analysis of sequence from tem39 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSKLRLTSPPEPTVMTHVPYQVL ALYNSTRELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVE KNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWLSFDVTDTVRE WLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLIL MMIPPHRLDNPGQGGQRKKRALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPY LRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator Info> Identical 7-residue fragments found in: Info> 1tfg.brk - > Tem39_gi|135684|sp|P10600|TGF3_HUMAN . . . . . 1 MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSK 50 ___HHHHHHHHHHHH__HHHHH_____________HHHHHHHHHHHHHHH . . . . . 51 LRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMHGEREEGCTQENTESEY 100 HH________EEEE__EEEEEE___HHHHHHHHHHHH________HHHHH . . . . . 101 YAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNRTNLFRAE 150 HHHHHH_HHHHHHHHH__EEEEE______EEEEEEEE______HHHHHHH . . . . . 151 FRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWL 200 HEEEE_________HHHHHHHHH________________________EEE . . . . . 201 SFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKF 250 E____HHHHHHHHHHH_____EEEEE__________HHHHHHHHHHHHHH . . . . . 251 KGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRKKR 300 ______________HHHHH________EEEEE______________HHHH . . . . . 301 ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPY 350 HHH______________E__EEEHHHH___EEEE_____EEEE_______ . . . . . 351 LRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQ 400 ___________________________EE_EEEEEEEEEEEE________ . 401 LSNMVVKSCKCS 412 ___EEEEEEEE_ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 30.8 % beta-contents : 25.6 % coil-contents : 43.6 % class : mixed method : 2 alpha-contents : 22.9 % beta-contents : 14.3 % coil-contents : 62.8 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -30.78 -3.09 -1.36 -0.50 -4.00 -4.00 -4.00 0.00 -0.25 -10.30 -3.10 -12.00 -12.00 0.00 -12.00 0.00 -97.39 -24.56 -0.96 -0.72 0.00 -4.00 0.00 0.00 0.00 -4.95 -9.96 -3.10 -12.00 -12.00 0.00 -12.00 0.00 -84.25 ID: Tem39_gi|135684|sp|P10600|TGF3_HUMAN AC: xxx Len: 350 1:I 327 Sc: -84.25 Pv: 8.562063e-01 NO_GPI_SITE GPI: learning from protozoa -44.43 -4.38 -0.16 0.00 -4.00 0.00 0.00 0.00 -0.83 -7.88 -10.82 -12.00 -12.00 0.00 -12.00 0.00 -108.50 -23.66 -3.19 -0.32 0.00 -4.00 0.00 -16.00 0.00 0.00 -8.75 -10.82 -12.00 -12.00 0.00 -12.00 0.00 -102.74 ID: Tem39_gi|135684|sp|P10600|TGF3_HUMAN AC: xxx Len: 350 1:I 337 Sc: -102.74 Pv: 8.991142e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? Tem39_gi|13 0.464 24 Y 0.588 24 Y 0.981 12 Y 0.947 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? Tem39_gi|13 0.548 375 Y 0.310 25 N 0.975 9 Y 0.869 Y # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? Tem39_gi|13 0.524 375 Y 0.475 375 Y 0.989 10 Y 0.197 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) 1-20 MKMHLQRALVVLALLNFATV slslstcttl 21-30 31-76 DFGHIKKKRVEAIRGQILSKLRLTSPPEPT VMTHVPYQVLALYNST relleemhgereeg 77-90 91-412 CTQENTESEYYAKEIHKFDMIQGLAEHNEL AVCPKGITSKVFRFNVSSVEKNRTNLFRAE FRVLRVPNPSSKRNEQRIELFQILRPDEHI AKQRYIGGKNLPTRGTAEWLSFDVTDTVRE WLLRRESNLGLEISIHCPCHTFQPNGDILE NIHEVMEIKFKGVDNEDDHGRGDLGRLKKQ KDHHNPHLILMMIPPHRLDNPGQGGQRKKR ALDTNYCFRNLEENCCVRPLYIDFRQDLGW KWVHEPKGYYANFCSGPCPYLRSADTTHST VLGLYNTLNPEASASPCCVPQDLEPLTILY YVGRTPKVEQLSNMVVKSCKCS low complexity regions: SEG 25 3.0 3.3 >Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) 1-7 MKMHLQR alvvlallnfatvslslstcttl 8-30 31-73 DFGHIKKKRVEAIRGQILSKLRLTSPPEPT VMTHVPYQVLALY nstrelleemhgereegctqentese 74-99 100-412 YYAKEIHKFDMIQGLAEHNELAVCPKGITS KVFRFNVSSVEKNRTNLFRAEFRVLRVPNP SSKRNEQRIELFQILRPDEHIAKQRYIGGK NLPTRGTAEWLSFDVTDTVREWLLRRESNL GLEISIHCPCHTFQPNGDILENIHEVMEIK FKGVDNEDDHGRGDLGRLKKQKDHHNPHLI LMMIPPHRLDNPGQGGQRKKRALDTNYCFR NLEENCCVRPLYIDFRQDLGWKWVHEPKGY YANFCSGPCPYLRSADTTHSTVLGLYNTLN PEASASPCCVPQDLEPLTILYYVGRTPKVE QLSNMVVKSCKCS low complexity regions: SEG 45 3.4 3.75 >Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) 1-412 MKMHLQRALVVLALLNFATVSLSLSTCTTL DFGHIKKKRVEAIRGQILSKLRLTSPPEPT VMTHVPYQVLALYNSTRELLEEMHGEREEG CTQENTESEYYAKEIHKFDMIQGLAEHNEL AVCPKGITSKVFRFNVSSVEKNRTNLFRAE FRVLRVPNPSSKRNEQRIELFQILRPDEHI AKQRYIGGKNLPTRGTAEWLSFDVTDTVRE WLLRRESNLGLEISIHCPCHTFQPNGDILE NIHEVMEIKFKGVDNEDDHGRGDLGRLKKQ KDHHNPHLILMMIPPHRLDNPGQGGQRKKR ALDTNYCFRNLEENCCVRPLYIDFRQDLGW KWVHEPKGYYANFCSGPCPYLRSADTTHST VLGLYNTLNPEASASPCCVPQDLEPLTILY YVGRTPKVEQLSNMVVKSCKCS 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 >Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSKLRLTSPPEPT VMTHVPYQVLALYNSTRELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEHNEL AVCPKGITSKVFRFNVSSVEKNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILRPDEHI AKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILE NIHEVMEIKFKGVDNEDDHGRGDLGRLkkqkdhhnphlilmmippHRLDNPGQGGQRKKR ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHST VLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS 1 - 267 MKMHLQRALV VLALLNFATV SLSLSTCTTL DFGHIKKKRV EAIRGQILSK LRLTSPPEPT VMTHVPYQVL ALYNSTRELL EEMHGEREEG CTQENTESEY YAKEIHKFDM IQGLAEHNEL AVCPKGITSK VFRFNVSSVE KNRTNLFRAE FRVLRVPNPS SKRNEQRIEL FQILRPDEHI AKQRYIGGKN LPTRGTAEWL SFDVTDTVRE WLLRRESNLG LEISIHCPCH TFQPNGDILE NIHEVMEIKF KGVDNEDDHG RGDLGRL 268 - 285 kkq kdhhnphlil mmipp 286 - 412 HRLDN PGQGGQRKKR ALDTNYCFRN LEENCCVRPL YIDFRQDLGW KWVHEPKGYY ANFCS GPCPY LRSADTTHST VLGLYNTLNP EASASPCCVP QDLEPLTILY YVGRTPKVEQ LSNMV VKSCK CS low complexity regions: DUST >Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSKLRLTSPPEPT VMTHVPYQVLALYNSTRELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEHNEL AVCPKGITSKVFRFNVSSVEKNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILRPDEHI AKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILE NIHEVMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRKKR ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHST VLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for Tem39_gi|135684|sp|P10600|TGF3_HUMAN sequence: 350 amino acids, 0 residue(s) in coiled coil state . | . | . | . | . | . 60 MKMHLQRALV VLALLNFATV SLSLSTCTTL DFGHIKKKRV EAIRGQILSK LRLTSPPEPT ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 VMTHVPYQVL ALYNSTRELL EEMHGEREEG CTQENTESEY YAKEIHKFDM IQGLAEHNEL ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~22222 222222222~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 180 AVCPKGITSK VFRFNVSSVE KNRTNLFRAE FRVLRVPNPS SKRNEQRIEL FQILRPDEHI ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . | . | . 240 AKQRYIGGKN LPTRGTAEWL SFDVTDTVRE WLLRRESNLG LEISIHCPCH TFQPNGDILE ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 NIHEVMEIKF KGVDNEDDHG RGDLGRLKKQ KDHHNPHLIL MMIPPHRLDN PGQGGQRKKR ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 . | . | . | . | . | ALDTNYCFRN LEENCCVRPL YIDFRQDLGW KWVHEPKGYY ANFCSGPCPY ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ---------- ---------- ---------- ---------- ---------- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** tem39.___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: tem39.___inter___ (1 sequences) MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSK LRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMHGEREEGCTQENTESEY YAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNRTNLFRAE FRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWL SFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKF KGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRKKR ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPY LRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQ LSNMVVKSCKCS (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 8 28 1.642 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 7 384 K+R profile 3.00 + CYT-EXT prof - -0.13 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 3.00 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: 0.13 -> Orientation: N-out ---------------------------------------------------------------------- "tem39" 412 8 28 #t 1.64167 ************************************ *TOPPREDM with prokaryotic function* ************************************ tem39.___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: tem39.___inter___ (1 sequences) MKMHLQRALVVLALLNFATVSLSLSTCTTLDFGHIKKKRVEAIRGQILSK LRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMHGEREEGCTQENTESEY YAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRFNVSSVEKNRTNLFRAE FRVLRVPNPSSKRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWL SFDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKF KGVDNEDDHGRGDLGRLKKQKDHHNPHLILMMIPPHRLDNPGQGGQRKKR ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPY LRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQ LSNMVVKSCKCS (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 8 28 1.642 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 7 384 K+R profile 2.00 + CYT-EXT prof - -0.13 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 2.00 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: 0.13 -> Orientation: N-out ---------------------------------------------------------------------- "tem39" 412 8 28 #t 1.64167 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem39.___saps___ SAPS. Version of April 11, 1996. Date run: Tue Oct 31 18:36:10 2000 File: /people/maria/tem39.___saps___ ID Tem39_gi|135684|sp|P10600|TGF3_HUMAN DE TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) number of residues: 412; molecular weight: 47.3 kdal 1 MKMHLQRALV VLALLNFATV SLSLSTCTTL DFGHIKKKRV EAIRGQILSK LRLTSPPEPT 61 VMTHVPYQVL ALYNSTRELL EEMHGEREEG CTQENTESEY YAKEIHKFDM IQGLAEHNEL 121 AVCPKGITSK VFRFNVSSVE KNRTNLFRAE FRVLRVPNPS SKRNEQRIEL FQILRPDEHI 181 AKQRYIGGKN LPTRGTAEWL SFDVTDTVRE WLLRRESNLG LEISIHCPCH TFQPNGDILE 241 NIHEVMEIKF KGVDNEDDHG RGDLGRLKKQ KDHHNPHLIL MMIPPHRLDN PGQGGQRKKR 301 ALDTNYCFRN LEENCCVRPL YIDFRQDLGW KWVHEPKGYY ANFCSGPCPY LRSADTTHST 361 VLGLYNTLNP EASASPCCVP QDLEPLTILY YVGRTPKVEQ LSNMVVKSCK CS -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 16( 3.9%); C : 14( 3.4%); D : 17( 4.1%); E : 33( 8.0%); F : 14( 3.4%) G : 23( 5.6%); H : 17( 4.1%); I : 19( 4.6%); K : 25( 6.1%); L : 45(10.9%) M : 9( 2.2%); N : 23( 5.6%); P : 24( 5.8%); Q : 15( 3.6%); R : 29( 7.0%) S : 23( 5.6%); T : 24( 5.8%); V : 25( 6.1%); W : 4( 1.0%); Y : 13( 3.2%) KR : 54 ( 13.1%); ED : 50 ( 12.1%); AGP : 63 ( 15.3%); KRED : 104 ( 25.2%); KR-ED : 4 ( 1.0%); FIKMNY : 103 ( 25.0%); LVIFM : 112 ( 27.2%); ST : 47 ( 11.4%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0+0000+000 0000000000 0000000000 -0000++++0 -00+00000+ 0+00000-00 61 0000000000 000000+-00 --000-+--0 000-00-0-0 00+-00+0-0 00000-00-0 121 0000+0000+ 00+000000- +0+0000+0- 0+00+00000 0++0-0+0-0 0000+0--00 181 0+0+0000+0 000+000-00 00-00-00+- 000++-0000 0-00000000 000000-00- 241 000-00-0+0 +00-0---00 +0-00+0++0 +-00000000 000000+0-0 000000++++ 301 00-00000+0 0--0000+00 00-0+0-000 +000-0+000 0000000000 0+00-00000 361 0000000000 -000000000 0-0-000000 000+00+0-0 000000+00+ 00 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 11/30 or 14/45 or 18/60): none Negative charge clusters (cmin = 10/30 or 14/45 or 17/60): none Mixed charge clusters (cmin = 17/30 or 23/45 or 28/60): 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 5 | 5 | 8 | 32 | 10 | 10 | 13 | 11 | 11 | 15 | 8 | 10 | lmin1 7 | 6 | 9 | 38 | 12 | 12 | 16 | 14 | 14 | 18 | 9 | 12 | lmin2 8 | 8 | 11 | 43 | 13 | 13 | 18 | 16 | 15 | 21 | 10 | 13 | (Significance level: 0.010000; Minimal displayed length: 6) There are no charge runs or patterns exceeding the given minimal lengths. Run count statistics: + runs >= 3: 2, at 36; 297; - runs >= 3: 1, at 256; * runs >= 5: 0 0 runs >= 21: 1, at 8; -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. There are no high scoring hydrophobic segments. ____________________________________ 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: -4.583 M_0.01= 49.71; M_0.05= 40.98; M_0.30= 30.59 1) From 8 to 24: length= 17, score=40.00 (pocket at 16 to 16: length= 1, score=-10.00) 8 ALVVLALL |N| F ATVSLSL L: 6(35.3%); A: 3(17.6%); S: 2(11.8%); V: 3(17.6%); 2. SPACINGS OF C. H2N-26-C-63-C-31-C-103-C-1-C-77-C-7-C-C-27-C-3-C-28-C-C-30-C-1-C-1-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-3-H-22-C-6 -H-29-H-19-H-6-C-14-H-10-H-5-C-55-H-46-H-C-1-C-H-12-H-15-H-13-H-H-2-H-8-H-20-C-7-C-C-17-H-9-C-3-C-9-H-18-C-C-30-C-1-C-1-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 4 Aligned matching blocks: [ 11- 14] VLAL [ 69- 72] VLAL 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: 28 (Expected range: 8-- 37) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 7 (6-10) 7 (11-20) 8 (>=21) 7 3. Clusters of amino acid multiplets (cmin = 12/30 or 15/45 or 18/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 10 (Expected range: 1-- 22) 5 +plets (f+: 13.1%), 5 -plets (f-: 12.1%) Total number of charge altplets: 7 (Critical number: 25) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 0 (6-10) 2 (11-20) 2 (>=21) 7 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 89- 108 5 E.... 4 4 0 B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 7) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core: 9) Location Period Element Copies Core Errors 89- 113 5 -00.0 5 5 /0/0/0/./1/ 278- 283 1 i 6 6 0 -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 224- 345 (3.) S( 121)S 1 of 24 0.0062 large 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: tem39 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TGFb_propeptide TGF-beta propeptide 242.4 6.5e-69 1 TGF-beta Transforming growth factor beta like 175.7 1.4e-56 1 cyclin Cyclin 0.6 35 1 DUF25 Domain of unknown function DUF25 0.5 86 1 enolase Enol-ase -1.4 62 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- DUF25 1/1 139 155 .. 1 17 [. 0.5 86 enolase 1/1 172 195 .. 417 440 .] -1.4 62 TGFb_propeptide 1/1 27 255 .. 1 250 [] 242.4 6.5e-69 cyclin 1/1 309 331 .. 31 54 .. 0.6 35 TGF-beta 1/1 315 412 .] 1 109 [] 175.7 1.4e-56 Alignments of top-scoring domains: DUF25: domain 1 of 1, from 139 to 155: score 0.5, E = 86 *->deewkavLspeqyrVlr<-* e+++ +L + ++rVlr Tem39_gi|1 139 VEKNRTNLFRAEFRVLR 155 enolase: domain 1 of 1, from 172 to 195: score -1.4, E = 62 *->qLLRIEEelgsaavyagknfrkak<-* q+LR E ++++ + +gkn+ + Tem39_gi|1 172 QILRPDEHIAKQRYIGGKNLPTRG 195 TGFb_propeptide: domain 1 of 1, from 27 to 255: score 242.4, E = 6.5e-69 *->crpldlrrrqkqkrleaiegeiLskLgLkrrPrpskeknphpkepas c++ld + +k kr+eai+g+iLskL+L+++P+p+ + + Tem39_gi|1 27 CTTLDFGHIKK-KRVEAIRGQILSKLRLTSPPEPT--------VMTH 64 vPefmldLYnalseleegk............eisdydgreasrantvrsf vP ++l+LYn+++el+e+++++++++ ++++ +s+y+++e++++++++ Tem39_gi|1 65 VPYQVLALYNSTRELLEEMhgereegctqenTESEYYAKEIHKFDMIQGL 114 sheesldreesteeshrkrfvFnlSsiPegetltalLarAELRlyrqdpl +++l ++ + ++k f+Fn+Ss++++ t+ L+rAE+R++r +p+ Tem39_gi|1 115 AEHNELAVCPKG--ITSKVFRFNVSSVEKNRTN---LFRAEFRVLR-VPN 158 anrfpawsraeqrveiYqvlkpgsdgsrdekGdpstrlLdsrlvdasnsg + + +r eqr+e++q+l+p+ + + +r+++ ++++++ + Tem39_gi|1 159 PSS----KRNEQRIELFQILRPDEHIAK-------QRYIGGKNLPTRGTA 197 ggWlsFDVTpavnrWlsnpqsnlGlqleveclcgdkapgrhvrpsragli +WlsFDVT++v++Wl +++snlGl+++++c+c+ +++p +++l Tem39_gi|1 198 -EWLSFDVTDTVREWLLRRESNLGLEISIHCPCH------TFQPNGDIL- 239 ge.gpqqkqPllvtff<-* ++ ++ ++ ++ +++ Tem39_gi|1 240 ENiHEVMEIKFKGVDN 255 cyclin: domain 1 of 1, from 309 to 331: score 0.6, E = 35 *->relEektlpnpdymdqQpseinps<-* r lEe ++++p y+d++ ++ ++ Tem39_gi|1 309 RNLEENCCVRPLYIDFRQ-DLGWK 331 TGF-beta: domain 1 of 1, from 315 to 412: score 175.7, E = 1.4e-56 *->CrrreLyVdFkdiGWddWIiaPkGYhAnYChGeCpfplagvgdslna C++r+Ly+dF+ +++++W+++PkGY+An+C+G Cp+ + + Tem39_gi|1 315 CCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRS------AD 355 tnhaivqtLvhslnPgtaapkPCCVPtkGtLsplsvLYyddnGdnvvlkq t+h++v+ L+++lnP+ a+++PCCVP++ L+pl++LYy ++ +++++q Tem39_gi|1 356 TTHSTVLGLYNTLNPE-ASASPCCVPQD--LEPLTILYYVGR--TPKVEQ 400 ypNMvVeeCGCr<-* ++NMvV++C+C+ Tem39_gi|1 401 LSNMVVKSCKCS 412 // 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: tem39 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- TGFb_propeptide TGF-beta propeptide 240.5 2.4e-68 1 TGF-beta Transforming growth factor beta like 175.7 1.4e-56 1 HTH_5 Bacterial regulatory protein, arsR fa 4.3 8.7 1 Bac_globin Protozoan/cyanobacterial globin 1.1 63 1 cyclin Cyclin 0.6 35 1 DUF25 Domain of unknown function DUF25 0.5 86 1 7tm_2 7 transmembrane receptor (Secretin fa -0.2 40 1 enolase Enol-ase -1.4 62 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Bac_globin 1/1 38 50 .. 106 118 .] 1.1 63 HTH_5 1/1 99 117 .. 62 82 .] 4.3 8.7 DUF25 1/1 139 155 .. 1 17 [. 0.5 86 enolase 1/1 172 195 .. 417 440 .] -1.4 62 TGFb_propeptide 1/1 27 255 .. 1 250 [] 240.5 2.4e-68 cyclin 1/1 309 331 .. 31 54 .. 0.6 35 7tm_2 1/1 383 393 .. 1 11 [. -0.2 40 TGF-beta 1/1 315 412 .] 1 109 [] 175.7 1.4e-56 Alignments of top-scoring domains: Bac_globin: domain 1 of 1, from 38 to 50: score 1.1, E = 63 *->aVvestrgdvlnk<-* ++ve +rg +l+k Tem39_gi|1 38 KRVEAIRGQILSK 50 HTH_5: domain 1 of 1, from 99 to 117: score 4.3, E = 8.7 *->yYslseldelvvdiielllel<-* +Y+ + +++++d+i+ l+e+ Tem39_gi|1 99 EYYAK--EIHKFDMIQGLAEH 117 DUF25: domain 1 of 1, from 139 to 155: score 0.5, E = 86 *->deewkavLspeqyrVlr<-* e+++ +L + ++rVlr Tem39_gi|1 139 VEKNRTNLFRAEFRVLR 155 enolase: domain 1 of 1, from 172 to 195: score -1.4, E = 62 *->qLLRIEEelgsaavyagknfrkak<-* q+LR E ++++ + +gkn+ + Tem39_gi|1 172 QILRPDEHIAKQRYIGGKNLPTRG 195 TGFb_propeptide: domain 1 of 1, from 27 to 255: score 240.5, E = 2.4e-68 *->crpldlrrrqkqkrleaiegeiLskLgLkrrPrpskeknphpkepas c++ld + +k kr+eai+g+iLskL+L+++P+p+ + + Tem39_gi|1 27 CTTLDFGHIKK-KRVEAIRGQILSKLRLTSPPEPT--------VMTH 64 vPefmldLYnalseleegk............eisdydgreasrantvrsf vP ++l+LYn+++el+e+++++++++ ++++ +s+y+++e++++++++ Tem39_gi|1 65 VPYQVLALYNSTRELLEEMhgereegctqenTESEYYAKEIHKFDMIQGL 114 sheesldreesteeshrkrfvFnlSsiPegetltalLarAELRlyrqdpl +++l ++ + ++k f+Fn+Ss++++ t+ L+rAE+R++r +p+ Tem39_gi|1 115 AEHNELAVCPKG--ITSKVFRFNVSSVEKNRTN---LFRAEFRVLR-VPN 158 anrfpawsraeqrveiYqvlkpgsdgsrdekGdpstrlLdsrlvdasnsg + + +r eqr+e++q+l+p+ + + +r+++ ++++++ + Tem39_gi|1 159 PSS----KRNEQRIELFQILRPDEHIAK-------QRYIGGKNLPTRGTA 197 ggWlsFDVTpavnrWlsnpqsnlGlqleveclcgdkapgrhvrpsragli +WlsFDVT++v++Wl +++snlGl+++++c+c+ +++p +++l Tem39_gi|1 198 -EWLSFDVTDTVREWLLRRESNLGLEISIHCPCH------TFQPNGDIL- 239 ge.gpqqkqPllvtff<-* ++ ++ ++ ++ +++ Tem39_gi|1 240 ENiHEVMEIKFKGVDN 255 cyclin: domain 1 of 1, from 309 to 331: score 0.6, E = 35 *->relEektlpnpdymdqQpseinps<-* r lEe ++++p y+d++ ++ ++ Tem39_gi|1 309 RNLEENCCVRPLYIDFRQ-DLGWK 331 7tm_2: domain 1 of 1, from 383 to 393: score -0.2, E = 40 *->allLkviytVG<-* ++ L+++y+VG Tem39_gi|1 383 LEPLTILYYVG 393 TGF-beta: domain 1 of 1, from 315 to 412: score 175.7, E = 1.4e-56 *->CrrreLyVdFkdiGWddWIiaPkGYhAnYChGeCpfplagvgdslna C++r+Ly+dF+ +++++W+++PkGY+An+C+G Cp+ + + Tem39_gi|1 315 CCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRS------AD 355 tnhaivqtLvhslnPgtaapkPCCVPtkGtLsplsvLYyddnGdnvvlkq t+h++v+ L+++lnP+ a+++PCCVP++ L+pl++LYy ++ +++++q Tem39_gi|1 356 TTHSTVLGLYNTLNPE-ASASPCCVPQD--LEPLTILYYVGR--TPKVEQ 400 ypNMvVeeCGCr<-* ++NMvV++C+C+ Tem39_gi|1 401 LSNMVVKSCKCS 412 // 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: tem39 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) 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: Tue Oct 31 18:39:44 2000 Sequence file: tem39 ---------------------------------------- Sequence Tem39_gi|135684|sp|P10600|TGF3_HUMAN (412 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 74: NSTR 135: NVSS 142: NRTN Total matches: 3 Matching pattern PS00004 CAMP_PHOSPHO_SITE: 214: RRES Total matches: 1 Matching pattern PS00005 PKC_PHOSPHO_SITE: 75: STR 128: TSK 160: SSK 161: SKR 207: TVR 395: TPK 408: SCK Total matches: 7 Matching pattern PS00006 CK2_PHOSPHO_SITE: 28: TTLD 55: SPPE 75: STRE 96: TESE 137: SSVE 207: TVRE Total matches: 6 Matching pattern PS00007 TYR_PHOSPHO_SITE: 331: KWVHEPKGY Total matches: 1 Matching pattern PS00008 MYRISTYL: 45: GQILSK 220: GLEISI 363: GLYNTL Total matches: 3 Matching pattern PS00016 RGD: 261: RGD Total matches: 1 Matching pattern PS00250 TGF_BETA: 333: VHEPKGYYANFCSGPC Total matches: 1 Total no of hits in this sequence: 23 ======================================== 1314 pattern(s) searched in 1 sequence(s), 412 residues. Total no of hits in all sequences: 23. 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 tem39 ***** 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, 412 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: tem39 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) 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: tem39 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) 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= Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) (412 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value PDE cyclic NMP phosphodiesterase domain 26 0.079 ARM Armadillo repeat 22 1.4 AAA AAA+ ATPase Module 21 2.0 BHLH basic helix-loop-helix domain 21 4.1 UBHYD Ubiquitin C-terminal hydrolase domain 20 5.9 SH2 Src Homology domain 2 20 7.1 HISDAC Histone deacetylase domain 20 7.6 SEC7 Sec7 like GDP exchange factor for ARF like GTPases 20 7.6 PTB Phospho-Tyrosine Binding domain 19 8.8 GAF GAF domain (Predicted Small-ligand binding domain) 19 9.9 >PDE cyclic NMP phosphodiesterase domain Length = 350 Score = 26.3 bits (57), Expect = 0.079 Identities = 46/200 (23%), Positives = 76/200 (38%), Gaps = 41/200 (20%) Query: 201 SFDVTDTVREWLLRRESNLGL------EISIHCPCH---------TFQPNG--------- 236 +FDVT TV +L + L + I C CH TFQ N Sbjct: 72 AFDVTQTVYTFLTSFNAAQYLTHLDIFALLISCMCHDLNHPGFNNTFQVNAQTELSLEYN 131 Query: 237 --DILENIHEVMEIK---------FKGVDNEDDHG--RGDLGRLKKQKDHHNPHLILMMI 283 +LEN H ++ K +G+ NED + R + +L D N H Sbjct: 132 DISVLENHHAMLTFKILRNSECNILEGL-NEDQYKELRRSVVQLILATDMQN-HFEHTNK 189 Query: 284 PPHRLDN-PGQGGQRKKRALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYAN 342 H L+N P +++ R + N+ + + + RP +++F L + +Y Sbjct: 190 FQHHLNNLPFDRNKKEDRQMILNFLIKCGDISNIARPWHLNFEWSLRVSDEFFQQSHYET 249 Query: 343 FCSGP-CPYLRSADTTHSTV 361 C P P++ TT + + Sbjct: 250 ICGYPVTPFMDKTKTTRARI 269 >ARM Armadillo repeat Length = 532 Score = 22.2 bits (47), Expect = 1.4 Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 2/46 (4%) Query: 143 RTNLFRAEFRVLRVPNPSS-KRNEQRIELFQILRPDEHIAKQRYIG 187 +T + R ++V +R + +E+ + R +E + K+R G Sbjct: 8 KTEVRRNRYKVAVDAEEGRRRREDNMVEIRKSKR-EESLMKKRREG 52 >AAA AAA+ ATPase Module Length = 298 Score = 21.4 bits (44), Expect = 2.0 Identities = 21/168 (12%), Positives = 49/168 (28%), Gaps = 26/168 (15%) Query: 78 ELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEH---------------NELAV 122 EL+++ GE + + +A I D I + EL Sbjct: 115 ELVQKFIGEGARMVRELFVMAREHAPSIIFMDEIDSIGSRLEGGSGGDSEVQRTMLELLN 174 Query: 123 CPKGITSKVFRFNV---SSVEKNRTNLFRAE--FRVLRVPNPSSKRNEQRIELFQILRPD 177 G + + + ++ + L R R + P P+ E R+++ +I Sbjct: 175 QLDGFEATKNIKVIMATNRIDILDSALLRPGRIDRKIEFPPPN---EEARLDILKIHSRK 231 Query: 178 EHIAKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGLEISI 225 ++ + + +V E + + ++ Sbjct: 232 MNLTRGINL---RKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQ 276 >BHLH basic helix-loop-helix domain Length = 103 Score = 20.7 bits (43), Expect = 4.1 Identities = 11/46 (23%), Positives = 21/46 (44%), Gaps = 1/46 (2%) Query: 130 KVFRFNVSSVEKNRTNLFRAEFRVLRVPNPSSKRNEQRIELFQILR 175 KV R + E+ R + +LR P + ++ Q++ + LR Sbjct: 7 KVRRVKANGRERARMHGLNNALDMLREYIPITTQH-QKLSKIETLR 51 >UBHYD Ubiquitin C-terminal hydrolase domain Length = 884 Score = 19.9 bits (41), Expect = 5.9 Identities = 9/48 (18%), Positives = 17/48 (34%), Gaps = 2/48 (4%) Query: 65 VPYQVLALYNSTRELLEEMHGEREEG--CTQENTESEYYAKEIHKFDM 110 +P Q++ + + + ER+E Q +E DM Sbjct: 318 IPQQLVERLQEEKRIEAQKRKERQEAHLYMQVQIVAEDQFCGHQGNDM 365 >SH2 Src Homology domain 2 Length = 119 Score = 19.8 bits (41), Expect = 7.1 Identities = 6/37 (16%), Positives = 11/37 (29%), Gaps = 3/37 (8%) Query: 93 QENTESEYYAKEIHKFDMIQGLAEH---NELAVCPKG 126 + YY F I + +H +C + Sbjct: 64 RSLDNGGYYISPRITFPCISDMIKHYQKQSDGLCRRL 100 >HISDAC Histone deacetylase domain Length = 433 Score = 19.8 bits (41), Expect = 7.6 Identities = 14/119 (11%), Positives = 34/119 (27%), Gaps = 11/119 (9%) Query: 75 STRELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEHNELAVCPKGITSKVFRF 134 L+ ++ + ++ + H + I L+ + + +F Sbjct: 47 MAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDN--LEMFKRESVKF 104 Query: 135 NVSSVEKNRTNLFRAEFRVLRVPNPSS-----KRNEQRIELFQILRPDEHIAKQRYIGG 188 NV +F + + S + N + ++ H AK+ G Sbjct: 105 NVGD----DCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASG 159 >SEC7 Sec7 like GDP exchange factor for ARF like GTPases Length = 192 Score = 19.8 bits (41), Expect = 7.6 Identities = 7/40 (17%), Positives = 16/40 (39%), Gaps = 5/40 (12%) Query: 99 EYYAKEIHKFDM-----IQGLAEHNELAVCPKGITSKVFR 133 +Y ++ F+ +Q L E + P G+ + + Sbjct: 6 RHYRIGLNLFNKKPEKGVQYLIERGFVPDTPVGVAHFLLQ 45 >PTB Phospho-Tyrosine Binding domain Length = 138 Score = 19.4 bits (40), Expect = 8.8 Identities = 7/26 (26%), Positives = 11/26 (41%), Gaps = 3/26 (11%) Query: 229 CHTFQPNG---DILENIHEVMEIKFK 251 C+ F DI I E ++ +K Sbjct: 110 CYAFTSEKLAEDITLTIGEAFDLAYK 135 >GAF GAF domain (Predicted Small-ligand binding domain) Length = 160 Score = 19.4 bits (40), Expect = 9.9 Identities = 9/44 (20%), Positives = 16/44 (35%), Gaps = 3/44 (6%) Query: 74 NSTRELLEEMHGEREEGCTQENTESEYYAKEIHKFDMIQGLAEH 117 N EL + ++ +E + EI F + G+ H Sbjct: 31 NGIAELATRLFNVHKDAVLEECLVAP--DSEIV-FPLDMGVVGH 71 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 10 Number of calls to ALIGN: 10 Length of query: 412 Total length of test sequences: 20182 Effective length of test sequences: 16637.0 Effective search space size: 6303507.0 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= Tem39_gi|135684|sp|P10600|TGF3_HUMAN TRANSFORMING GROWTH FACTOR BETA 3 PRECURSOR (TGF-BETA 3) (412 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|1504014 [3..727] P-loop containing nucleotide triphosphat... 26 1.6 gi|584960 [16..180] EF Hand-like 26 1.6 gi|121286 [210..431] Double-stranded beta-helix 24 4.4 gi|2150113 [49..445] Ferritin-like 23 6.7 gi|136297 [237..503] beta/alpha (TIM)-barrel 24 6.7 gi|1051321 [353..924] P-loop containing nucleotide triphosph... 23 6.8 gi|730692 [7..211] beta/alpha (TIM)-barrel 23 6.9 gi|1354131 [16..303] Protein kinases (PK), catalytic core 24 6.9 gi|2308977 [178..600] P-loop containing nucleotide triphosph... 23 7.2 gi|544221 [55..339] beta/alpha (TIM)-barrel 23 9.1 gi|1709211 [75..820] P-loop containing nucleotide triphospha... 23 9.5 >gi|1504014 [3..727] P-loop containing nucleotide triphosphate hydrolases Length = 725 Score = 25.7 bits (56), Expect = 1.6 Identities = 20/84 (23%), Positives = 33/84 (38%), Gaps = 6/84 (7%) Query: 5 LQRALVVLALLNFATVSLSLST----CTTLDFGHIKKKRVEAIRGQILSKLRLTSPPEPT 60 ++ A N T+ +T +LDF + +I+ +L KLR+ P Sbjct: 73 QALYTLLEAFGNSPTIINGNATRFSQILSLDFDQAGQVASASIQTMLLEKLRVARRPASE 132 Query: 61 VMTHVPYQVLALYNSTRELLEEMH 84 +V Y +LA L E+H Sbjct: 133 ATFNVFYYLLA--CGDGTLRTELH 154 >gi|584960 [16..180] EF Hand-like Length = 165 Score = 25.5 bits (55), Expect = 1.6 Identities = 7/95 (7%), Positives = 17/95 (17%), Gaps = 4/95 (4%) Query: 202 FDVTDTVREWLLRRESNLGLEISIHCPCHTFQPNGDILENIHEVMEIKFKGVDNEDDH-- 259 F + + + + + F D + Sbjct: 60 FKKIGMDYGKEVEFPAFVDGWKELANYDLKLWSQNKKSLIRDWGEAV-FDIFDKDGSGSI 118 Query: 260 GRGDLGR-LKKQKDHHNPHLILMMIPPHRLDNPGQ 293 + + + LDN G+ Sbjct: 119 SLDEWKAYGRISGICSSDEDAEKTFKHCDLDNSGK 153 >gi|121286 [210..431] Double-stranded beta-helix Length = 222 Score = 24.1 bits (52), Expect = 4.4 Identities = 7/33 (21%), Positives = 15/33 (45%), Gaps = 1/33 (3%) Query: 59 PTVMTHVPYQVLAL-YNSTRELLEEMHGEREEG 90 + + +L Y++ E + ++ REEG Sbjct: 157 QSYLQGFSKNILEASYDTKFEEINKVLFGREEG 189 >gi|2150113 [49..445] Ferritin-like Length = 397 Score = 23.4 bits (50), Expect = 6.7 Identities = 25/117 (21%), Positives = 36/117 (30%), Gaps = 32/117 (27%) Query: 264 LGRLKKQKD--HHNPHLILMMIPPHRLDNPGQGGQRKKRA-LDTNY---------CFRNL 311 +Q D HH HL + P NP G +R L+ Y C+ + Sbjct: 270 WDTFLQQLDQQHHGMHLGVWFWRPTVWWNPAAGVTPAERDWLEEKYPGWNSTWGQCWDVI 329 Query: 312 EEN-----------------CCVRPLYIDFRQDLGWK---WVHEPKGYYANFCSGPC 348 EN C + L I++ W + E G +F S P Sbjct: 330 IENLVDGNVAQTYPETLPIVCNMSQLPINYTPGDAWAVKDYQLEYNGRLYHFGSEPD 386 >gi|136297 [237..503] beta/alpha (TIM)-barrel Length = 267 Score = 23.6 bits (50), Expect = 6.7 Identities = 12/121 (9%), Positives = 31/121 (24%), Gaps = 18/121 (14%) Query: 162 KRNEQRIELFQILRPDEHIAKQRYIGGKNLPTRGTAEWLSFDVTDTVREWLLRRESNLGL 221 K E + L ++ + G T V Sbjct: 48 KAAEVKPALMAEVKRASPSKGPIAMNGNAAQQALTYALAGASV----------------- 90 Query: 222 EISIHCPCHTFQPNGDILENIHEVMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILM 281 IS+ F+ + + + ++ D ++ + + H ++L+ Sbjct: 91 -ISVLTEPTWFKGSLLDMRLARQAIDNLPHRPAILRKDFIIDEYQIDEARLHGADTVLLI 149 Query: 282 M 282 + Sbjct: 150 V 150 >gi|1051321 [353..924] P-loop containing nucleotide triphosphate hydrolases Length = 572 Score = 23.3 bits (50), Expect = 6.8 Identities = 7/55 (12%), Positives = 16/55 (28%), Gaps = 2/55 (3%) Query: 30 LDFGHIKKKRVEAIRGQILSKLRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMH 84 L + + L R+ S ++ Y+V + E+ + Sbjct: 75 LLYKRNVLTGLNLKYTVPLEVPRVISQKPGERNFNIFYEVYH--GLSDEMKAKFG 127 >gi|730692 [7..211] beta/alpha (TIM)-barrel Length = 205 Score = 23.3 bits (50), Expect = 6.9 Identities = 4/37 (10%), Positives = 13/37 (34%) Query: 245 VMEIKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILM 281 KF + + + + KK+ + + ++ Sbjct: 38 STNGKFIPYWDTEKVTPEVIKKFKKKYEPTALRVKVL 74 >gi|1354131 [16..303] Protein kinases (PK), catalytic core Length = 288 Score = 23.6 bits (49), Expect = 6.9 Identities = 7/84 (8%), Positives = 14/84 (16%), Gaps = 5/84 (5%) Query: 279 ILMMIPPHRLDNPGQGGQRKKRALDTNYCFRNLEENCCV-----RPLYIDFRQDLGWKWV 333 + + P +N EN R D + + Sbjct: 200 LEFFVTPFDGSPMKIIRGSYDLPKPIEDTEKNWLENTLEIDQNKRWNSQDLFNAVKTNSI 259 Query: 334 HEPKGYYANFCSGPCPYLRSADTT 357 + + T Sbjct: 260 VPKQHLKEQITITEKQVSKQPSDT 283 >gi|2308977 [178..600] P-loop containing nucleotide triphosphate hydrolases Length = 423 Score = 23.3 bits (50), Expect = 7.2 Identities = 10/42 (23%), Positives = 16/42 (37%), Gaps = 2/42 (4%) Query: 43 IRGQILSKLRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMH 84 I L + R+ S P HV Y +LA ++ + Sbjct: 1 IIDHRLERSRIASVPTGERSFHVLYYLLA--GTSAAEKAHLG 40 >gi|544221 [55..339] beta/alpha (TIM)-barrel Length = 285 Score = 23.0 bits (49), Expect = 9.1 Identities = 5/34 (14%), Positives = 10/34 (28%) Query: 248 IKFKGVDNEDDHGRGDLGRLKKQKDHHNPHLILM 281 V N + R K K + + ++ Sbjct: 51 NDKVFVSNNPNVQHLLTNRAKYLKPLQDKGIKVI 84 >gi|1709211 [75..820] P-loop containing nucleotide triphosphate hydrolases Length = 746 Score = 22.9 bits (49), Expect = 9.5 Identities = 10/42 (23%), Positives = 20/42 (46%), Gaps = 2/42 (4%) Query: 43 IRGQILSKLRLTSPPEPTVMTHVPYQVLALYNSTRELLEEMH 84 I +L K + H+ YQ+L+ ++ EL E+++ Sbjct: 208 ILAYLLEKSGIVRQVYNERNYHIFYQLLS--GASEELKEKLN 247 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 11 Number of calls to ALIGN: 11 Length of query: 412 Total length of test sequences: 256703 Effective length of test sequences: 209547.0 Effective search space size: 78128845.0 Initial X dropoff for ALIGN: 25.0 bits