analysis of sequence from tem19 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >tem19partial RTREEGPADGASLRVVASSRSVGRSGPCSPRAAGHGHGGAESPRHRLPVALTATLVLIC AGQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFVEQLAHKFISPQLRMSFIV FSTRGTTLMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTAS VIIALTDGELHEDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVN DGFQALQGIIHSILKKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKI NDSVTLNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTHCSDG SILAIALLILFLLLALALLWWFWPLCCTVIIKEVPPPPAEESEEEDDDGLPKKKWPTVD ASYYGGRGVGGIKRMEVRWGEKGSTEEGAKLEKAKNARVKMPEQEYEFPEPRNLNNNMR RPSSPRKWYSPIKGKLDALWVLLRKGYDRVSVMRPQPGDTGRCINFTRVKNNQPAKYPL NNAYHTSSPPPAPIYTPPPPAPHCPPPPPSAPTPPIPSPPSTLPPPPQAPPPNRAPPPS RPPPRPSV ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > tem19partial . . . . . 1 RTREEGPADGASLRVVASSRSVGRSGPCSPRAAGHGHGGAESPRHRLPVA 50 ___________EEEEEEE____________________________HHHH . . . . . 51 LTATLVLICAGQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFV 100 HHHHHHEEE__________________EEEEEE_____EEEE_HHHHHHH . . . . . 101 EQLAHKFISPQLRMSFIVFSTRGTTLMKLTEDREQIRQGLEELQKVLPGG 150 HHHHHHH_HHHHHHHEEEE______EEE_____HHHHHHHHHHHHH____ . . . . . 151 DTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELHEDLFFYSEREAN 200 _______HHHHHHHHHHH_______EEEEEEE_______EEEEEHHHHHH . . . . . 201 RSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVNDGFQALQGIIHSIL 250 H_____EEEEEEE_____HHHHHHHHHH_EEEE_____HHHHHHHHHHHH . . . . . 251 KKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKINDSVT 300 _HHHHHHHH__________EEEEEEE___________EEEEE______EE . . . . . 301 LNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTH 350 E_________EEE_____HHHHH_HHHHHHHHH_____EEEEEEEEEE__ . . . . . 351 CSDGSILAIALLILFLLLALALLWWFWPLCCTVIIKEVPPPPAEESEEED 400 _______HHHHHHHHHHHHHHHHHH____EEEEEEEE_____________ . . . . . 401 DDGLPKKKWPTVDASYYGGRGVGGIKRMEVRWGEKGSTEEGAKLEKAKNA 450 ___________________________EEE_______HHHHHHHHHHHHH . . . . . 451 RVKMPEQEYEFPEPRNLNNNMRRPSSPRKWYSPIKGKLDALWVLLRKGYD 500 HH__________________________________HHHHHHHHHHH___ . . . . . 501 RVSVMRPQPGDTGRCINFTRVKNNQPAKYPLNNAYHTSSPPPAPIYTPPP 550 _EEEEE_______EEEEEEE______________________________ . . . . 551 PAPHCPPPPPSAPTPPIPSPPSTLPPPPQAPPPNRAPPPSRPPPRPSV 598 ________________________________________________ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 21.4 % beta-contents : 13.6 % coil-contents : 65.0 % class : mixed method : 2 alpha-contents : 0.0 % beta-contents : 13.6 % coil-contents : 86.4 % class : beta ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -5.59 -1.12 -1.50 -1.27 0.00 -4.00 0.00 0.00 0.00 -12.94 -3.96 -12.00 -12.00 -4.00 -12.00 0.00 -70.38 -10.18 -0.05 -0.10 -0.20 0.00 -4.00 0.00 0.00 0.00 -9.97 -3.96 -12.00 -12.00 -4.00 -12.00 0.00 -68.47 ID: tem19partial AC: xxx Len: 590 1:I 561 Sc: -68.47 Pv: 5.332868e-01 NO_GPI_SITE GPI: learning from protozoa -23.32 -0.03 -0.11 -0.01 -4.00 -4.00 0.00 0.00 0.00 -8.65 -13.18 -12.00 -12.00 -4.00 -12.00 0.00 -93.29 -12.30 -1.22 -0.08 -0.26 0.00 -4.00 0.00 0.00 0.00 -10.89 -13.18 -12.00 -12.00 -4.00 -12.00 0.00 -81.93 ID: tem19partial AC: xxx Len: 590 1:I 572 Sc: -81.93 Pv: 5.441371e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? tem19partia 1.000 372 Y 0.750 383 Y 0.999 368 Y 0.171 N # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? tem19partia 0.474 284 N 0.410 372 Y 0.986 364 Y 0.176 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? tem19partia 0.524 33 Y 0.367 33 Y 0.992 363 Y 0.311 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >tem19partial 1-9 RTREEGPAD gaslrvvassrsvgrsg 10-26 27-339 PCSPRAAGHGHGGAESPRHRLPVALTATLV LICAGQGGRREDGGPACYGGFDLYFILDKS GSVLHHWNEIYYFVEQLAHKFISPQLRMSF IVFSTRGTTLMKLTEDREQIRQGLEELQKV LPGGDTYMHEGFERASEQIYYENRQGYRTA SVIIALTDGELHEDLFFYSEREANRSRDLG AIVYCVGVKDFNETQLARIADSKDHVFPVN DGFQALQGIIHSILKKSCIEILAAEPSTIC AGESFQVVVRGNGFRHARNVDRVLCSFKIN DSVTLNEKPFSVEDTYLLCPAPILKEVGMK AALQVSMNDGLSF isssviittt 340-349 350-355 HCSDGS ilaiallilflllalallwwfw 356-377 378-386 PLCCTVIIK evppppaeeseee 387-399 400-537 DDDGLPKKKWPTVDASYYGGRGVGGIKRME VRWGEKGSTEEGAKLEKAKNARVKMPEQEY EFPEPRNLNNNMRRPSSPRKWYSPIKGKLD ALWVLLRKGYDRVSVMRPQPGDTGRCINFT RVKNNQPAKYPLNNAYHT sspppapiytppppaphcpppppsaptppi 538-597 psppstlppppqapppnrapppsrppprps 598-598 V low complexity regions: SEG 25 3.0 3.3 >tem19partial rtreegpadgaslrvvassrsvgrsgpcsp 1-57 raaghghggaesprhrlpvaltatlvl 58-355 ICAGQGGRREDGGPACYGGFDLYFILDKSG SVLHHWNEIYYFVEQLAHKFISPQLRMSFI VFSTRGTTLMKLTEDREQIRQGLEELQKVL PGGDTYMHEGFERASEQIYYENRQGYRTAS VIIALTDGELHEDLFFYSEREANRSRDLGA IVYCVGVKDFNETQLARIADSKDHVFPVND GFQALQGIIHSILKKSCIEILAAEPSTICA GESFQVVVRGNGFRHARNVDRVLCSFKIND SVTLNEKPFSVEDTYLLCPAPILKEVGMKA ALQVSMNDGLSFISSSVIITTTHCSDGS ilaiallilflllalallwwfw 356-377 378-385 PLCCTVII kevppppaeeseeedddglpkkkwp 386-410 411-537 TVDASYYGGRGVGGIKRMEVRWGEKGSTEE GAKLEKAKNARVKMPEQEYEFPEPRNLNNN MRRPSSPRKWYSPIKGKLDALWVLLRKGYD RVSVMRPQPGDTGRCINFTRVKNNQPAKYP LNNAYHT sspppapiytppppaphcpppppsaptppi 538-597 psppstlppppqapppnrapppsrppprps 598-598 V low complexity regions: SEG 45 3.4 3.75 >tem19partial rtreegpadgaslrvvassrsvgrsgpcsp 1-76 raaghghggaesprhrlpvaltatlvlica gqggrredggpacygg 77-355 FDLYFILDKSGSVLHHWNEIYYFVEQLAHK FISPQLRMSFIVFSTRGTTLMKLTEDREQI RQGLEELQKVLPGGDTYMHEGFERASEQIY YENRQGYRTASVIIALTDGELHEDLFFYSE REANRSRDLGAIVYCVGVKDFNETQLARIA DSKDHVFPVNDGFQALQGIIHSILKKSCIE ILAAEPSTICAGESFQVVVRGNGFRHARNV DRVLCSFKINDSVTLNEKPFSVEDTYLLCP APILKEVGMKAALQVSMNDGLSFISSSVII TTTHCSDGS ilaiallilflllalallwwfw 356-377 378-537 PLCCTVIIKEVPPPPAEESEEEDDDGLPKK KWPTVDASYYGGRGVGGIKRMEVRWGEKGS TEEGAKLEKAKNARVKMPEQEYEFPEPRNL NNNMRRPSSPRKWYSPIKGKLDALWVLLRK GYDRVSVMRPQPGDTGRCINFTRVKNNQPA KYPLNNAYHT sspppapiytppppaphcpppppsaptppi 538-597 psppstlppppqapppnrapppsrppprps 598-598 V 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 >tem19partial RTREEGPADGASLRVVASSRSVGRSGPCSPRAAghghggaesprhrlpvaltatlvliCA GQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFVEQLAHKFISPQLRMSFIVFS TRGTTLMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVII ALTDGELHEDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVNDGFQ ALQGIIHSILKKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKINDSVT LNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFIsssviitttHCSDGSIlaia llilflllalallwwfwPLcctviikevppppaeeseeedddGLPKKKWPTVDASYYGGR GVGGIKRMEVRWGEKGSTEEGAKLEKAKNARVKMPEQEYEFPEPRNLNNNMRRPSSPRKW YSPIKGKLDALWVLLRKGYDRVSVMRPQPGDTGRCINFTRVKNNQPAKYPLNNAYHtssp ppapiytppppaphcpppppsaptppipsppstlppppqapppnrapppsrppprpsV 1 - 33 RTREEGPADG ASLRVVASSR SVGRSGPCSP RAA 34 - 58 ghghgga esprhrlpva ltatlvli 59 - 340 CA GQGGRREDGG PACYGGFDLY FILDKSGSVL HHWNEIYYFV EQLAHKFISP QLRMSFIV FS TRGTTLMKLT EDREQIRQGL EELQKVLPGG DTYMHEGFER ASEQIYYENR QGYRTASV II ALTDGELHED LFFYSEREAN RSRDLGAIVY CVGVKDFNET QLARIADSKD HVFPVNDG FQ ALQGIIHSIL KKSCIEILAA EPSTICAGES FQVVVRGNGF RHARNVDRVL CSFKINDS VT LNEKPFSVED TYLLCPAPIL KEVGMKAALQ VSMNDGLSFI 341 - 349 sssviittt 350 - 356 H CSDGSI 357 - 377 laia llilflllal allwwfw 378 - 379 PL 380 - 402 c ctviikevpp ppaeeseeed dd 403 - 536 GLPKKKWP TVDASYYGGR GVGGIKRMEV RWGEKGSTEE GAKLEKAKNA RVKMPEQEYE FP EPRNLNNN MRRPSSPRKW YSPIKGKLDA LWVLLRKGYD RVSVMRPQPG DTGRCINFTR VK NNQPAKYP LNNAYH 537 - 597 tssp ppapiytppp paphcppppp saptppipsp pstlppppqa pppnrappps rppprp s 598 - 598 V low complexity regions: DUST >tem19partial RTREEGPADGASLRVVASSRSVGRSGPCSPRAAGHGHGGAESPRHRLPVALTATLVLICA GQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFVEQLAHKFISPQLRMSFIVFS TRGTTLMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVII ALTDGELHEDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVNDGFQ ALQGIIHSILKKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKINDSVT LNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTHCSDGSILAIA LLILFLLLALALLWWFWPLCCTVIIKEVPPPPAEESEEEDDDGLPKKKWPTVDASYYGGR GVGGIKRMEVRWGEKGSTEEGAKLEKAKNARVKMPEQEYEFPEPRNLNNNMRRPSSPRKW YSPIKGKLDALWVLLRKGYDRVSVMRPQPGDTGRCINFTRVKNNQPAKYPLNNAYHTSSP PPAPIYTPPPPAPHCPPPPPSAPTPPIPSPPSTLPPPPQAPPPNRAPPPSRPPPRPSV ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for tem19partial sequence: 590 amino acids, 25 residue(s) in coiled coil state Coil 1 * 123* 148* TTLMKLTEDREQIRQGLEELQKVLPG . | . | . | . | . | . 60 RTREEGPADG ASLRVVASSR SVGRSGPCSP RAAGHGHGGA ESPRHRLPVA LTATLVLICA ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 GQGGRREDGG PACYGGFDLY FILDKSGSVL HHWNEIYYFV EQLAHKFISP QLRMSFIVFS ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 TRGTTLMKLT EDREQIRQGL EELQKVLPGG DTYMHEGFER ASEQIYYENR QGYRTASVII ~~29999999 9999999999 999999962~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border --efgabcde fgabcdefga bcdefgabc- ---------- ---------- ---------- * 21 M'95 -w register ~~89999999 9999999999 999999997~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~15777777 7777777777 7777766~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~1555566 9999999999 9999877~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 240 ALTDGELHED LFFYSEREAN RSRDLGAIVY CVGVKDFNET QLARIADSKD HVFPVNDGFQ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . | . | . 300 ALQGIIHSIL KKSCIEILAA EPSTICAGES FQVVVRGNGF RHARNVDRVL CSFKINDSVT ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . | . | . 360 LNEKPFSVED TYLLCPAPIL KEVGMKAALQ VSMNDGLSFI SSSVIITTTH CSDGSILAIA ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . | . | . 420 LLILFLLLAL ALLWWFWPLC CTVIIKEVPP PPAEESEEED DDGLPKKKWP TVDASYYGGR ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . | . | . 480 GVGGIKRMEV RWGEKGSTEE GAKLEKAKNA RVKMPEQEYE FPEPRNLNNN MRRPSSPRKW ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~111111 11111111~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 540 YSPIKGKLDA LWVLLRKGYD RVSVMRPQPG DTGRCINFTR VKNNQPAKYP LNNAYHTSSP ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . | . | PPAPIYTPPP PAPHCPPPPP SAPTPPIPSP PSTLPPPPQA PPPNRAPPPS ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ---------- ---------- ---------- ---------- ---------- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** tem8.___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: tem8.___inter___ (1 sequences) RTREEGPADGASLRVVASSRSVGRSGPCSPRAAGHGHGGAESPRHRLPVA LTATLVLICAGQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFV EQLAHKFISPQLRMSFIVFSTRGTTLMKLTEDREQIRQGLEELQKVLPGG DTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELHEDLFFYSEREAN RSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVNDGFQALQGIIHSIL KKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKINDSVT LNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTH CSDGSILAIALLILFLLLALALLWWFWPLCCTVIIKEVPPPPAEESEEED DDGLPKKKWPTVDASYYGGRGVGGIKRMEVRWGEKGSTEEGAKLEKAKNA RVKMPEQEYEFPEPRNLNNNMRRPSSPRKWYSPIKGKLDALWVLLRKGYD RVSVMRPQPGDTGRCINFTRVKNNQPAKYPLNNAYHTSSPPPAPIYTPPP PAPHCPPPPPSAPTPPIPSPPSTLPPPPQAPPPNRAPPPSRPPPRPSV (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 1 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 45 65 1.189 Certain 2 332 352 1.038 Certain 3 356 376 2.603 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 Loop length 44 266 3 222 K+R profile 9.00 0.00 + + CYT-EXT prof - - 0.28 0.83 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -0.3333 NEG: 4.0000 POS: 8.0000 -> Orientation: N-in CYT-EXT difference: -1.12 -> Orientation: N-in ---------------------------------------------------------------------- "tem8" 598 45 65 #t 1.18854 332 352 #t 1.0375 356 376 #t 2.60313 ************************************ *TOPPREDM with prokaryotic function* ************************************ tem8.___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: tem8.___inter___ (1 sequences) RTREEGPADGASLRVVASSRSVGRSGPCSPRAAGHGHGGAESPRHRLPVA LTATLVLICAGQGGRREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFV EQLAHKFISPQLRMSFIVFSTRGTTLMKLTEDREQIRQGLEELQKVLPGG DTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELHEDLFFYSEREAN RSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVNDGFQALQGIIHSIL KKSCIEILAAEPSTICAGESFQVVVRGNGFRHARNVDRVLCSFKINDSVT LNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTH CSDGSILAIALLILFLLLALALLWWFWPLCCTVIIKEVPPPPAEESEEED DDGLPKKKWPTVDASYYGGRGVGGIKRMEVRWGEKGSTEEGAKLEKAKNA RVKMPEQEYEFPEPRNLNNNMRRPSSPRKWYSPIKGKLDALWVLLRKGYD RVSVMRPQPGDTGRCINFTRVKNNQPAKYPLNNAYHTSSPPPAPIYTPPP PAPHCPPPPPSAPTPPIPSPPSTLPPPPQAPPPNRAPPPSRPPPRPSV (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 1 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 45 65 1.189 Certain 2 332 352 1.038 Certain 3 356 376 2.603 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 Loop length 44 266 3 222 K+R profile 9.00 0.00 + + CYT-EXT prof - - 0.28 0.83 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 9.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 3.00 (NEG-POS)/(NEG+POS): -0.3333 NEG: 4.0000 POS: 8.0000 -> Orientation: N-in CYT-EXT difference: -1.12 -> Orientation: N-in ---------------------------------------------------------------------- "tem8" 598 45 65 #t 1.18854 332 352 #t 1.0375 356 376 #t 2.60313 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem8.___saps___ SAPS. Version of April 11, 1996. Date run: Thu Dec 14 16:46:48 2000 File: /people/maria/tem8.___saps___ ID tem19partial DE - number of residues: 598; molecular weight: 66.0 kdal 1 RTREEGPADG ASLRVVASSR SVGRSGPCSP RAAGHGHGGA ESPRHRLPVA LTATLVLICA 61 GQGGRREDGG PACYGGFDLY FILDKSGSVL HHWNEIYYFV EQLAHKFISP QLRMSFIVFS 121 TRGTTLMKLT EDREQIRQGL EELQKVLPGG DTYMHEGFER ASEQIYYENR QGYRTASVII 181 ALTDGELHED LFFYSEREAN RSRDLGAIVY CVGVKDFNET QLARIADSKD HVFPVNDGFQ 241 ALQGIIHSIL KKSCIEILAA EPSTICAGES FQVVVRGNGF RHARNVDRVL CSFKINDSVT 301 LNEKPFSVED TYLLCPAPIL KEVGMKAALQ VSMNDGLSFI SSSVIITTTH CSDGSILAIA 361 LLILFLLLAL ALLWWFWPLC CTVIIKEVPP PPAEESEEED DDGLPKKKWP TVDASYYGGR 421 GVGGIKRMEV RWGEKGSTEE GAKLEKAKNA RVKMPEQEYE FPEPRNLNNN MRRPSSPRKW 481 YSPIKGKLDA LWVLLRKGYD RVSVMRPQPG DTGRCINFTR VKNNQPAKYP LNNAYHTSSP 541 PPAPIYTPPP PAPHCPPPPP SAPTPPIPSP PSTLPPPPQA PPPNRAPPPS RPPPRPSV -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 43( 7.2%); C : 13( 2.2%); D : 25( 4.2%); E : 40( 6.7%); F : 21( 3.5%) G : 46( 7.7%); H : 14( 2.3%); I : 32( 5.4%); K : 28( 4.7%); L : 50( 8.4%) M : 9( 1.5%); N : 21( 3.5%); P+ : 64(10.7%); Q : 17( 2.8%); R : 41( 6.9%) S : 45( 7.5%); T : 26( 4.3%); V : 36( 6.0%); W : 8( 1.3%); Y : 19( 3.2%) KR : 69 ( 11.5%); ED : 65 ( 10.9%); AGP : 153 ( 25.6%); KRED : 134 ( 22.4%); KR-ED : 4 ( 0.7%); FIKMNY : 130 ( 21.7%); LVIFM : 148 ( 24.7%); ST : 71 ( 11.9%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 +0+--000-0 000+00000+ 000+000000 +000000000 -00+0+0000 0000000000 61 0000++--00 0000000-00 000-+00000 0000-00000 -0000+0000 00+0000000 121 0+00000+00 --+-00+000 --00+00000 -0000-00-+ 00-0000-0+ 000+000000 181 000-0-00-- 00000-+-00 +0+-000000 0000+-00-0 000+00-0+- 000000-000 241 0000000000 ++000-0000 -0000000-0 00000+0000 +00+00-+00 000+00-000 301 00-+0000-- 0000000000 +-000+0000 0000-00000 0000000000 00-0000000 361 0000000000 0000000000 00000+-000 000--0---- --000+++00 00-000000+ 421 00000++0-0 +00-+000-- 00+0-+0+00 +0+00-0-0- 00-0+00000 0++0000++0 481 0000+0+0-0 00000++00- +0000+0000 -00+00000+ 0+00000+00 0000000000 541 0000000000 0000000000 0000000000 0000000000 0000+00000 +000+000 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 10/30 or 13/45 or 16/60): none Negative charge clusters (cmin = 10/30 or 13/45 or 16/60): none Mixed charge clusters (cmin = 15/30 or 21/45 or 26/60): 1) From 394 to 465: see sequence above see sequence above quartile: 3; size: 72, +count: 14, -count: 18, 0count: 40; t-value: 4.48 * G: 9 (12.5%); K: 9 (12.5%); E: 14 (19.4%); 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. ________________________________ High scoring uncharged segments: score= 1.00 frequency= 0.776 ( LAGSVTIPNFQYHMCW ) score= 0.00 frequency= 0.000 ( BZX ) score= -8.00 frequency= 0.224 ( KEDR ) Expected score/letter: -1.017 M_0.01= 41.93; M_0.05= 34.23 1) From 336 to 385: length= 50, score=41.00 * 336 GLSFISSSVI ITTTHCSDGS ILAIALLILF LLLALALLWW FWPLCCTVII L: 12(24.0%); S: 6(12.0%); I: 8(16.0%); 2) From 529 to 584: length= 56, score=56.00 ** 529 YPLNNAYHTS SPPPAPIYTP PPPAPHCPPP PPSAPTPPIP SPPSTLPPPP 579 QAPPPN P: 28(50.0%); C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 5 | 5 | 7 | 37 | 10 | 10 | 13 | 12 | 11 | 15 | 7 | 9 | lmin1 6 | 6 | 9 | 45 | 12 | 12 | 16 | 14 | 14 | 19 | 8 | 11 | lmin2 8 | 7 | 10 | 50 | 13 | 13 | 18 | 16 | 16 | 21 | 10 | 12 | (Significance level: 0.010000; Minimal displayed length: 6) (0) 57(2,0,0); at 327- 385: see sequence above (3. quartile) L: 13 (22.0%); A: 6 (10.2%); S: 7 (11.9%); I: 8 (13.6%); LVIFM: 28 (47.5%); ST: 11 (18.6%); (-) 8(1,0,0); at 394- 402: EESEEEDDD (3. quartile) --0------ (0) 61(1,0,0); at 523- 584: see sequence above (4. quartile) P: 29 (46.8%); (0) 64(2,0,0); at 529- 594: see sequence above (4. quartile) P: 34 (51.5%); ST: 10 (15.2%); Run count statistics: + runs >= 3: 1, at 406; - runs >= 3: 1, at 397; * runs >= 5: 1, at 397; 0 runs >= 25: 2, at 354; 529; -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. __________________________________ High scoring hydrophobic segments: 2.00 (LVIFM) 1.00 (AGYCW) 0.00 (BZX) -2.00 (PH) -4.00 (STNQ) -8.00 (KEDR) Expected score/letter: -2.072 M_0.01= 23.31; M_0.05= 19.43 1) From 356 to 385: length= 30, score=41.00 ** 356 ILAIALLILF LLLALALLWW FWPLCCTVII L: 11(36.7%); A: 4(13.3%); I: 5(16.7%); W: 3(10.0%); ____________________________________ High scoring transmembrane segments: 5.00 (LVIF) 2.00 (AGM) 0.00 (BZX) -1.00 (YCW) -2.00 (ST) -6.00 (P) -8.00 (H) -10.00 (NQ) -16.00 (KR) -17.00 (ED) Expected score/letter: -3.973 M_0.01= 54.08; M_0.05= 44.84; M_0.30= 33.84 1) From 356 to 385: length= 30, score=90.00 ** 356 ILAIALLILF LLLALALLWW FWPLCCTVII L: 11(36.7%); A: 4(13.3%); I: 5(16.7%); W: 3(10.0%); 2. SPACINGS OF C. H2N-27-C-30-C-13-C-137-C-42-C-11-C-24-C-23-C-35-C-28-C-C-133-C-39-C-43-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-27-C-6-H-1-H-7-H-13-C-13-C-17-H-H-12-H-49-H-32-H-22-C-19-H-15-H-6-C-11-C-15-H-8-C-23-C-34-H-C-28-C-C-133-C-20-H-17-H-C-43-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 5 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: 9 -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 57 (Expected range: 17-- 52) high 1 ...EE..... ....VV.SS. .......... .AA....GG. .......... .......... 61 ..GGRR..GG ....GG.... .......... HH....YY.. .......... .......... 121 ...TT..... .......... EE......GG .......... .....YY... ........II 181 .......... .FF....... .......... .......... .......... .......... 241 ....II.... KK......AA .......... ..VVV..... .......... .......... 301 .......... ..LL...... ......AA.. .......... SSS.IITTT. .......... 361 LL...LLL.. .LLWW....C C..II...PP PP.EE.EEED DD...KKK.. .....YYGG. 421 ..GG...... ........EE .......... .......... .......NNN .RR.SS.... 481 .......... ...LL..... .......... .......... ..NN...... .NN....SSP 541 PP.....PPP P....PPPPP ....PP...P P...PPPP.. PPP...PPP. .PPP.... 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 34 (6-10) 6 (11-20) 12 (>=21) 6 3. Clusters of amino acid multiplets (cmin = 15/30 or 19/45 or 23/60): none 4. Long amino acid multiplets (>= 5; Letter/Length/Position): P/5/556 B. CHARGE ALPHABET. 1. Total number of charge multiplets: 16 (Expected range: 2-- 25) 7 +plets (f+: 11.5%), 9 -plets (f-: 10.9%) Total number of charge altplets: 16 (Critical number: 28) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 5 (6-10) 1 (11-20) 3 (>=21) 8 3. Long charge multiplets (>= 5; Letter/Length/Position): -/6/397 --------------------------------------------------------------- ----------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 362- 373 2 L. 6 6 ! 0 389- 392 1 P 4 4 0 541- 579 3 PP. 10 4 /3/4/./ 548- 551 1 P 4 4 0 548- 597 5 P..P. 9 5 ! /1/././3/./ 556- 560 1 P 5 5 ! 0 575- 578 1 P 4 4 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 81- 134 9 i..0.*.0. 6 6 /0/././2/./2/./2/./ 225- 284 10 i..0....00 6 6 /0/././1/././././2/2/ 361- 368 1 i 8 8 0 361- 390 3 i.. 9 7 1 362- 373 2 i. 6 6 0 394- 402 1 - 8 6 ! 1 399- 440 7 *..00.. 6 6 /0/././2/1/././ -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 148- 234 (2.) P( 86)P 1 of 65 0.0017 large 1. maximal spacing 288- 420 (3.) R( 132)R 1 of 42 0.0010 large 1. maximal spacing 318- 378 (3.) P( 60)P 2 of 65 0.0005 large 2. maximal spacing 322- 387 (3.) E( 65)E 2 of 41 0.0294 large 2. maximal spacing 353- 386 (3.) *( 33)* 2 of 135 0.0002 large 2. maximal spacing 463- 599 (4.) E( 136)E 1 of 41 0.0009 large 1. maximal spacing 511- 599 (4.) -( 88)- 1 of 66 0.0011 large maximal spacing 520- 585 (4.) R( 65)R 2 of 42 0.0238 large 2. maximal spacing 528- 585 (4.) *( 57)* 1 of 135 0.0000 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: tem8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem19partial Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- vwa von Willebrand factor type A domain 37.9 2.3e-07 1 Man-6-P_recep Cation-dependent mannose-6-phosphate r 0.9 20 1 beta-lactamase Beta-lactamase 0.6 38 1 Glyco_hydro_1 Glycosyl hydrolase family 1 -1.2 57 1 Bacteriofer Bacterioferritin -110.1 1e+02 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- vwa 1/1 78 249 .. 1 200 [] 37.9 2.3e-07 Bacteriofer 1/1 132 255 .. 1 155 [] -110.1 1e+02 Glyco_hydro_1 1/1 271 284 .. 515 528 .] -1.2 57 Man-6-P_recep 1/1 394 406 .. 266 278 .] 0.9 20 beta-lactamase 1/1 438 452 .. 1 15 [. 0.6 38 Alignments of top-scoring domains: vwa: domain 1 of 1, from 78 to 249: score 37.9, E = 2.3e-07 *->DivFLlDGSgSigsqnFervKdFvervverLdvgprdkkeedavrVg D++F+lD SgS+ ++ ++++ Fve+++ ++ + + r + tem19parti 78 DLYFILDKSGSVLHH-WNEIYYFVEQLAHKFIS---PQ-----LRMS 115 lvQYSdnvrtEikfklndyqnkdevlqalqkiryedyyggggtnTgaALq + +S++ +t++k + + q + l+ lqk++ gg t ++ tem19parti 116 FIVFSTRGTTLMKLTEDREQIRQ-GLEELQKVL-----PGGDTYMHEGFE 159 yvvrnlft.easGsRiepvaeegapkvlVvlTDGrsqddpspTi.dirdv + ++++ + ++G R + v++ lTDG+ ++d + + ++ tem19parti 160 RASEQIYYeNRQGYR--------TASVIIALTDGELHED-L--FfYSERE 198 lnelkkeagvevfaiGvGnadnnnleeLreIAskpddhvfkvsdfea.Ld +n+ ++ g +v+ +Gv++ +n + +L +IA + dhvf v+d ++ L+ tem19parti 199 ANRSRD-LGAIVYCVGVKD-FN--ETQLARIADSK-DHVFPVNDGFQaLQ 243 tlqelL<-* +++ + tem19parti 244 GIIHSI 249 Bacteriofer: domain 1 of 1, from 132 to 255: score -110.1, E = 1e+02 *->MKGdpkVIeyLNklLggELaAinQYFlHsRmyedWGltkLaererhE d++ I++ + L L + Y m e G+++ e ++ E tem19parti 132 ---DREQIRQGLEELQKVLPGGDTY-----MHE--GFERASEQIYYE 168 SieEMkHADklIeRILfLEGlPNLqeLdkLrIGetvrEmLeaDLalEyev + A+ +I+ L + Ge + + + E e+ tem19parti 169 NRQGYRTASVIIA----------LTD------GELHEDLFFY---SEREA 199 .rkaLkeAialCeevqDYvSRdLleeilaDTEEdHiDWLEtQLdLidKIG +r + Ai +C v+D +L + +aD dH+ ++ I tem19parti 200 nRSRDLGAIVYCVGVKDFNETQL--ARIAD-SKDHVFPVNDGFQALQGII 246 lenYlQsqa<-* s++ tem19parti 247 HSILKKSCI 255 Glyco_hydro_1: domain 1 of 1, from 271 to 284: score -1.2, E = 57 *->YkevirnNgfplkr<-* ++ v+r+Ngf+ +r tem19parti 271 FQVVVRGNGFRHAR 284 Man-6-P_recep: domain 1 of 1, from 394 to 406: score 0.9, E = 20 *->EEsEERDDHLLPm<-* EEsEE DD LP tem19parti 394 EESEEEDDDGLPK 406 beta-lactamase: domain 1 of 1, from 438 to 452: score 0.6, E = 38 *->eedlaalekqfdArl<-* +e++a+lek ++Ar+ tem19parti 438 TEEGAKLEKAKNARV 452 // 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: tem8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem19partial Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- vwa von Willebrand factor type A domain 36.1 1.7e-09 1 GIDA Glucose inhibited division protein A 4.0 2.9 1 TarH Tar ligand binding domain homologues 2.5 20 1 IRS PTB domain (IRS-1 type) 2.5 30 1 CBFB_NFYA CCAAT-binding transcription factor (CB 1.6 15 1 Man-6-P_recep Cation-dependent mannose-6-phosphate r 0.9 20 1 SIS SIS domain 0.6 77 1 beta-lactamase Beta-lactamase 0.6 38 1 Flavi_capsid Flavivirus capsid protein C 0.5 94 1 Glyco_hydro_1 Glycosyl hydrolase family 1 -1.2 57 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- CBFB_NFYA 1/1 133 156 .. 17 40 .. 1.6 15 TarH 1/1 154 177 .. 119 142 .] 2.5 20 vwa 1/1 78 249 .. 1 200 [] 36.1 1.7e-09 SIS 1/1 203 249 .. 94 140 .. 0.6 77 Glyco_hydro_1 1/1 271 284 .. 515 528 .] -1.2 57 IRS 1/1 267 291 .. 1 28 [. 2.5 30 GIDA 1/1 331 348 .. 140 157 .. 4.0 2.9 Flavi_capsid 1/1 352 371 .. 107 126 .] 0.5 94 Man-6-P_recep 1/1 394 406 .. 266 278 .] 0.9 20 beta-lactamase 1/1 438 452 .. 1 15 [. 0.6 38 Alignments of top-scoring domains: CBFB_NFYA: domain 1 of 1, from 133 to 156: score 1.6, E = 15 *->RRqaRakleaelklikarkkYLHe<-* R q R+ le+ +k+ Y+He tem19parti 133 REQIRQGLEELQKVLPGGDTYMHE 156 TarH: domain 1 of 1, from 154 to 177: score 2.5, E = 20 *->mqdgfdpayrdwlqqavklkgeav<-* m +gf+ a ++++ ++ + +++a+ tem19parti 154 MHEGFERASEQIYYENRQGYRTAS 177 vwa: domain 1 of 1, from 78 to 249: score 36.1, E = 1.7e-09 *->DivFLlDGSgSigsqnFervKdFvervverLdvgprdkkeedavrVg D++F+lD SgS+ ++ ++++ Fve+++ ++ + + r + tem19parti 78 DLYFILDKSGSVLHH-WNEIYYFVEQLAHKFIS---PQ-----LRMS 115 lvQYSdnvrtEikfklndyqnkdevlqalqkiryedyyggggtnTgaALq + +S++ +t++k + + q + l+ lqk++ gg t ++ tem19parti 116 FIVFSTRGTTLMKLTEDREQIRQ-GLEELQKVL-----PGGDTYMHEGFE 159 yvvrnlft.easGsRiepvaeegapkvlVvlTDGrsqddpspTi.dirdv + ++++ + ++G R + v++ lTDG+ ++d + + ++ tem19parti 160 RASEQIYYeNRQGYR--------TASVIIALTDGELHED-L--FfYSERE 198 lnelkkeagvevfaiGvGnadnnnleeLreIAskpddhvfkvsdfea.Ld +n+ ++ g +v+ +Gv++ +n + +L +IA + dhvf v+d ++ L+ tem19parti 199 ANRSRD-LGAIVYCVGVKD-FN--ETQLARIADSK-DHVFPVNDGFQaLQ 243 tlqelL<-* +++ + tem19parti 244 GIIHSI 249 SIS: domain 1 of 1, from 203 to 249: score 0.6, E = 77 *->karga.akiiaiTnndgsslareasiddlilripaepealqaastsa +++ga ++++ + +++ lar a d++++++ + +alq+ ++++ tem19parti 203 RDLGAiVYCVGVKDFNETQLARIADSKDHVFPVNDGFQALQG-IIHS 248 i<-* i tem19parti 249 I 249 Glyco_hydro_1: domain 1 of 1, from 271 to 284: score -1.2, E = 57 *->YkevirnNgfplkr<-* ++ v+r+Ngf+ +r tem19parti 271 FQVVVRGNGFRHAR 284 IRS: domain 1 of 1, from 267 to 291: score 2.5, E = 30 *->gkevwvvnvkteglercknLlsGsyrLr<-* + e+++v+v+++g +++n + +L+ tem19parti 267 AGESFQVVVRGNGFRHARN---VDRVLC 291 GIDA: domain 1 of 1, from 331 to 348: score 4.0, E = 2.9 *->VvtqdGlefrAkaVviTT<-* V ++dGl f +++V+iTT tem19parti 331 VSMNDGLSFISSSVIITT 348 Flavi_capsid: domain 1 of 1, from 352 to 371: score 0.5, E = 94 *->SedsltwlflllaLlpmamA<-* S +s+ ++ll+ l+ a+A tem19parti 352 SDGSILAIALLILFLLLALA 371 Man-6-P_recep: domain 1 of 1, from 394 to 406: score 0.9, E = 20 *->EEsEERDDHLLPm<-* EEsEE DD LP tem19parti 394 EESEEEDDDGLPK 406 beta-lactamase: domain 1 of 1, from 438 to 452: score 0.6, E = 38 *->eedlaalekqfdArl<-* +e++a+lek ++Ar+ tem19parti 438 TEEGAKLEKAKNARV 452 // 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: tem8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem19partial 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: Thu Dec 14 16:49:06 2000 Sequence file: tem8 ---------------------------------------- Sequence tem19partial (598 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 200: NRSR 218: NETQ 296: NDSV 517: NFTR Total matches: 4 Matching pattern PS00004 CAMP_PHOSPHO_SITE: 472: RRPS Total matches: 1 Matching pattern PS00005 PKC_PHOSPHO_SITE: 12: SLR 18: SSR 29: SPR 42: SPR 120: STR 195: SER 292: SFK 476: SPR 512: TGR Total matches: 9 Matching pattern PS00006 CK2_PHOSPHO_SITE: 2: TREE 183: TDGE 195: SERE 253: SCIE 300: TLNE 307: SVED 332: SMND 396: SEEE 437: STEE Total matches: 9 Matching pattern PS00008 MYRISTYL: 69: GGPACY 244: GIIHSI 324: GMKAAL 354: GSILAI Total matches: 4 Matching pattern PS00009 AMIDATION: 63: GGRR Total matches: 1 Total no of hits in this sequence: 28 ======================================== 1314 pattern(s) searched in 1 sequence(s), 598 residues. Total no of hits in all sequences: 28. Search time: 00:00 min ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Profile Search ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with motif search against own library ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** argv[1]=P argv[2]=-m /data/patterns/own/motif.fa argv[4]=-seq tem8 ***** 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, 598 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: tem8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem19partial 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: tem8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: tem19partial 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 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= tem19partial (598 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value VWA Von Willebrand factor A domain 79 2e-17 PCNA Proliferating Cell nuclear antigen like domain 26 0.21 SGTP Small GTPAses 25 0.24 ARR Arrestin domain 24 0.61 INSL Insulinase like Metallo protease domain 24 0.66 14-3-3 14-3-3 protein alpha Helical domain 23 1.3 PAP Papain/bleomycin hydrolase like domain 22 2.6 KIN Protein kinase domain 22 3.4 DSP Dual specificity protein phosphatase 21 3.6 SH3 Src Homology domain 3 21 3.8 RHOGAP RHO-type GTPase GTP hydrolysis activating protein 21 4.1 PP2C PP2C type phosphatase domain 21 5.9 CBS cystathionine beta -synthase domain (A predicted ligand... 20 6.7 BRIGHT BRIGHT domain (Alpha helical DNA binding domain) 20 8.3 SNARE Alpha helical domains which are involved in vesicle fu... 20 8.5 AP2 A plant specific DNA binding domain (Apetala 2 like) 20 9.4 >VWA Von Willebrand factor A domain Length = 255 Score = 78.7 bits (192), Expect = 2e-17 Identities = 20/202 (9%), Positives = 20/202 (9%), Gaps = 22/202 (10%) Query: 78 DLYFILDKSGSV-LHHWNEIYYFVEQLAHKFI-------SPQLRMSFIVFSTRGT-TLMK 128 Sbjct: 55 SLILTLDCSEAMLEKDLRPNRHAMIIQYAIDFVHEFFDQNPISQMGIIIMRNGLAQLVSQ 114 Query: 129 LTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELH 188 Sbjct: 115 VSGNPQDHIDALKSIRKQEPKGNPSLQNALEMARG--LLLPVPAHCTREVLIVFGSLSTT 172 Query: 189 EDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIAD---SKD-HVFPVNDGFQALQG 244 Sbjct: 173 DPG--DIHQTIDSLVSEKIRVKVLGL-SAQVAICKELCKATNYGDESFYKILLDETHLK- 228 Query: 245 IIHSILKKSCIEILAAEPSTIC 266 Sbjct: 229 ---ELFNEAVTPLPVNKINKGF 247 >PCNA Proliferating Cell nuclear antigen like domain Length = 280 Score = 25.6 bits (56), Expect = 0.21 Identities = 5/64 (7%), Positives = 5/64 (7%), Gaps = 2/64 (3%) Query: 292 SFKINDSVTLNEKPFSVEDTYLLCPAPILKEVGMKAALQVSMNDGLSFISSSVIITTTHC 351 Sbjct: 125 EGGVVTVCKITTQEPEETLDFDFCSTNVMNKIILQSEGLREAFSELDMTGDVLQITVS-- 182 Query: 352 SDGS 355 Sbjct: 183 PDKP 186 >SGTP Small GTPAses Length = 164 Score = 25.1 bits (55), Expect = 0.24 Identities = 13/65 (20%), Positives = 13/65 (20%), Gaps = 7/65 (10%) Query: 284 RNVDRVLCSFKINDSVTLNEKPFSVEDTYLLCP--APILKEVGMKAAL----QVSMNDGL 337 Sbjct: 71 RGAAGALLVYDITSRETYNALTNWLTDARMLASQNIVIIL-CGNKKDLDADREVTFLEAS 129 Query: 338 SFISS 342 Sbjct: 130 RFAQE 134 >ARR Arrestin domain Length = 454 Score = 23.7 bits (51), Expect = 0.61 Identities = 5/25 (20%), Positives = 5/25 (20%) Query: 569 SPPSTLPPPPQAPPPNRAPPPSRPP 593 Sbjct: 380 SKPPESPERTDRGLPSIEATNGSEP 404 >INSL Insulinase like Metallo protease domain Length = 433 Score = 23.8 bits (51), Expect = 0.66 Identities = 15/80 (18%), Positives = 15/80 (18%), Gaps = 13/80 (16%) Query: 155 HEGFERASEQIYYENRQGYRTASVIIALTDGELHE-------DLFFYSEREANRSRDLGA 207 Sbjct: 327 PENYEKVKKRVFEL------LKETYENLTDEQVEEAKSRIINSRLFEEERVENDAFDIGY 380 Query: 208 IVYCVGVKDFNETQLARIAD 227 Sbjct: 381 SYTVVRDLDFYRFFDKNLSR 400 >14-3-3 14-3-3 protein alpha Helical domain Length = 270 Score = 22.6 bits (48), Expect = 1.3 Identities = 16/52 (30%), Positives = 16/52 (30%), Gaps = 2/52 (3%) Query: 126 LMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTAS 177 Sbjct: 12 LAKLAEQAERYEGMVENMKSVASTDQELTVE--ERNLLSVAYKNVIGARRAS 61 >PAP Papain/bleomycin hydrolase like domain Length = 376 Score = 21.9 bits (46), Expect = 2.6 Identities = 4/19 (21%), Positives = 4/19 (21%) Query: 560 PSAPTPPIPSPPSTLPPPP 578 Sbjct: 358 PLTARVQKPDMKPRVSCPP 376 Score = 20.8 bits (43), Expect = 4.7 Identities = 4/16 (25%), Positives = 4/16 (25%) Query: 542 PAPIYTPPPPAPHCPP 557 Sbjct: 361 ARVQKPDMKPRVSCPP 376 Score = 20.0 bits (41), Expect = 9.2 Identities = 3/16 (18%), Positives = 3/16 (18%) Query: 526 PAKYPLNNAYHTSSPP 541 Sbjct: 361 ARVQKPDMKPRVSCPP 376 >KIN Protein kinase domain Length = 313 Score = 21.6 bits (45), Expect = 3.4 Identities = 9/67 (13%), Positives = 9/67 (13%), Gaps = 4/67 (5%) Query: 125 TLMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTD 184 Sbjct: 61 KISKAFDNLKDTKRTLREIHLL----RHFKHENLISIKDILKPNSKEQFEDVYIVSELMD 116 Query: 185 GELHEDL 191 Sbjct: 117 TDLHQII 123 >DSP Dual specificity protein phosphatase Length = 185 Score = 21.5 bits (45), Expect = 3.6 Identities = 4/27 (14%), Positives = 4/27 (14%) Query: 317 APILKEVGMKAALQVSMNDGLSFISSS 343 Sbjct: 48 IPKLQKLGITHVLNAAEGRSFMHVNTN 74 >SH3 Src Homology domain 3 Length = 90 Score = 21.3 bits (45), Expect = 3.8 Identities = 6/17 (35%), Positives = 6/17 (35%) Query: 576 PPPQAPPPNRAPPPSRP 592 Sbjct: 1 PRVQAWSPPVRGIPQLP 17 Score = 20.9 bits (44), Expect = 4.5 Identities = 5/14 (35%), Positives = 5/14 (35%) Query: 558 PPPSAPTPPIPSPP 571 Sbjct: 1 PRVQAWSPPVRGIP 14 >RHOGAP RHO-type GTPase GTP hydrolysis activating protein Length = 194 Score = 21.0 bits (44), Expect = 4.1 Identities = 4/26 (15%), Positives = 4/26 (15%), Gaps = 4/26 (15%) Query: 126 LMKLT----EDREQIRQGLEELQKVL 147 Sbjct: 164 ILQHSHGIEEERQDLTTALGLVKELL 189 >PP2C PP2C type phosphatase domain Length = 254 Score = 20.6 bits (43), Expect = 5.9 Identities = 7/49 (14%), Positives = 7/49 (14%) Query: 181 ALTDGELHEDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIADSK 229 Sbjct: 79 LLRDALMDANEGILEDQKINLERRDMGTTAVLIAFREDGAWRAHVGDSR 127 >CBS cystathionine beta -synthase domain (A predicted ligand binding domain) Length = 214 Score = 20.3 bits (42), Expect = 6.7 Identities = 7/76 (9%), Positives = 7/76 (9%), Gaps = 8/76 (10%) Query: 273 VVVRGN----GFRHARNVDRVL---CSFKINDSVTLNEKPFSV-EDTYLLCPAPILKEVG 324 Sbjct: 36 PIVDKEDRLVGWVTTLELLGISEKDFKKPITEFMRPVEEVITVYEDDEARNVVLKFVKYK 95 Query: 325 MKAALQVSMNDGLSFI 340 Sbjct: 96 VVSIPVLTRDGRVIGM 111 Score = 20.3 bits (42), Expect = 6.8 Identities = 9/53 (16%), Positives = 9/53 (16%), Gaps = 3/53 (5%) Query: 209 VYCVGVKDFNETQLARIADSKDHVFPVNDGFQALQGIIHSILKKSCIEILAAE 261 Sbjct: 75 VITVYEDDEARNVVLKFVKYKVVSIPVLTRDGRVIGMVR---NCDVVKTLAKL 124 >BRIGHT BRIGHT domain (Alpha helical DNA binding domain) Length = 172 Score = 20.3 bits (42), Expect = 8.3 Identities = 6/29 (20%), Positives = 6/29 (20%), Gaps = 1/29 (3%) Query: 16 VASSRSVGRSGPCSPRAAGHGHGGAESPR 44 Sbjct: 125 IDGNRREGRRSSYGQYEAMH-NQMPMTPI 152 >SNARE Alpha helical domains which are involved in vesicle fusion Length = 254 Score = 20.2 bits (42), Expect = 8.5 Identities = 4/20 (20%), Positives = 4/20 (20%) Query: 357 LAIALLILFLLLALALLWWF 376 Sbjct: 187 PATLSGIVAFILSLLCGALN 206 >AP2 A plant specific DNA binding domain (Apetala 2 like) Length = 218 Score = 20.1 bits (41), Expect = 9.4 Identities = 7/25 (28%), Positives = 7/25 (28%) Query: 446 KAKNARVKMPEQEYEFPEPRNLNNN 470 Sbjct: 83 KGASAILNFPDLAGSFPRPSSLSPR 107 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 16 Number of calls to ALIGN: 20 Length of query: 598 Total length of test sequences: 20182 Effective length of test sequences: 16637.0 Effective search space size: 9391311.1 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= tem19partial (598 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|420193 [185..357] Integrin A (or I) domain 86 1e-18 gi|2582830 [161..353] Integrin A (or I) domain 81 4e-17 gi|2645090 [1..155] Integrin A (or I) domain 76 2e-15 gi|102029 [2..423] Phosphoglycerate kinase 28 0.38 gi|1001744 [209..396] alpha/beta-Hydrolases 28 0.45 gi|2499877 [3..454] Cysteine proteinases 28 0.45 gi|555731 [3..383] Serpins 28 0.64 gi|1346563 [21..174] Periplasmic binding protein-like I 27 0.78 gi|543771 [1..98] Ferredoxin-like 27 0.89 gi|116871 [267..480] 4-bladed beta-propeller 27 1.1 gi|2622097 [427..630] ATP-grasp 26 1.7 gi|1572759 [30..280] Trypsin-like serine proteases 25 3.1 gi|124505 [1..400] Sugar phosphatases 25 4.3 gi|398985 [18..447] PLP-dependent transferases 24 5.1 gi|416621 [37..465] Serpins 25 5.2 gi|127815 [6..138] Bleomycin resistance protein/Dihydroxybip... 24 5.7 gi|2194029 [140..303] Ferredoxin reductase-like, C-terminal ... 24 6.5 gi|1001472 [191..704] N-terminal nucleophile aminohydrolases... 24 7.3 gi|1086887 [26..189] P-loop containing nucleotide triphospha... 24 7.4 gi|1350557 [4..271] P-loop containing nucleotide triphosphat... 24 7.7 gi|483174 [15..156] Four-helical up-and-down bundle 24 8.1 gi|229680 [2..306] Periplasmic binding protein-like I 24 8.8 gi|1706496 [2..127] DNA clamp 24 8.9 gi|2414449 [42..312] alpha/beta-Hydrolases 24 9.5 >gi|420193 [185..357] Integrin A (or I) domain Length = 173 Score = 86.1 bits (211), Expect = 1e-18 Identities = 36/179 (20%), Positives = 36/179 (20%), Gaps = 20/179 (11%) Query: 78 DLYFILDKSGSV-LHHWNEIYYFVEQL------AHKFISP-QLRMSFIVFSTRGTTLMKL 129 Sbjct: 1 DIVFLLDGSERLGEQNFHKVRRFVEDVSRRLTLARRDDDPLNARMALLQYGSQNQQQVAF 60 Query: 130 TE--DREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTAS--VIIALTDG 185 Sbjct: 61 PLTYNVTTIHEALERAT--YLNSFSHVGTGIVHAINNVVRGARGGARRHAELSFVFLTDG 118 Query: 186 ELHEDLFFYSEREANRSRDLGAIVYCVGVK-DFNETQLARIA-DSKDHVFPVNDGFQAL 242 Sbjct: 119 VTGND---SLEESVHSMRKQNVVPTVVAVGGDVDMDVLTKISLGDRAAIFREKD-FDSL 173 >gi|2582830 [161..353] Integrin A (or I) domain Length = 193 Score = 81.5 bits (199), Expect = 4e-17 Identities = 34/196 (17%), Positives = 34/196 (17%), Gaps = 26/196 (13%) Query: 78 DLYFILDKSGSVLHHWNEIYYFVEQLAHKF-ISPQL-RMSFIVFSTRGTTLMKLTEDREQ 135 Sbjct: 2 DIVIVLDGSNSI-YPWESVTAFLNSLLRNMDIGPQQTQVGIVQYGQTVVHEFYLN-TYST 59 Query: 136 IRQGLEELQKV--LPGGDTYMHEGFERASEQIYYE---NRQGYRTASVIIALTDGELHED 190 Sbjct: 60 TEEVMDAALRIRQRGGTQTMTALGIDTAREEAFTEAHGARRGVQK--VMVIVTDGE--SH 115 Query: 191 LFFYSEREANRSRDLGAIVYCVGVK-DFNETQLARIADSK-----------DHVFPVNDG 238 Sbjct: 116 DNYRLQEVIDKCEDENIQRFAIAILGSYSRGNLSTEKFVEEIKSIASKPTEKHFFNVSD- 174 Query: 239 FQALQGIIHSILKKSC 254 Sbjct: 175 ELALVTIVEALGERIF 190 >gi|2645090 [1..155] Integrin A (or I) domain Length = 155 Score = 76.0 bits (185), Expect = 2e-15 Identities = 34/159 (21%), Positives = 34/159 (21%), Gaps = 16/159 (10%) Query: 79 LYFILDKSGSV-LHHWNEIYYFVEQLAHKFISPQL--RMSFIVFSTRGTTLMKLTE--DR 133 Sbjct: 1 MLFLLDSSGSVGDENFDKMKEFVKSIVLNFDVDNQLTRIGIIRFDSDAEIIIQLSDHKTL 60 Query: 134 EQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTDG-----ELH 188 Sbjct: 61 KDLLNDIDSI-RYNEGIQTRIDKALERAMEAFSEKNGGRADATKALVLLADGQNSFIEGS 119 Query: 189 EDLFFYSEREANRSRDLGAIVYCVGV-KDFNETQLARIA 226 Sbjct: 120 QDL----NEELKPLIDAKVFRYVIGIGRELDLKELEDIA 154 >gi|102029 [2..423] Phosphoglycerate kinase Length = 422 Score = 28.3 bits (63), Expect = 0.38 Identities = 17/74 (22%), Positives = 17/74 (22%), Gaps = 10/74 (13%) Query: 172 GYRTASVIIALTDGE--LHEDLFFYSEREANRSRDLGAIVYCVGVKDFNE--TQLARIAD 227 Sbjct: 106 GPEVEAIVNKADNGAVILLENLRFHIEEEGSSKDKEGNKTK-ADKAKVEEFRKGLTALGD 164 Query: 228 SKDHVFPVNDGFQA 241 Sbjct: 165 ----VY-VNDAFGT 173 >gi|1001744 [209..396] alpha/beta-Hydrolases Length = 188 Score = 28.0 bits (62), Expect = 0.45 Identities = 12/72 (16%), Positives = 12/72 (16%), Gaps = 10/72 (13%) Query: 117 IVFSTRGT-TLMKLTEDREQIRQGLEELQKVLPG-GDTYMHEGFERASEQIYYE-----N 169 Sbjct: 10 NLIVFRGTQTTMEWVNN---LRAQQIPFTERRSGQYFGKIHQGFIENYLRIVSPIPREIA 66 Query: 170 RQGYRTASVIIA 181 Sbjct: 67 QQLDPAVPCYVT 78 >gi|2499877 [3..454] Cysteine proteinases Length = 452 Score = 27.8 bits (61), Expect = 0.45 Identities = 4/23 (17%), Positives = 4/23 (17%) Query: 556 PPPPPSAPTPPIPSPPSTLPPPP 578 Sbjct: 424 KKHVPEEVLAVLEQEPIVLPAWD 446 >gi|555731 [3..383] Serpins Length = 381 Score = 27.6 bits (61), Expect = 0.64 Identities = 9/68 (13%), Positives = 9/68 (13%), Gaps = 11/68 (16%) Query: 108 ISPQLRMSFIVFSTRGTTLMKLTEDREQIRQGLE----ELQKVLPGGDTYMHEGFERASE 163 Sbjct: 25 VLFTLGILLGSGGAQGKT-------SYQIAKTMRLKSANFPWNISETQQEMKSLYKELSD 77 Query: 164 QIYYENRQ 171 Sbjct: 78 SLTMENTS 85 >gi|1346563 [21..174] Periplasmic binding protein-like I Length = 154 Score = 27.2 bits (60), Expect = 0.78 Identities = 22/155 (14%), Positives = 22/155 (14%), Gaps = 25/155 (16%) Query: 135 QIRQGLEELQKVLPGGDTYM-HEGFERASEQIYYENRQGYRTASVIIALTDGELHEDLFF 193 Sbjct: 17 LLRNGMEDYAKTLDGVDLQIEDALNDVAKQQSQIQNFIAAGVDAIIVQPVDTDATTVM-- 74 Query: 194 YSEREANRSRDLGAIVYCVGVKDFNETQLARIADSKDHVFPVND-----GFQALQGIIHS 248 Sbjct: 75 --SKLAA-DAGIPLVYV--------NREPVNIDTLPEKQAFVASNEVDSGTLQTREICKL 123 Query: 249 ILKKSCIEILAAEPSTICAGESFQVVVRGNGFRHA 283 Sbjct: 124 LDGKGKAVVIMGELSNQAARM------RTKDIHDV 152 >gi|543771 [1..98] Ferredoxin-like Length = 98 Score = 26.8 bits (59), Expect = 0.89 Identities = 11/52 (21%), Positives = 11/52 (21%), Gaps = 6/52 (11%) Query: 98 YFVEQLAHKFISPQLRMSFIVFST-RGTTLMKLTEDREQIRQGLEELQKVLP 148 Sbjct: 24 MYTEGEAKK-----IGVVGWVKNTSKGTVTGQVQGPEEKVNSMKSWLSKVGS 70 >gi|116871 [267..480] 4-bladed beta-propeller Length = 214 Score = 26.8 bits (59), Expect = 1.1 Identities = 6/26 (23%), Positives = 6/26 (23%), Gaps = 2/26 (7%) Query: 557 PPPPSAPTPPIPSPPSTLPPPPQAPP 582 Sbjct: 2 TPALGPQAGIDTNEIA--PLEPDAPP 25 >gi|2622097 [427..630] ATP-grasp Length = 204 Score = 26.1 bits (57), Expect = 1.7 Identities = 13/100 (13%), Positives = 13/100 (13%), Gaps = 11/100 (11%) Query: 127 MKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTDGE 186 Sbjct: 52 MEIVYDDVELEEYMREAVRVSPEHPILVDKFLEDAIEVDVDALCDGTDVYIGGIMEHIEE 111 Query: 187 LHEDLFFYSEREANRSRDLGAIVYCVGVKDFNETQLARIA 226 Sbjct: 112 -----------AGVHSGDSACVIPPQSIPEDIIDTIKEYT 140 >gi|1572759 [30..280] Trypsin-like serine proteases Length = 251 Score = 25.1 bits (54), Expect = 3.1 Identities = 5/88 (5%), Positives = 5/88 (5%), Gaps = 8/88 (9%) Query: 460 EFPEPRNLNNNMRRPSSPRKWYSPIKGK--LDALWVLLRKGYDRVSVMRPQPGDTGRCIN 517 Sbjct: 116 RISSDLSKLGIKPVCLVHDDSKLLKQYKNGVVIGYGLTLGEDSSGEPKLINS-QTLQSTS 174 Query: 518 FTRVKNNQPAKYPLNNAYHTSSPPPAPI 545 Sbjct: 175 VPIISDDD-----CVKTWRFLSLLSVKI 197 >gi|124505 [1..400] Sugar phosphatases Length = 400 Score = 24.6 bits (53), Expect = 4.3 Identities = 17/71 (23%), Positives = 17/71 (23%), Gaps = 4/71 (5%) Query: 149 GGDTYMHEGFERASEQIYYENRQGYR----TASVIIALTDGELHEDLFFYSEREANRSRD 204 Sbjct: 289 AGAGYKSLCVILGLADIYIFSEDTTFKWDSCAAHAILRAMGGGMVDLKECLERNPDTGLD 348 Query: 205 LGAIVYCVGVK 215 Sbjct: 349 LPQLVYHVGNE 359 >gi|398985 [18..447] PLP-dependent transferases Length = 430 Score = 24.4 bits (52), Expect = 5.1 Identities = 7/43 (16%), Positives = 7/43 (16%) Query: 221 QLARIADSKDHVFPVNDGFQALQGIIHSILKKSCIEILAAEPS 263 Sbjct: 95 GPFYLAHDRISFVQTLSGTGALAVAAKFLALFISRDIWIPDPS 137 >gi|416621 [37..465] Serpins Length = 429 Score = 24.6 bits (53), Expect = 5.2 Identities = 10/89 (11%), Positives = 10/89 (11%), Gaps = 13/89 (14%) Query: 107 FISP---QLRMSFIVFSTRGTTLMKLTEDREQIRQGLEELQKVLPGGDTYMHEGFERASE 163 Sbjct: 74 FLSPLSISTAFAMTKLGACNDT-------LKQLMEVF-KFDTISEKTSDQIHFFFAKLNC 125 Query: 164 QIYYENRQGY--RTASVIIALTDGELHED 190 Sbjct: 126 RLYRKANKSSDLVSANRLFGDKSLTFNES 154 >gi|127815 [6..138] Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase Length = 133 Score = 24.1 bits (52), Expect = 5.7 Identities = 5/42 (11%), Positives = 5/42 (11%), Gaps = 4/42 (9%) Query: 65 RREDGGPACYGGFDLYFILDKSGSVLHHWNEIYYFVEQLAHK 106 Sbjct: 89 VCDKVEAQERMVLGLMKTEDPGG----NPTEIFWGPRIDMSN 126 >gi|2194029 [140..303] Ferredoxin reductase-like, C-terminal NADP-linked domain Length = 164 Score = 24.1 bits (52), Expect = 6.5 Identities = 7/75 (9%), Positives = 7/75 (9%), Gaps = 15/75 (20%) Query: 134 EQIRQGLEELQKVLPGGDTYMH----EGFERASEQIYYENRQGYRTASVIIALTDGELHE 189 Sbjct: 99 DRVAEHADQLWQLIKNQKTHTYICGLRGMEEGIDAALSA-----------AAAKEGVTWS 147 Query: 190 DLFFYSEREANRSRD 204 Sbjct: 148 DYQKDLKKAGRWHVE 162 >gi|1001472 [191..704] N-terminal nucleophile aminohydrolases (Ntn hydrolases) Length = 514 Score = 23.8 bits (51), Expect = 7.3 Identities = 13/89 (14%), Positives = 13/89 (14%), Gaps = 7/89 (7%) Query: 457 QEYEFPEPRNLNNNMRRPSSPRKWYSPIKGKLDALWVLLRKGYDRVSVMR------PQPG 510 Sbjct: 366 QWNPAD-PLNTPSGMADINKFMAVLEGVAAQVKFLYDDLAISWGEVVQMQVGNFTAPANG 424 Query: 511 DTGRCINFTRVKNNQPAKYPLNNAYHTSS 539 Sbjct: 425 APSNLGSFRVLALSTIANQRFQAVAGDSY 453 >gi|1086887 [26..189] P-loop containing nucleotide triphosphate hydrolases Length = 164 Score = 24.1 bits (51), Expect = 7.4 Identities = 13/120 (10%), Positives = 13/120 (10%), Gaps = 14/120 (11%) Query: 144 QKVLPGGDTYMHEGFERASEQIYYENRQGYRTASVIIALTDGELHEDLFFYSEREANRSR 203 Sbjct: 47 TVELIEKDLGGLTNEDNGFKKTEMRDVDA---VLLFYAADDLESFKQLKENLVHVQRKIP 103 Query: 204 DLGAIVYCVGVKD-----FNETQLARIADSKD-HVFPV----NDGF-QALQGIIHSILKK 252 Sbjct: 104 PNANITVVGTKADVKEMQVQWQEVDSFAENQGFSCFETSSKTGVNVEIILHDILETIFER 163 >gi|1350557 [4..271] P-loop containing nucleotide triphosphate hydrolases Length = 268 Score = 23.9 bits (50), Expect = 7.7 Identities = 10/71 (14%), Positives = 10/71 (14%), Gaps = 4/71 (5%) Query: 443 KLEKAKNARVKMPEQEYEFPEPRNLNNNMRRPSSPRKWYSPIKGKLDALWVLLRKGYDRV 502 Sbjct: 3 EKEKAIELAMSAVERQFGKGSIMRLGNDEPMMRDVQAIPTGSISLDIALGVGGVPKGRII 62 Query: 503 SVMRPQPGDTG 513 Sbjct: 63 EIF----GPES 69 >gi|483174 [15..156] Four-helical up-and-down bundle Length = 142 Score = 23.7 bits (51), Expect = 8.1 Identities = 5/20 (25%), Positives = 5/20 (25%) Query: 128 KLTEDREQIRQGLEELQKVL 147 Sbjct: 118 HMRKLRKRVLRDAEDLQRRL 137 >gi|229680 [2..306] Periplasmic binding protein-like I Length = 305 Score = 23.8 bits (51), Expect = 8.8 Identities = 19/162 (11%), Positives = 19/162 (11%), Gaps = 32/162 (19%) Query: 161 ASEQIYYENRQGYRTASVIIALTDGELHEDLFFYSEREANRSRDLGAIVYCVGVKDFNET 220 Sbjct: 43 EKTLNAIDSLAASGAKGFVICTPDPKLGSAI----VAKARG-YDMKVIAV-----DDQFV 92 Query: 221 QLARIADSKDHVFPVND-----GFQALQGIIHSILKK-----SCIEILAAEPSTICAGES 270 Sbjct: 93 NAK--GKPMDTVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARR- 149 Query: 271 FQVVVRGNGFRHARNVDRVLCSFKINDSVTLNEKPFSVEDTY 312 Sbjct: 150 -----RTTGSMDALKAA----GFPEKQIYQVPTKSNDIPGAF 182 >gi|1706496 [2..127] DNA clamp Length = 126 Score = 23.7 bits (51), Expect = 8.9 Identities = 6/26 (23%), Positives = 6/26 (23%) Query: 127 MKLTEDREQIRQGLEELQKVLPGGDT 152 Sbjct: 1 MEFTIKRDYFITQLNDTLKAISPRTT 26 >gi|2414449 [42..312] alpha/beta-Hydrolases Length = 271 Score = 23.7 bits (51), Expect = 9.5 Identities = 11/70 (15%), Positives = 11/70 (15%), Gaps = 11/70 (15%) Query: 117 IVFSTRGTTLMKLTEDREQIRQGLEELQKVLPGGD-TYMHEGFERASEQIYYENR----- 170 Sbjct: 54 ITVVFRGT-----KTSSQLLLEGWTTLKPSSDFYGMGLVNTYFRSGHEKTWQYVQDALSI 108 Query: 171 QGYRTASVII 180 Sbjct: 109 SQYRNYDVYV 118 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 24 Number of calls to ALIGN: 24 Length of query: 598 Total length of test sequences: 256703 Effective length of test sequences: 209547.0 Effective search space size: 117038708.7 Initial X dropoff for ALIGN: 25.0 bits