analysis of sequence from orf6.1620.prot.fa ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp MIFKLPLILL RLYITSFIIW IFQTTILPQT LTKLTNVSIK TQTFQHYYPY TSLVNTPKNS NSINIITNSN ITYIIAHPDD EVMFFAPSII ELKKPKYNNQ INLICFSKGN YIKSMDEIRQ SELIQSSRIL GIDQVSILDY QDGMNETWQL NDIVQSLHEN LSPTSSGSDT NSNNKPSVLI TFDDQGVSNH PNHISLFHGT KKYIQELRRK SENKNKTRIK TTTTTINYID IDSSSSTKFY VLKSLNFFEK YSFTILGNIE ILFNFISLLI KKFINININV SFFSNQIIKS KFDNNNNNLQ LQNLNDIRFY SDLNMLSLSY AAMAYGHFSQ MVWFRYAWLL LSRYLTYNHL IEQ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > orf6.1620.prot . . . . . 1 MIFKLPLILLRLYITSFIIWIFQTTILPQTLTKLTNVSIKTQTFQHYYPY 50 ____HHHHHHHHHHHHHHHHHHHHH_________________________ . . . . . 51 TSLVNTPKNSNSINIITNSNITYIIAHPDDEVMFFAPSIIELKKPKYNNQ 100 ___________EEEEEE___EEEEEE____EEEEE___EEEE________ . . . . . 101 INLICFSKGNYIKSMDEIRQSELIQSSRILGIDQVSILDYQDGMNETWQL 150 EEEEEE_____HHHHHHHHHHHHHHHHH_____EEEEEE___________ . . . . . 151 NDIVQSLHENLSPTSSGSDTNSNNKPSVLITFDDQGVSNHPNHISLFHGT 200 HHHHHHHH___________________EEEEE___________EEEE___ . . . . . 201 KKYIQELRRKSENKNKTRIKTTTTTINYIDIDSSSSTKFYVLKSLNFFEK 250 HHHHHHHHHHH_______EEEE__EEEEE________EEEEEEE______ . . . . . 251 YSFTILGNIEILFNFISLLIKKFINININVSFFSNQIIKSKFDNNNNNLQ 300 EEEEE___HHHHHHHHHHHHHHHH_____________EEE__________ . . . . . 301 LQNLNDIRFYSDLNMLSLSYAAMAYGHFSQMVWFRYAWLLLSRYLTYNHL 350 ________________HHHHHHHHH____HHHHHHHHHHHHHHHHHHHH_ 351 IEQ 353 ___ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 3.7 % beta-contents : 60.4 % coil-contents : 35.9 % class : beta method : 2 alpha-contents : 37.8 % beta-contents : 26.8 % coil-contents : 35.3 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -18.89 -0.10 -0.22 0.00 -4.00 0.00 0.00 0.00 -0.35 -2.41 -1.67 0.00 -12.00 0.00 0.00 0.00 -39.64 -6.15 -2.43 -3.34 -5.71 0.00 0.00 -4.00 0.00 -0.02 -2.76 -1.67 0.00 -12.00 0.00 0.00 0.00 -38.07 ID: orf6.1620.prot AC: xxx Len: 353 1:I 321 Sc: -38.07 Pv: 1.184515e-01 NO_GPI_SITE GPI: learning from protozoa -29.59 -0.07 -0.19 -0.56 -4.00 0.00 0.00 0.00 -0.04 -2.24 -6.68 0.00 -12.00 0.00 0.00 0.00 -55.36 -21.89 -1.49 -2.01 -0.55 -4.00 0.00 0.00 0.00 -2.74 -1.43 -6.68 0.00 -12.00 0.00 0.00 0.00 -52.79 ID: orf6.1620.prot AC: xxx Len: 353 1:I 327 Sc: -52.79 Pv: 1.606118e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? orf6.1620.p 0.523 33 Y 0.568 33 Y 0.989 9 Y 0.824 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? orf6.1620.p 0.421 325 N 0.197 20 N 0.960 9 Y 0.683 Y # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? orf6.1620.p 0.363 169 N 0.238 35 N 0.994 9 Y 0.791 Y ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp 1-54 MIFKLPLILLRLYITSFIIWIFQTTILPQT LTKLTNVSIKTQTFQHYYPYTSLV ntpknsnsiniitnsnityii 55-75 76-212 AHPDDEVMFFAPSIIELKKPKYNNQINLIC FSKGNYIKSMDEIRQSELIQSSRILGIDQV SILDYQDGMNETWQLNDIVQSLHENLSPTS SGSDTNSNNKPSVLITFDDQGVSNHPNHIS LFHGTKKYIQELRRKSE nknktriktttttinyididsssst 213-237 238-264 KFYVLKSLNFFEKYSFTILGNIEILFN fisllikkfinininvsffsnqii 265-288 289-293 KSKFD nnnnnlqlqnln 294-305 306-353 DIRFYSDLNMLSLSYAAMAYGHFSQMVWFR YAWLLLSRYLTYNHLIEQ low complexity regions: SEG 25 3.0 3.3 >orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp 1-1 M ifklplillrlyitsfiiwifqttilpqtl 2-45 tkltnvsiktqtfq 46-46 H yypytslvntpknsnsiniitnsnityii 47-75 76-199 AHPDDEVMFFAPSIIELKKPKYNNQINLIC FSKGNYIKSMDEIRQSELIQSSRILGIDQV SILDYQDGMNETWQLNDIVQSLHENLSPTS SGSDTNSNNKPSVLITFDDQGVSNHPNHIS LFHG tkkyiqelrrksenknktriktttttinyi 200-238 didsssstk 239-241 FYV lkslnffekysftilgnieilfnfisllik 242-320 kfinininvsffsnqiikskfdnnnnnlql qnlndirfysdlnmlslsy 321-353 AAMAYGHFSQMVWFRYAWLLLSRYLTYNHL IEQ low complexity regions: SEG 45 3.4 3.75 >orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp 1-1 M ifklplillrlyitsfiiwifqttilpqtl 2-75 tkltnvsiktqtfqhyypytslvntpknsn siniitnsnityii 76-191 AHPDDEVMFFAPSIIELKKPKYNNQINLIC FSKGNYIKSMDEIRQSELIQSSRILGIDQV SILDYQDGMNETWQLNDIVQSLHENLSPTS SGSDTNSNNKPSVLITFDDQGVSNHP nhislfhgtkkyiqelrrksenknktrikt 192-314 ttttinyididsssstkfyvlkslnffeky sftilgnieilfnfisllikkfinininvs ffsnqiikskfdnnnnnlqlqnlndirfys dln 315-353 MLSLSYAAMAYGHFSQMVWFRYAWLLLSRY LTYNHLIEQ low complexity regions: XNU # Score cutoff = 21, Search from offsets 1 to 4 # both members of each repeat flagged # lambda = 0.347, K = 0.200, H = 0.664 >orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp MIFKLPLILLRLYITSFIIWIFQTTILPQTLTKLTNVSIKTQTFQHYYPYTSLVNTPKNS NSINIITNSNITYIIAHPDDEVMFFAPSIIELKKPKYNNQINLICFSKGNYIKSMDEIRQ SELIQSSRILGIDQVSILDYQDGMNETWQLNDIVQSLHENLsptssgsdtnsnnkPSVLI TFDDQGVSNHPNHISLFHGTKKYIQELrrksenknktriktttttinyididsssstKFY VLKSLNFFEKYSFTILGNIEILFNFISLLIKKFinininvsFFSNQIIKSKFdnnnnnlq lqNLNDIRFYSDLNMLSLSYAAMAYGHFSQMVWFRYAWLLLSRYLTYNHLIEQ 1 - 161 MIFKLPLILL RLYITSFIIW IFQTTILPQT LTKLTNVSIK TQTFQHYYPY TSLVNTPKNS NSINIITNSN ITYIIAHPDD EVMFFAPSII ELKKPKYNNQ INLICFSKGN YIKSMDEIRQ SELIQSSRIL GIDQVSILDY QDGMNETWQL NDIVQSLHEN L 162 - 175 sptssgsdt nsnnk 176 - 207 PSVLI TFDDQGVSNH PNHISLFHGT KKYIQEL 208 - 237 rrk senknktrik tttttinyid idsssst 238 - 273 KFY VLKSLNFFEK YSFTILGNIE ILFNFISLLI KKF 274 - 281 inininv s 282 - 292 FFSNQIIKS KF 293 - 302 dnnnnnlq lq 303 - 353 NLNDIRFY SDLNMLSLSY AAMAYGHFSQ MVWFRYAWLL LSRYLTYNHL IEQ low complexity regions: DUST >orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp MIFKLPLILLRLYITSFIIWIFQTTILPQTLTKLTNVSIKTQTFQHYYPYTSLVNTPKNS NSINIITNSNITYIIAHPDDEVMFFAPSIIELKKPKYNNQINLICFSKGNYIKSMDEIRQ SELIQSSRILGIDQVSILDYQDGMNETWQLNDIVQSLHENLSPTSSGSDTNSNNKPSVLI TFDDQGVSNHPNHISLFHGTKKYIQELRRKSENKNKTRIKTTTTTINYIDIDSSSSTKFY VLKSLNFFEKYSFTILGNIEILFNFISLLIKKFINININVSFFSNQIIKSKFDNNNNNLQ LQNLNDIRFYSDLNMLSLSYAAMAYGHFSQMVWFRYAWLLLSRYLTYNHLIEQ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for orf6.1620.prot sequence: 353 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MIFKLPLILL RLYITSFIIW IFQTTILPQT LTKLTNVSIK TQTFQHYYPY TSLVNTPKNS ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 120 NSINIITNSN ITYIIAHPDD EVMFFAPSII ELKKPKYNNQ INLICFSKGN YIKSMDEIRQ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 180 SELIQSSRIL GIDQVSILDY QDGMNETWQL NDIVQSLHEN LSPTSSGSDT NSNNKPSVLI ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~22 2222222222 22~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 240 TFDDQGVSNH PNHISLFHGT KKYIQELRRK SENKNKTRIK TTTTTINYID IDSSSSTKFY ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~1 3336666666 66666664~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 300 VLKSLNFFEK YSFTILGNIE ILFNFISLLI KKFINININV SFFSNQIIKS KFDNNNNNLQ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~11 1122222222 * 14 M'95 -w local . | . | . | . | . | LQNLNDIRFY SDLNMLSLSY AAMAYGHFSQ MVWFRYAWLL LSRYLTYNHL IEQ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~ ---------- ---------- ---------- ---------- ---------- --- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~ 222222~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** orf6.1620.prot.fa.___inter___ is a single sequence Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok Using sequence file: orf6.1620.prot.fa.___inter___ (1 sequences) MIFKLPLILLRLYITSFIIWIFQTTILPQTLTKLTNVSIKTQTFQHYYPY TSLVNTPKNSNSINIITNSNITYIIAHPDDEVMFFAPSIIELKKPKYNNQ INLICFSKGNYIKSMDEIRQSELIQSSRILGIDQVSILDYQDGMNETWQL NDIVQSLHENLSPTSSGSDTNSNNKPSVLITFDDQGVSNHPNHISLFHGT KKYIQELRRKSENKNKTRIKTTTTTINYIDIDSSSSTKFYVLKSLNFFEK YSFTILGNIEILFNFISLLIKKFINININVSFFSNQIIKSKFDNNNNNLQ LQNLNDIRFYSDLNMLSLSYAAMAYGHFSQMVWFRYAWLLLSRYLTYNHL IEQ (p)rokaryotic or (e)ukaryotic: e Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 12 32 1.559 Certain 2 251 271 0.892 Putative 3 314 334 1.060 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 Loop length 11 218 42 19 K+R profile 3.00 5.00 + 2.00 CYT-EXT prof - - 0.65 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 6.00 Tm probability: 0.73 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 2.0000 -> Orientation: undecided CYT-EXT difference: -0.65 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 3 Loop length 11 281 19 K+R profile 3.00 2.00 + CYT-EXT prof - - 0.57 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 5.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 2.0000 -> Orientation: undecided CYT-EXT difference: -0.57 -> Orientation: N-in ---------------------------------------------------------------------- "orf6" 353 12 32 #t 1.55938 251 271 #f 0.891667 314 334 #t 1.06042 ************************************ *TOPPREDM with prokaryotic function* ************************************ orf6.1620.prot.fa.___inter___ is a single sequence Using hydrophobicity file: /bio_software/2D/toppredm/lib/Engelman-Steitz.scale Using cyt/ext file: /bio_software/2D/toppredm/lib/Cyt-Ext.prok Using sequence file: orf6.1620.prot.fa.___inter___ (1 sequences) MIFKLPLILLRLYITSFIIWIFQTTILPQTLTKLTNVSIKTQTFQHYYPY TSLVNTPKNSNSINIITNSNITYIIAHPDDEVMFFAPSIIELKKPKYNNQ INLICFSKGNYIKSMDEIRQSELIQSSRILGIDQVSILDYQDGMNETWQL NDIVQSLHENLSPTSSGSDTNSNNKPSVLITFDDQGVSNHPNHISLFHGT KKYIQELRRKSENKNKTRIKTTTTTINYIDIDSSSSTKFYVLKSLNFFEK YSFTILGNIEILFNFISLLIKKFINININVSFFSNQIIKSKFDNNNNNLQ LQNLNDIRFYSDLNMLSLSYAAMAYGHFSQMVWFRYAWLLLSRYLTYNHL IEQ (p)rokaryotic or (e)ukaryotic: p Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 12 32 1.559 Certain 2 251 271 0.892 Putative 3 314 334 1.060 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 Loop length 11 218 42 19 K+R profile 2.00 5.00 + 2.00 CYT-EXT prof - - 0.65 - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 5.00 Tm probability: 0.73 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 2.0000 -> Orientation: undecided CYT-EXT difference: -0.65 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 3 Loop length 11 281 19 K+R profile 2.00 2.00 + CYT-EXT prof - - 0.57 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 4.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 0.00 (NEG-POS)/(NEG+POS): -1.0000 NEG: 0.0000 POS: 2.0000 -> Orientation: undecided CYT-EXT difference: -0.57 -> Orientation: N-in ---------------------------------------------------------------------- "orf6" 353 12 32 #t 1.55938 251 271 #f 0.891667 314 334 #t 1.06042 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Fri Mar 8 15:24:04 2002 File: /people/b_eisen/orf6.1620.prot.fa.___saps___ ID orf6.1620.prot DE orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp number of residues: 353; molecular weight: 41.1 kdal 1 MIFKLPLILL RLYITSFIIW IFQTTILPQT LTKLTNVSIK TQTFQHYYPY TSLVNTPKNS 61 NSINIITNSN ITYIIAHPDD EVMFFAPSII ELKKPKYNNQ INLICFSKGN YIKSMDEIRQ 121 SELIQSSRIL GIDQVSILDY QDGMNETWQL NDIVQSLHEN LSPTSSGSDT NSNNKPSVLI 181 TFDDQGVSNH PNHISLFHGT KKYIQELRRK SENKNKTRIK TTTTTINYID IDSSSSTKFY 241 VLKSLNFFEK YSFTILGNIE ILFNFISLLI KKFINININV SFFSNQIIKS KFDNNNNNLQ 301 LQNLNDIRFY SDLNMLSLSY AAMAYGHFSQ MVWFRYAWLL LSRYLTYNHL IEQ -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A--: 6( 1.7%); C : 1( 0.3%); D : 15( 4.2%); E : 11( 3.1%); F : 22( 6.2%) G- : 8( 2.3%); H : 8( 2.3%); I++: 44(12.5%); K : 23( 6.5%); L : 37(10.5%) M : 7( 2.0%); N++: 38(10.8%); P : 10( 2.8%); Q : 18( 5.1%); R : 9( 2.5%) S : 38(10.8%); T : 26( 7.4%); V- : 10( 2.8%); W : 4( 1.1%); Y : 18( 5.1%) KR : 32 ( 9.1%); ED : 26 ( 7.4%); AGP --: 24 ( 6.8%); KRED : 58 ( 16.4%); KR-ED : 6 ( 1.7%); FIKMNY++: 152 ( 43.1%); LVIFM : 120 ( 34.0%); ST : 64 ( 18.1%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 000+000000 +000000000 0000000000 00+000000+ 0000000000 0000000+00 61 0000000000 00000000-- -000000000 -0++0+0000 0000000+00 00+00--0+0 121 0-00000+00 00-00000-0 0-000-0000 0-000000-0 00000000-0 0000+00000 181 00--000000 0000000000 ++000-0+++ 0-0+0+0+0+ 000000000- 0-00000+00 241 00+00000-+ 000000000- 0000000000 ++00000000 00000000+0 +0-0000000 301 00000-0+00 0-00000000 0000000000 0000+00000 00+0000000 0-0 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 9/30 or 11/45 or 14/60): none Negative charge clusters (cmin = 7/30 or 10/45 or 12/60): none Mixed charge clusters (cmin = 13/30 or 17/45 or 21/60): none B. HIGH SCORING (UN)CHARGED SEGMENTS. There are no high scoring positive charge segments. There are no high scoring negative charge segments. There are no high scoring mixed charge segments. There are no high scoring uncharged segments. C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 4 | 4 | 6 | 48 | 9 | 8 | 11 | 11 | 10 | 14 | 6 | 8 | lmin1 6 | 5 | 7 | 59 | 11 | 10 | 14 | 13 | 13 | 17 | 8 | 10 | lmin2 7 | 6 | 8 | 65 | 12 | 11 | 15 | 15 | 14 | 19 | 9 | 11 | (Significance level: 0.010000; Minimal displayed length: 6) (+0) 9(0,0,0); at 213- 221: NKNKTRIKT (3. quartile) 0+0+0+0+0 (*0) 12(0,0,0); at 210- 221: KSENKNKTRIKT (3. quartile) +0-0+0+0+0+0 Run count statistics: + runs >= 3: 1, at 208; - runs >= 3: 1, at 79; * runs >= 4: 0 0 runs >= 32: 0 -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. There are no high scoring hydrophobic segments. There are no high scoring transmembrane segments. 2. SPACINGS OF C. H2N-104-C-248-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-45-H-30-H-27-C-52-H-31-H-2-H-4-H-128-H-21-H-4-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 4 Aligned matching blocks: [ 67- 70] TNSN [ 170- 173] TNSN ______________________________ [ 150- 153] LNDI [ 304- 307] LNDI B. SEPARATED AND TANDEM REPEATS: 11-letter reduced alphabet. (i= LVIF; += KR; -= ED; s= AG; o= ST; n= NQ; a= YW; p= P; h= H; m= M; c= C) Repeat core block length: 8 -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 27 (Expected range: 9-- 39) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 8 (6-10) 9 (11-20) 7 (>=21) 4 3. Clusters of amino acid multiplets (cmin = 13/30 or 16/45 or 20/60): none 4. Long amino acid multiplets (>= 5; Letter/Length/Position): T/5/221 N/5/294 B. CHARGE ALPHABET. 1. Total number of charge multiplets: 7 (Expected range: 0-- 11) 4 +plets (f+: 9.1%), 3 -plets (f-: 7.4%) Total number of charge altplets: 1 (Critical number: 13) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 0 (6-10) 1 (11-20) 2 (>=21) 5 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 221- 225 1 T 5 5 ! 0 233- 236 1 S 4 4 0 253- 292 10 F......... 4 4 0 266- 281 4 I... 4 4 0 294- 298 1 N 5 5 ! 0 B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 6) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9) Location Period Element Copies Core Errors 2- 31 5 i..0. 6 6 /0/././2/./ 206- 221 2 *. 8 8 0 248- 292 5 i.... 8 6 1 253- 270 3 i.. 6 6 0 262- 285 4 i... 6 6 0 299- 346 8 i..00.00 6 6 /0/././2/2/./2/1/ -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 72- 147 (2.) T( 75)T 2 of 27 0.0001 large 2. maximal spacing 86- 321 (3.) A( 235)A 1 of 7 0.0090 large maximal spacing 187- 241 (3.) V( 54)V 1 of 11 0.9926 small maximal spacing 211- 233 (3.) S( 22)S 1 of 39 0.9916 small maximal spacing 254- 346 (4.) T( 92)T 1 of 27 0.0075 large 1. maximal spacing ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Pfam (from /data/patterns/pfam) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/pfam/Pfam Sequence file: orf6.1620.prot.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Glyco_hydro_28 Polygalacturonase (pectinase) 2.6 9.7 1 DUF158 Uncharacterized LmbE-like protein, CO -72.7 0.25 1 Ribosomal_L27e Ribosomal L27e protein family -75.2 36 1 SCO1-SenC SCO1/SenC -90.3 65 1 MHCK_EF2_kinase MHCK/EF2 kinase domain family -164.4 89 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- MHCK_EF2_kinase 1/1 18 154 .. 1 245 [] -164.4 89 Glyco_hydro_28 1/1 147 166 .. 343 362 .] 2.6 9.7 SCO1-SenC 1/1 71 248 .. 1 188 [] -90.3 65 Ribosomal_L27e 1/1 153 253 .. 1 137 [] -75.2 36 DUF158 1/1 67 283 .. 1 292 [] -72.7 0.25 Alignments of top-scoring domains: MHCK_EF2_kinase: domain 1 of 1, from 18 to 154: score -164.4, E = 89 *->IkWeydpGdditkkWtedivlvkvepkPFAeGAlReAYrtkdlSkgt I W + +i ++ + + v++ + F Y +l + orf6.1620. 18 IIWIFQT--TILPQTLTKLTNVSIKTQTF-----QHYYPYTSLVN-- 55 DenYPLGtttkLFPPiemisPisknneamtqlkqdwklvgkyvaKryikq k+ + + + + orf6.1620. 56 ------------------------------TPKNSNS--INIIT---NSN 70 tdRdvYFeDVkmQMvakkWAekYNrkKPPKkIefLqscViELiDrppssn + Y + P + f +iEL+ +p+ n orf6.1620. 71 IT--------------------YIIAHPDDEVMFFAPSIIELK--KPKYN 98 Gq.dplcglEPyiEGkYkKyNsNSGfVsnddaRnTPQaFSHFTYElSNHQ q ++c + G Y+K s d +R Q+ + orf6.1620. 99 NQiNLIC----FSKGNYIK--------SMDEIR---QS-----------E 122 Ll....vVDIQGVgDlYTDPQIHTkdGtGFGdGNLGkrGfakFlqtHkCN L++++++ I V l ++ + G++ +t N orf6.1620. 123 LIqssrILGIDQVSIL------------DY------QDGMN---ETWQLN 151 aiC<-* +i orf6.1620. 152 DIV 154 Glyco_hydro_28: domain 1 of 1, from 147 to 166: score 2.6, E = 9.7 *->tssCeNvppslkGkqspasc<-* t++++++ +sl + +sp+s+ orf6.1620. 147 TWQLNDIVQSLHENLSPTSS 166 SCO1-SenC: domain 1 of 1, from 71 to 248: score -90.3, E = 65 *->ialilgvgallsyLfyrskRlLetsKeaeakrlni..YgDknslggP i i++ ++ +f s +e +K++++++ n+ + n+++ orf6.1620. 71 ITYIIAHPDDEVMFFAPS--IIELKKPKYNNQINLicFSKGNYIKS- 114 FtlidqnGkkftsdnLkG..klsLiYFGFTnCPdiCPaaLdkltdiikkL +i q + +s +G +++s+++ ++ l di+ L orf6.1620. 115 MDEIRQSELIQSSR-ILGidQVSILDYQDGMN------ETWQLNDIVQSL 157 kekenIdvqvvFIsvDPe.rDtPkvLKeY....lknFdpsFigLTGtvde +e+ + + + D ++ +P vL +++++ +n + + Gt + orf6.1620. 158 HEN----LSPTSSGSDTNsNNKPSVLITFddqgVSNHPNHISLFHGTKKY 203 iksvakkfKVfyskviqdkpeq.dYlVdHSsf...fYLIdpdGkilkhYg i+++ k + + i + +Y + Ss++++fY +lk + orf6.1620. 204 IQELRRKSENKNKTRIKTTTTTiNYIDIDSSSstkFY-------VLKSL- 245 rnld<-* n orf6.1620. 246 -NFF 248 Ribosomal_L27e: domain 1 of 1, from 153 to 253: score -75.2, E = 36 *->MvKfLKpGKVvlvlrGRYAG.......kKaVIVkafDeGtsdrPYgH v L + l+ +G+++++++k V + D+G+s +P orf6.1620. 153 IVQSLHEN-----LSPTSSGsdtnsnnKPSVLITFDDQGVSNHPNHI 194 ALVAGieRYPlKVtkkmgaKKiaKrskvKpFiKvVNYnHLmPTRYtLDvd L G ++Y + +k K ++++K+ ++NY +D+d orf6.1620. 195 SLFHGTKKYIQELRRKSENK---NKTRIKTTTTTINY---------IDID 232 lkkKtvvnadalkapskKveArkevKkkfEEryktGKNrWFFtKLRF<-* s K + K+ FF K F orf6.1620. 233 SS------------SSTKFYVL--------------KSLNFFEKYSF 253 DUF158: domain 1 of 1, from 67 to 283: score -72.7, E = 0.25 *->ssenrLkdAkkVLavhAHPDDesigmGATiakft..dqGkrVlvvtl + n + AHPDDe++ + i + +++ ++ +++ orf6.1620. 67 TNSNIT-------YIIAHPDDEVMFFAPSIIELKkpKYNNQINLICF 106 TeGeegstlgsRWAqllaDsadeLaeiRreElaeAAriLGVkkhiqLgla G + s + eiR El + riLG + L + orf6.1620. 107 SKG---NYIKS------------MDEIRQSELIQSSRILGIDQVSILDYQ 141 drgldkGdlgt.qlpDrgLaqsdLeev..tkalVkviRelrPHvllVFdp G+ t ql D +qs e +++t + + P vl +Fd+ orf6.1620. 142 -----DGMNETwQLND--IVQSLHENLspTSSGSDTNSNNKPSVLITFDD 184 nggyPYEgHPDHrrtHtVtaAaveaAgafagtpdfpgdpwtvpklYyvvl g+ HP H+ f gt ++ + l orf6.1620. 185 QGVS---NHPNHIS-------------LFHGTKKY------IQEL----- 207 fLrekvsklsaeflasfhRGPFEeWllkrdddidFfvsdDGiddliEakk r k + ++ + + ++d id + orf6.1620. 208 --RRKSENKNKTRIKTTT--------TTIN------YID--IDSS--SST 237 qaRlrklaAlfahatqsvsePllraiaellgereklykeEgfrl.argsf ++ +l++l + s + + +e+l + l+ ++ +sf orf6.1620. 238 KF--YVLKSLNFFEKYSF---TILGNIEILFNFISLLIKKFINInINVSF 282 p<-* orf6.1620. 283 F 283 // Start with PfamFrag (from /data/patterns/pfam) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/pfam/PfamFrag Sequence file: orf6.1620.prot.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Glyco_hydro_28 Polygalacturonase (pectinase) 2.6 9.7 1 Polysac_deacet Polysaccharide deacetylase 2.2 18 1 Histone_HNS H-NS histone family 0.6 83 1 Peptidase_C16 Peptidase C16 family 0.4 26 1 DUF158 Uncharacterized LmbE-like protein, COG 0.4 31 1 MOZ_SAS MOZ/SAS family -0.5 78 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- MOZ_SAS 1/1 96 107 .. 193 204 .] -0.5 78 Peptidase_C16 1/1 104 113 .. 241 250 .] 0.4 26 Glyco_hydro_28 1/1 147 166 .. 343 362 .] 2.6 9.7 Polysac_deacet 1/1 174 184 .. 1 11 [. 2.2 18 DUF158 1/1 176 194 .. 134 155 .. 0.4 31 Histone_HNS 1/1 298 308 .. 1 12 [. 0.6 83 Alignments of top-scoring domains: MOZ_SAS: domain 1 of 1, from 96 to 107: score -0.5, E = 78 *->kyykgqylqvLn<-* ky+++++l++ + orf6.1620. 96 KYNNQINLICFS 107 Peptidase_C16: domain 1 of 1, from 104 to 113: score 0.4, E = 26 *->vCFvKGDviK<-* +CF KG iK orf6.1620. 104 ICFSKGNYIK 113 Glyco_hydro_28: domain 1 of 1, from 147 to 166: score 2.6, E = 9.7 *->tssCeNvppslkGkqspasc<-* t++++++ +sl + +sp+s+ orf6.1620. 147 TWQLNDIVQSLHENLSPTSS 166 Polysac_deacet: domain 1 of 1, from 174 to 184: score 2.2, E = 18 *->ddksvyLTFDD<-* +++sv +TFDD orf6.1620. 174 NKPSVLITFDD 184 DUF158: domain 1 of 1, from 176 to 194: score 0.4, E = 31 *->PHvllVFdpnggyPYEgHPDHr<-* P vl +Fd+ g+ HP H+ orf6.1620. 176 PSVLITFDDQGVS---NHPNHI 194 Histone_HNS: domain 1 of 1, from 298 to 308: score 0.6, E = 83 *->MnelLkiLnNiR<-* n+ L++Ln iR orf6.1620. 298 -NLQLQNLNDIR 308 // Start with Repeat Library (from /data/patterns/repeats-Miguel-Andrade/hmm) hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/repeats-Miguel-Andrade/hmm/repeats.hmm-lib Sequence file: orf6.1620.prot.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Prosite --------------------------------------------------------- | ppsearch (c) 1994 EMBL Data Library | | based on MacPattern (c) 1990-1994 R. Fuchs | --------------------------------------------------------- PROSITE pattern search started: Fri Mar 8 15:26:00 2002 Sequence file: orf6.1620.prot.fa ---------------------------------------- Sequence orf6.1620.prot (353 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 36: NVSI 70: NITY 145: NETW 215: NKTR 279: NVSF Total matches: 5 Matching pattern PS00004 CAMP_PHOSPHO_SITE: 208: RRKS Total matches: 1 Matching pattern PS00005 PKC_PHOSPHO_SITE: 38: SIK 56: TPK 126: SSR 200: TKK 236: STK Total matches: 5 Matching pattern PS00006 CK2_PHOSPHO_SITE: 88: SIIE 114: SMDE 136: SILD 156: SLHE 166: SGSD 181: TFDD 290: SKFD Total matches: 7 Matching pattern PS00008 MYRISTYL: 143: GMNETW 167: GSDTNS Total matches: 2 Total no of hits in this sequence: 20 ======================================== 1314 pattern(s) searched in 1 sequence(s), 353 residues. Total no of hits in all sequences: 20. Search time: 00:00 min ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Profile Search ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with motif search against own library ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** SeqTyp=2 : PROTEIN search; >APC D-Box is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >INTRA-SIGNAL-M minimal SH3 binding is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >INTRA-SIGNAL-M deubiquitinating enzyme SH3 domain binding motif (Kato, 2000) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >INTRA-SIGNAL-M minimal class I consensus-SH3 binding motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >INTRA-SIGNAL-M minimal class II consensus-SH3 binding motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >INTRA-SIGNAL-M exact 14-3-3 binding consensus (Muslin 1996 Cell 84 889) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >INTRA-SIGNAL-M 14-3-3 binding motif in RAF and others (Muslin 1996 Cell 84 889) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >INTRA-SIGNAL-M WW domain binding motif in formins (Bedford 1997) is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >INTRA-SIGNAL-M PY motif for WW domain is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >TM-CYTOPLASMIC-M di-hydrophobic endocytosis motifs for internalized transmembrane proteins is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >TM-CYTOPLASMIC-M tyrosine-based endocytosis motif for internalized transmembrane proteins is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >TM-EXTRACELL-M Endocytosis signal for internalized transmembrane proteins is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >EXTRACELL-M minimal furin protease cleavage site motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >EXTRACELL-M extended furin protease cleavage site motif is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >EXTRACELL-M zinc binding motif in MMPs is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >EXTRACELL-M g alpha binding go loco is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS PDX-1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS QKI-5 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS HCDA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS SV40 LrgT experimentally determined is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS H2B experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS v-Rel experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Amida experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS RanBP3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Pho4p experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS DNAhelicaseQ1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS LEF-1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS TCF-1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR p53-NLS1 NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS hum-Ku70 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS GAL4 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS act/inh betaA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS BDV-P experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS BDV-P experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS BDV-P experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS TR2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS THOV NP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS polyomaVP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS HIV-1 Tat experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS HIV-1 Rev experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Rex experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS SRY experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS SOX9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS NS5A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS DNAse EBV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS DNAse EBV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS adenovE1a experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS ystDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS hVDR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS CPV capsid experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS hGlu.cort.experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS cFOS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS cJUN experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS hDNApolalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS hDNAtopoII experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS hBLM experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS hARNT experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS influenzaNP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS p54 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS hProTalpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Tst1/Oct6 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS protHsc9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS protHsci experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS protHsc3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Ta alpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Pax-QNR experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Hunt.Dis.pro experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS MyoD experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS opaque2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS CTP experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS HCV experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS p110RB1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS VirD2-Nterm experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS VirD2-Cterm experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Nucloplasmin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Nucleolin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS ICP-8 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Nab2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS M9 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS lscMyc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS humKprotein experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS FluA experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Mat-alpha experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS polyoma Lrg-T experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS polyoma Lrg-T experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS SV40 VP1 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS SV40 VP2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS polyoma VP2 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS c-myb experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS N-myc experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS p53 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS c-erb-A experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS yeast SKI3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS L29 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS Max experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS L3 experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >NUCLEAR NLS dyskerin experimentally determined NLS is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >PDZ domain binding motif science 278_2075_pawson is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units >WW domain binding motif science 278_2075_pawson is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 353 units ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~ ~~~ Start with HMM-search search against own library hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/own/own-hmm.lib Sequence file: orf6.1620.prot.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/own/own-hmm-f.lib Sequence file: orf6.1620.prot.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ L. Aravind's signalling DB+ PSSM from other authors IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp (353 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value VWA Von Willebrand factor A domain 26 0.084 SCP SCP/PR1 domain (Domain found in plant pathogenesis relat... 25 0.17 FKBP FK506 binding protein (Peptidyl prolyl isomerase) 23 0.68 PTB Phospho-Tyrosine Binding domain 22 1.2 UBHYD Ubiquitin C-terminal hydrolase domain 22 1.8 SEC7 Sec7 like GDP exchange factor for ARF like GTPases 21 2.0 KH HnRNP K homology domain (A RNA binding domain) 21 2.1 PAP Papain/bleomycin hydrolase like domain 20 3.4 HISDAC Histone deacetylase domain 20 4.0 UBA Ubiquitin pathway associated domain 20 5.1 INSL Insulinase like Metallo protease domain 19 7.3 PDE cyclic NMP phosphodiesterase domain 19 8.2 ACET NH2 acetyltransferase domain 19 8.9 >VWA Von Willebrand factor A domain Length = 255 Score = 26.1 bits (57), Expect = 0.084 Identities = 12/131 (9%), Positives = 12/131 (9%), Gaps = 13/131 (9%) Query: 204 IQELRRKSENKNKTRIKTTTTTINYIDIDSSSSTKFYVLKSLNFFEKYSFTILGNIEILF 263 Sbjct: 33 VEARKKRTAKKNITPYQRGIIRSLILTLDCSEA-----MLEKDLRPNRHAMIIQYAI--- 84 Query: 264 NFISLLIKKFINININVSFFSNQIIKSKFDNNNN----NLQLQNLNDIRFYSDLNM-LSL 318 Sbjct: 85 DFVHEFFDQNPISQMGIIIMRNGLAQLVSQVSGNPQDHIDALKSIRKQEPKGNPSLQNAL 144 Query: 319 SYAAMAYGHFS 329 Sbjct: 145 EMARGLLLPVP 155 Score = 19.5 bits (40), Expect = 6.5 Identities = 13/84 (15%), Positives = 13/84 (15%), Gaps = 21/84 (25%) Query: 132 IDQVSILDYQDGMNET-WQLNDIVQSLHENLS---PTSSGSDTN---------------- 171 Sbjct: 96 ISQMGIIIMRNGLAQLVSQVSGNPQDHIDALKSIRKQEPKGNPSLQNALEMARGLLLPVP 155 Query: 172 SNNKPSVLITFDDQGVSNHPNHIS 195 Sbjct: 156 AHCTREVLIVFGS-LSTTDPGDIH 178 >SCP SCP/PR1 domain (Domain found in plant pathogenesis related proteins and animal trypsin inhibitors) Length = 159 Score = 24.9 bits (54), Expect = 0.17 Identities = 6/17 (35%), Positives = 6/17 (35%) Query: 317 SLSYAAMAYGHFSQMVW 333 Sbjct: 108 FSGNNFLKTGHYTQMVW 124 >FKBP FK506 binding protein (Peptidyl prolyl isomerase) Length = 149 Score = 22.9 bits (49), Expect = 0.68 Identities = 7/37 (18%), Positives = 7/37 (18%), Gaps = 1/37 (2%) Query: 176 PSVLITFDDQGVSNHPNHISLFHGTKKYIQELRRKSE 212 Sbjct: 110 PGVIREINGDSITVDFNH-PLAGQTVHFDIEVLEIDP 145 >PTB Phospho-Tyrosine Binding domain Length = 138 Score = 22.1 bits (47), Expect = 1.2 Identities = 8/61 (13%), Positives = 8/61 (13%), Gaps = 6/61 (9%) Query: 128 RILGIDQVSILDYQDGMNETWQLNDIVQSLHENLSPTSSGSDTNSNNKPSVLITFDDQGV 187 Sbjct: 10 RFLGCVET---PKANGSD---VAREAIHAIRFQRDLKRSEQTRETAKLQKVEIRISIDNV 63 Query: 188 S 188 Sbjct: 64 I 64 Score = 19.4 bits (40), Expect = 8.1 Identities = 5/15 (33%), Positives = 5/15 (33%) Query: 70 NITYIIAHPDDEVMF 84 Sbjct: 81 RISFCADDKDDKRMF 95 >UBHYD Ubiquitin C-terminal hydrolase domain Length = 884 Score = 21.5 bits (45), Expect = 1.8 Identities = 4/82 (4%), Positives = 4/82 (4%), Gaps = 3/82 (3%) Query: 85 FAPSIIELKKPKYNNQINLICFSKGNYIKSMDEIRQSELIQSSRILGIDQVSILDYQDGM 144 Sbjct: 20 LRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQ 79 Query: 145 NETWQLNDIVQSLHENLSPTSS 166 Sbjct: 80 -ELCRV--LLDNVENKMKGTCV 98 Score = 19.2 bits (39), Expect = 9.6 Identities = 15/72 (20%), Positives = 15/72 (20%), Gaps = 1/72 (1%) Query: 173 NNKPSVLITFDDQGVSNHPNHISLFHGTKKYIQELRRKSENKNKTRIKTTTTTINYIDID 232 Sbjct: 613 NTDPMLLQFFKSQGYRDGPGN-PLRHNYEGTLRDLLQFFKPRQPKKLYYQQLKMKITDFE 671 Query: 233 SSSSTKFYVLKS 244 Sbjct: 672 NRRSFKCIWLNS 683 >SEC7 Sec7 like GDP exchange factor for ARF like GTPases Length = 192 Score = 21.3 bits (45), Expect = 2.0 Identities = 13/65 (20%), Positives = 13/65 (20%), Gaps = 4/65 (6%) Query: 247 FFEKYSFTILGNIEILFNFISLLIKKFINININVSFFSNQIIKSK----FDNNNNNLQLQ 302 Sbjct: 111 FSQRYCICNPGVVRQFRNPDTIFILAFAIILLNTDMYSPNVKPERKMKLEDFIKNLRGVD 170 Query: 303 NLNDI 307 Sbjct: 171 DGEDI 175 >KH HnRNP K homology domain (A RNA binding domain) Length = 92 Score = 21.4 bits (45), Expect = 2.1 Identities = 9/44 (20%), Positives = 9/44 (20%), Gaps = 2/44 (4%) Query: 74 IIAHPDDEVMFFAPSIIELKKPKYNNQINLICFSKGNYIKSMDE 117 Sbjct: 13 SQNPRPQYGFPRAQTTIDIAIPP--NRCGLIIGKSGDTIRQLQE 54 >PAP Papain/bleomycin hydrolase like domain Length = 376 Score = 20.4 bits (42), Expect = 3.4 Identities = 4/36 (11%), Positives = 4/36 (11%) Query: 48 YPYTSLVNTPKNSNSINIITNSNITYIIAHPDDEVM 83 Sbjct: 215 YPFQGKVRAHRCHPKKYQKVAWIQDFIMLQNNEHRI 250 >HISDAC Histone deacetylase domain Length = 433 Score = 20.2 bits (42), Expect = 4.0 Identities = 7/18 (38%), Positives = 7/18 (38%), Gaps = 1/18 (5%) Query: 194 ISLFHGTKKYIQELRRKS 211 Sbjct: 74 MCQFH-TDEYIDFLSRVT 90 >UBA Ubiquitin pathway associated domain Length = 255 Score = 20.0 bits (41), Expect = 5.1 Identities = 2/20 (10%), Positives = 2/20 (10%) Query: 278 INVSFFSNQIIKSKFDNNNN 297 Sbjct: 29 MEMGYQREEVERALRAAFNN 48 >INSL Insulinase like Metallo protease domain Length = 433 Score = 19.5 bits (40), Expect = 7.3 Identities = 9/21 (42%), Positives = 9/21 (42%), Gaps = 1/21 (4%) Query: 183 DDQGVSNHPNHISLFHGTKKY 203 Sbjct: 59 DEKGMAHFLEHM-LFNGTEKY 78 >PDE cyclic NMP phosphodiesterase domain Length = 350 Score = 19.3 bits (39), Expect = 8.2 Identities = 21/98 (21%), Positives = 21/98 (21%), Gaps = 22/98 (22%) Query: 2 IFKLPLILLRLYITSFIIWIFQTTILPQTLTKLTNVSIKTQTFQHYYPYTSLVNTPKNSN 61 Sbjct: 41 IFKIPIEKLQRFI--------------MTVNALYRKNNRYHNFTHAFDVTQTVYT----- 81 Query: 62 SINIITNSNITYIIAHPDDEVMFFAPSIIELKKPKYNN 99 Sbjct: 82 ---FLTSFNAAQYLTHLDIFALLISCMCHDLNHPGFNN 116 >ACET NH2 acetyltransferase domain Length = 173 Score = 19.2 bits (39), Expect = 8.9 Identities = 4/15 (26%), Positives = 4/15 (26%) Query: 243 KSLNFFEKYSFTILG 257 Sbjct: 130 DAVHSWQKAGFDIVG 144 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 13 Number of calls to ALIGN: 16 Length of query: 353 Total length of test sequences: 20182 Effective length of test sequences: 16435.0 Effective search space size: 5216262.4 Initial X dropoff for ALIGN: 25.0 bits Y. Wolf's SCOP PSSM IMPALA version 1.1 [20-December-1999] Reference: Alejandro A. Schaffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul (1999), "IMPALA: Matching a Protein Sequence Against a Collection of "PSI-BLAST-Constructed Position-Specific Score Matrices", Bioinformatics 15:1000-1011. Query= orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp (353 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|2308977 [178..600] P-loop containing nucleotide triphosph... 25 1.9 gi|2605611 [15..455] Ferritin-like 25 2.3 gi|2129405 [8..201] S-adenosyl-L-methionine-dependent methyl... 24 3.1 gi|2194045 [11..394] Ferritin-like 24 3.2 gi|1072178 [17..364] Phosphoglycerate mutase-like 24 3.2 gi|2498161 [23..196] N-terminal nucleophile aminohydrolases ... 24 3.3 gi|1172028 [272..600] beta-Lactamase/D-ala carboxypeptidase 24 3.6 gi|117300 [20..406] Cytochrome P450 24 4.4 gi|1125790 [25..414] Phosphoglycerate mutase-like 24 4.5 gi|1053218 [1393..1540] Trypsin-like serine proteases 23 7.2 gi|544105 [9..172] 4-helical cytokines 23 8.9 gi|515162 [1..146] Bacteriophage T7 lysozyme (Zn amidase) 23 9.2 >gi|2308977 [178..600] P-loop containing nucleotide triphosphate hydrolases Length = 423 Score = 24.9 bits (54), Expect = 1.9 Identities = 10/75 (13%), Positives = 10/75 (13%), Gaps = 1/75 (1%) Query: 42 QTFQHYYPYTSLVNTPKNSNSINIITNSNITYIIAHPDDEVMFFAPSIIELKK-PKYNNQ 100 Sbjct: 324 RRFENKNPAITAGASGSGNGYGMVSQNARSSFTVKHFAGEVDYSATGLLEENGEVISGDL 383 Query: 101 INLICFSKGNYIKSM 115 Sbjct: 384 MNLMKSTRSDFVREL 398 >gi|2605611 [15..455] Ferritin-like Length = 441 Score = 24.9 bits (54), Expect = 2.3 Identities = 7/57 (12%), Positives = 7/57 (12%) Query: 297 NNLQLQNLNDIRFYSDLNMLSLSYAAMAYGHFSQMVWFRYAWLLLSRYLTYNHLIEQ 353 Sbjct: 122 IASQMQSIDELRHVQTQIHAMSHYNKFFDGFQDWAHMHDRVWYLSVPKSFFEDARSA 178 >gi|2129405 [8..201] S-adenosyl-L-methionine-dependent methyltransferases Length = 194 Score = 24.4 bits (53), Expect = 3.1 Identities = 6/66 (9%), Positives = 6/66 (9%), Gaps = 7/66 (10%) Query: 72 TYIIAHPDDEVMFFAPSIIELKKPKYNNQINLIC-------FSKGNYIKSMDEIRQSELI 124 Sbjct: 44 THEENHGWANHYHARIEELYPPNVVDPGSVTLLTGGPECTHFSNARGGKPVSDQKRASAW 103 Query: 125 QSSRIL 130 Sbjct: 104 HVLDWI 109 >gi|2194045 [11..394] Ferritin-like Length = 384 Score = 24.2 bits (52), Expect = 3.2 Identities = 7/57 (12%), Positives = 7/57 (12%) Query: 297 NNLQLQNLNDIRFYSDLNMLSLSYAAMAYGHFSQMVWFRYAWLLLSRYLTYNHLIEQ 353 Sbjct: 170 QTAVFAALDKVDNAQMIQMERLFIAKLVPGFDASTDVPKKIWTTDPIYSGARATVQE 226 >gi|1072178 [17..364] Phosphoglycerate mutase-like Length = 348 Score = 24.1 bits (52), Expect = 3.2 Identities = 5/58 (8%), Positives = 5/58 (8%), Gaps = 1/58 (1%) Query: 288 IKSKFDNNNNNLQLQNLNDIRFYSDLNMLSLSYAAMAYGHFSQMVWFRYAWLLLSRYL 345 Sbjct: 155 DAELLQLVRNHADEPIVEAVKYNHVIDSLKVRYILQDDR-LPYPEWARGYENRILNMS 211 >gi|2498161 [23..196] N-terminal nucleophile aminohydrolases (Ntn hydrolases) Length = 174 Score = 24.2 bits (52), Expect = 3.3 Identities = 7/46 (15%), Positives = 7/46 (15%) Query: 223 TTTINYIDIDSSSSTKFYVLKSLNFFEKYSFTILGNIEILFNFISL 268 Sbjct: 60 ETCLDSLVIDASVSSSMVVIENIFCRDGMRVGAVANLHRIRDAARV 105 >gi|1172028 [272..600] beta-Lactamase/D-ala carboxypeptidase Length = 329 Score = 24.1 bits (52), Expect = 3.6 Identities = 20/191 (10%), Positives = 20/191 (10%), Gaps = 13/191 (6%) Query: 145 NETWQLNDIVQSLHENLSPTSSGSDTNSNNKPSVLITFDD--QGVSNHP-NHISLFHGTK 201 Sbjct: 80 ENVITPNTTIFDPGYWVLPNSTKRFRDWKKTGHGDTDLNKAITESSDTYFYQVAYNMGID 139 Query: 202 KYIQELRRKSENKNKTRIKTTTTTINYIDIDSSSSTKFYVLKSLNFFEKYSFTILGNIEI 261 Sbjct: 140 RLSNWMKDFGF-GMPTGIEIQEETAANIPTREWKQKRYKRPWVQGDTISVGI-GQGYWTA 197 Query: 262 LFNFISLLIKKFINININVSFFSNQIIKSKFDNNNNNLQLQNLNDIRFYSDLNMLSLSYA 321 Sbjct: 198 TPLQVAKATTILVN---NGKVNTPHLMKAIEGAV-----LEPYEDPLLYPDINTPKVAAW 249 Query: 322 AMAYGHFSQMV 332 Sbjct: 250 EAAKRGMYNVV 260 >gi|117300 [20..406] Cytochrome P450 Length = 387 Score = 23.9 bits (51), Expect = 4.4 Identities = 14/120 (11%), Positives = 14/120 (11%) Query: 225 TINYIDIDSSSSTKFYVLKSLNFFEKYSFTILGNIEILFNFISLLIKKFINININVSFFS 284 Sbjct: 128 EICGPVAARILAHILGICEASDVEIIRWSQRLIDGAGNFGWRSELFERSDEANAEMNCLF 187 Query: 285 NQIIKSKFDNNNNNLQLQNLNDIRFYSDLNMLSLSYAAMAYGHFSQMVWFRYAWLLLSRY 344 Sbjct: 188 NDLVKKHRSAPNPSAFATMLNAPDPIPLSQIYANIKIAIGGGVNEPRDALGTILYGLLTN 247 >gi|1125790 [25..414] Phosphoglycerate mutase-like Length = 390 Score = 23.7 bits (51), Expect = 4.5 Identities = 10/66 (15%), Positives = 10/66 (15%), Gaps = 1/66 (1%) Query: 281 SFFSNQIIKSKFDNNNNNLQLQNLNDIRFYSDLNMLSLSYAAMAYGHFSQMVWFRYAWLL 340 Sbjct: 161 SFVNSADVQAVLG-NLTNYCGQPVDIDNLWIITNALYIEQIYYNATLRTKNNWFTDAFYA 219 Query: 341 LSRYLT 346 Sbjct: 220 KADAIN 225 >gi|1053218 [1393..1540] Trypsin-like serine proteases Length = 148 Score = 23.1 bits (49), Expect = 7.2 Identities = 9/51 (17%), Positives = 9/51 (17%), Gaps = 8/51 (15%) Query: 70 NITYIIAHPD-------DEVMFFAPSIIELKKP-KYNNQINLICFSKGNYI 112 Sbjct: 10 AIKSLYIRKGYVGDGCIDRESFNDIAVFELEEPIEFSKDIFPACLPSAPKI 60 >gi|544105 [9..172] 4-helical cytokines Length = 164 Score = 22.9 bits (49), Expect = 8.9 Identities = 8/69 (11%), Positives = 8/69 (11%), Gaps = 6/69 (8%) Query: 188 SNHPNHISLFHGTKKYIQELRRKSENKNKTRIKTTTTTINYIDIDSSSSTK----FYVLK 243 Sbjct: 90 ELAPTLDTLQLDVTDFATNIWLQMEDLGA--APAVQPTQGAMPTFTSAFQRRAGGVLVAS 147 Query: 244 SLNFFEKYS 252 Sbjct: 148 QLHRFLELA 156 >gi|515162 [1..146] Bacteriophage T7 lysozyme (Zn amidase) Length = 146 Score = 22.8 bits (48), Expect = 9.2 Identities = 10/31 (32%), Positives = 10/31 (32%) Query: 277 NINVSFFSNQIIKSKFDNNNNNLQLQNLNDI 307 Sbjct: 72 SIGVCLVGGIDDKGKFDANFTPAQMQSLRSL 102 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 12 Number of calls to ALIGN: 12 Length of query: 353 Total length of test sequences: 256703 Effective length of test sequences: 206078.0 Effective search space size: 64052053.3 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Fri Mar 8 15:26:36 2002 ***** Copyright 2000, Richard Mott, Wellcome Trust Centre for Human Genetics, University of Oxford For help see http://www.well.ox.ac.uk/ariadne For usage use -help using gap penalty 11+1k using matrix BLOSUM62 printing all alignments with eval < 0.100000 using sequence1 orf6.1620.prot using self-comparison > 1 orf6.1620.prot len 353 from 39 to 103 vs orf6.1620.prot len 353 from 242 to 301 score 51 eval 5.975219e-02 identity 31.67% K 1.224573e-02 L 1.983776e-01 H 1.034815e+00 alpha 1.580019e-01 39 IKTQTFQHYYPYTSLVNTPKNSNSINIITNSNITYIIAHPDDEVMFFAPSIIELKKPKYN 98 orf6.1620.prot :|: | | :| | | | |::: | | | ||: ||: | | 242 LKSLNFFEKYSFTILGNIEILFNFISLLIKKFININI-----NVSFFSNQIIKSKFDNNN 296 orf6.1620.prot 99 NQINL 103 orf6.1620.prot | : | 297 NNLQL 301 orf6.1620.prot ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ TIGRFAM hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/tigrfam/tigrfam.hmm Sequence file: orf6.1620.prot.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00181 pepF: oligoendopeptidase F -1.4 51 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00181 1/1 110 162 .. 562 614 .] -1.4 51 Alignments of top-scoring domains: TIGR00181: domain 1 of 1, from 110 to 162: score -1.4, E = 51 *->nyikflssGgskyPletlkllGvdltspepweeahnefkrwleevek nyik + +++ ++lG+d s ++ ++ne ++ ++v+ orf6.1620. 110 NYIKSMDEIRQSELIQSSRILGIDQVSILDYQDGMNETWQLNDIVQS 156 lfkkle<-* l + l orf6.1620. 157 LHENLS 162 // hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/tigrfam/tigrfam.hmm-f Sequence file: orf6.1620.prot.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TIGR00602 rad24: checkpoint protein rad24 0.6 12 1 TIGR00181 pepF: oligoendopeptidase F -1.4 47 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- TIGR00602 1/1 145 159 .. 656 670 .] 0.6 12 TIGR00181 1/1 110 162 .. 562 614 .] -1.4 47 Alignments of top-scoring domains: TIGR00602: domain 1 of 1, from 145 to 159: score 0.6, E = 12 *->pEtfsledsdnSlse<-* +Et+ l d+ Sl e orf6.1620. 145 NETWQLNDIVQSLHE 159 TIGR00181: domain 1 of 1, from 110 to 162: score -1.4, E = 47 *->nyikflssGgskyPletlkllGvdltspepweeahnefkrwleevek nyik + +++ ++lG+d s ++ ++ne ++ ++v+ orf6.1620. 110 NYIKSMDEIRQSELIQSSRILGIDQVSILDYQDGMNETWQLNDIVQS 156 lfkkle<-* l + l orf6.1620. 157 LHENLS 162 // SMART hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/iprscan/data/smart.HMMs Sequence file: orf6.1620.prot.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // COG hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/cogs/cogs.hmm Sequence file: orf6.1620.prot.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG2120 -112.1 12 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG2120 1/1 46 299 .. 1 317 [] -112.1 12 Alignments of top-scoring domains: COG2120: domain 1 of 1, from 46 to 299: score -112.1, E = 12 *->mfeinspleeaffkllreVlemtstsplaselrvLavfpHPDDEsiG +l+ + ++s+ + + +HPDDE+ orf6.1620. 46 HYYPYTSLVNTPKNSNSINIITNSN--------ITYIIAHPDDEVMF 84 cGGTLakya..aaGveVglvclTlGEmGenltqplldthetlgeiRreEl + ++++ +++ + l+c+ +++ eiR+ El orf6.1620. 85 FAPSIIELKkpKYNNQINLICF-----------SKGNYIKSMDEIRQSEL 123 aeAArvLGvekrillglgsrypDggLetepddqearvdlvqaqtalvatd + ++r+LG++ + l+ y Dg e +++d+vq+ orf6.1620. 124 IQSSRILGIDQVSILD----YQDGMNE-----TWQLNDIVQS-------- 156 Lravirel.............rPhvVltpdPwnGgdgHPDHrathelava + + l++++++++++++++P+v++t+d+ G+ HP H+ + ++ orf6.1620. 157 ---LHENLsptssgsdtnsnnKPSVLITFDD-QGVSNHPNHISLFHGTKK 202 AvasagipkrpndwgvsaavayytdlgasplqagsryqlnatldPdvlll + +++ +++ + +++ + ++++ ++++ + ++ orf6.1620. 203 YIQELRRKSEN-KN---------KTRIKTTTTTINYIDIDSSSSTKFY-- 240 tsdelavtqkvvdisavaevKlaAiraHrtQfadtalferafplenerle v s + +K + +t ++ + + + l++ orf6.1620. 241 -----------VLKSLNFFEKYS-----FTILGNIEILFNFISLLI---- 270 lrveaaltwygleagvtyaegfrgeeslllailgl<-* ++ + v+ + + + + l orf6.1620. 271 ------KKFINININVSFFSNQIIKSKFDNNNNNL 299 // hmmpfam - search a single seq against HMM database HMMER 2.1.1 (Dec 1998) Copyright (C) 1992-1998 Washington University School of Medicine HMMER is freely distributed under the GNU General Public License (GPL). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data/patterns/cogs/cogs.hmm-f Sequence file: orf6.1620.prot.fa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: orf6.1620.prot orf6-1954:5366-4305:e 1062 bp, 353 aa, contig 8759 bp Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- COG2120 7.4 0.3 1 COG0817 5.6 1.7 1 COG3324 1.8 25 1 COG0262 0.2 82 1 COG1665 -0.6 62 1 COG1859 -0.7 81 1 COG3202 -2.1 94 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- COG3202 1/1 18 40 .. 501 523 .] -2.1 94 COG0262 1/1 45 58 .. 176 189 .] 0.2 82 COG1665 1/1 111 124 .. 348 361 .] -0.6 62 COG0817 1/1 115 133 .. 1 19 [. 5.6 1.7 COG2120 1/1 117 143 .. 89 119 .. 7.4 0.3 COG1859 1/1 202 215 .. 229 247 .] -0.7 81 COG3324 1/1 217 240 .. 1 29 [. 1.8 25 Alignments of top-scoring domains: COG3202: domain 1 of 1, from 18 to 40: score -2.1, E = 94 *->ilWIyavkkLnkeYqaaialsek<-* i+WI+ ++ L + +++++ s+k orf6.1620. 18 IIWIFQTTILPQTLTKLTNVSIK 40 COG0262: domain 1 of 1, from 45 to 58: score 0.2, E = 82 *->qnyYdykfeiyeRr<-* q+yY+y++++++++ orf6.1620. 45 QHYYPYTSLVNTPK 58 COG1665: domain 1 of 1, from 111 to 124: score -0.6, E = 62 *->YIkSLDLikksrLk<-* YIkS+D i +s L orf6.1620. 111 YIKSMDEIRQSELI 124 COG0817: domain 1 of 1, from 115 to 133: score 5.6, E = 1.7 *->mvkiandttymmmrILGID<-* m +i+ +++rILGID orf6.1620. 115 MDEIRQSELIQSSRILGID 133 COG2120: domain 1 of 1, from 117 to 143: score 7.4, E = 0.3 *->eiRreElaeAArvLGvekrillglgsrypDg<-* eiR+ El+ ++r+LG++ + l+ y Dg orf6.1620. 117 EIRQSELIQSSRILGIDQVSILD----YQDG 143 COG1859: domain 1 of 1, from 202 to 215: score -0.7, E = 81 *->eyIqkvvvkevlfdeesks<-* +yIq e+++ +e k+ orf6.1620. 202 KYIQ-----ELRRKSENKN 215 COG3324: domain 1 of 1, from 217 to 240: score 1.8, E = 25 *->vPkRSmarqgtpNwvdlaakDlekakkFY<-* +R ++ t+N++d+ D ++ kFY orf6.1620. 217 --TRIKTTTTTINYIDI---DSSSSTKFY 240 //