analysis of sequence from tem21_2hypoth ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFNWTALKPNQIPSGTVFSELDD EKILEDKFEELFKTKAQGPALDLICSKNKTAQKAASKVTLLEANRAKNLAITLRKAGRSAEEICRAIHTF DLQTLPVDFVECLMRFLPTEAEVKLLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMAGMAFLGNFQD NLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGNYMNSSKRGAVYGFKLQSLDLLLDTKSTDRKMTL LHFIALTVKEKYPDLANFWHELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNE GKLDKLQRDAKTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEAEQENEARKKQEEVMREKQLA QEAKKLDAKTPSQRNKWQQQELIAELRRRQAKEHRPVYEGKDGTIEDIITVLKSVPFTARTAKRGSRFFC DAAHHDESNC ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > Tem21.2_gi|7328133|emb|CAB82400.1| . . . . . 1 LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFN 50 ___________________EEEEEE___EEEEEE_______________E . . . . . 51 WTALKPNQIPSGTVFSELDDEKILEDKFEELFKTKAQGPALDLICSKNKT 100 EE___________________HHHHHHHHHHHHHHH____EEEEE____H . . . . . 101 AQKAASKVTLLEANRAKNLAITLRKAGRSAEEICRAIHTFDLQTLPVDFV 150 HHHHHHHHHHHHHHHHHHHHHHHHHH___HHHHHHHHHH________HHH . . . . . 151 ECLMRFLPTEAEVKLLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMA 200 HHHHH_____HHHHHHHHHHHH___HHHHHHHHHHHHHHHHHHHHHHHHH . . . . . 201 GMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGNYMN 250 HHHHHH____HHHHHH_HHHHHHHHHHHHHHHHHHHHHHHHHHHH_____ . . . . . 251 SSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWH 300 ______EEEEE_HHHHHHHH_____HHHHHHHHHHHHHHH_____HHHHH . . . . . 301 ELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNE 350 HHHHHHHHHHHHHHHHHHHHH_____HHHHHHHHH____HHHHHH_____ . . . . . 351 GKLDKLQRDAKTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEA 400 ___HHHHHHHHHHHHHHHHHEEEEE___________HHHHHHHHHHHHHH . . . . . 401 EQENEARKKQEEVMREKQLAQEAKKLDAKTPSQRNKWQQQELIAELRRRQ 450 HHHHHHHHHHHHHHHHHHHHHHHHHH_________HHHHHHHHHHHHHHH . . . . . 451 AKEHRPVYEGKDGTIEDIITVLKSVPFTARTAKRGSRFFCDAAHHDESNC 500 HHHH___________HHHHHHH______________EEEE__________ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 81.1 % beta-contents : 0.0 % coil-contents : 18.9 % class : alpha method : 2 alpha-contents : 52.0 % beta-contents : 0.0 % coil-contents : 48.0 % class : alpha ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -21.87 -2.28 -0.17 0.00 -4.00 0.00 -4.00 0.00 0.00 -4.61 -3.54 0.00 -12.00 0.00 -12.00 0.00 -64.47 -3.25 -0.49 -0.29 -1.35 0.00 0.00 0.00 -0.13 -0.50 -6.73 -3.54 -12.00 -12.00 0.00 -12.00 0.00 -52.30 ID: Tem21.2_gi|7328133|emb|CAB82400.1| AC: xxx Len: 490 1:I 462 Sc: -52.30 Pv: 2.536860e-01 NO_GPI_SITE GPI: learning from protozoa -26.78 -0.48 -0.23 -0.13 -4.00 0.00 0.00 -0.35 -0.09 -5.83 -12.03 -12.00 -12.00 0.00 -12.00 0.00 -85.92 -26.85 0.00 -0.23 0.00 -4.00 0.00 0.00 -0.35 -0.09 -5.14 -12.03 -12.00 -12.00 0.00 -12.00 0.00 -84.69 ID: Tem21.2_gi|7328133|emb|CAB82400.1| AC: xxx Len: 490 1:I 461 Sc: -84.69 Pv: 5.955505e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? Tem21.2_gi| 0.537 162 Y 0.157 32 N 0.508 30 N 0.190 N # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? Tem21.2_gi| 0.421 222 N 0.280 496 N 0.726 104 N 0.134 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? Tem21.2_gi| 0.487 257 Y 0.359 485 Y 0.955 480 Y 0.223 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] 1-1 L ppppdkcppapplpgaap 2-19 20-31 SVVLTVPPGLSA irikkpppik 32-41 42-220 TKFRLPVFNWTALKPNQIPSGTVFSELDDE KILEDKFEELFKTKAQGPALDLICSKNKTA QKAASKVTLLEANRAKNLAITLRKAGRSAE EICRAIHTFDLQTLPVDFVECLMRFLPTEA EVKLLRQYERERQPLEELAAEDRFMLLFSK VERLTQRMAGMAFLGNFQDNLQMLTPQLN aiiaasasvkss 221-232 233-260 QKLKQMLEIILALGNYMNSSKRGAVYGF klqsldllldtkst 261-274 275-381 DRKMTLLHFIALTVKEKYPDLANFWHELHF VEKAAAVSLENVLLDVKELGRGMELIRREC SIHDNSVLRNFLSTNEGKLDKLQRDAKTAE EAYNAVVRYFGESPKTT ppsvffpvfv 382-391 392-500 RFIRSYKEAEQENEARKKQEEVMREKQLAQ EAKKLDAKTPSQRNKWQQQELIAELRRRQA KEHRPVYEGKDGTIEDIITVLKSVPFTART AKRGSRFFCDAAHHDESNC low complexity regions: SEG 25 3.0 3.3 >Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] lppppdkcppapplpgaapsvvltvppgls 1-49 airikkpppiktkfrlpvf 50-152 NWTALKPNQIPSGTVFSELDDEKILEDKFE ELFKTKAQGPALDLICSKNKTAQKAASKVT LLEANRAKNLAITLRKAGRSAEEICRAIHT FDLQTLPVDFVEC lmrflpteaevkllrqyererqpleelaae 153-188 drfmll 189-217 FSKVERLTQRMAGMAFLGNFQDNLQMLTP qlnaiiaasasvkssqklkqmleiilal 218-245 246-397 GNYMNSSKRGAVYGFKLQSLDLLLDTKSTD RKMTLLHFIALTVKEKYPDLANFWHELHFV EKAAAVSLENVLLDVKELGRGMELIRRECS IHDNSVLRNFLSTNEGKLDKLQRDAKTAEE AYNAVVRYFGESPKTTPPSVFFPVFVRFIR SY keaeqenearkkqeevmrekqlaqeakkld 398-429 ak 430-500 TPSQRNKWQQQELIAELRRRQAKEHRPVYE GKDGTIEDIITVLKSVPFTARTAKRGSRFF CDAAHHDESNC low complexity regions: SEG 45 3.4 3.75 >Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] lppppdkcppapplpgaapsvvltvppgls 1-60 airikkpppiktkfrlpvfnwtalkpnqip 61-397 SGTVFSELDDEKILEDKFEELFKTKAQGPA LDLICSKNKTAQKAASKVTLLEANRAKNLA ITLRKAGRSAEEICRAIHTFDLQTLPVDFV ECLMRFLPTEAEVKLLRQYERERQPLEELA AEDRFMLLFSKVERLTQRMAGMAFLGNFQD NLQMLTPQLNAIIAASASVKSSQKLKQMLE IILALGNYMNSSKRGAVYGFKLQSLDLLLD TKSTDRKMTLLHFIALTVKEKYPDLANFWH ELHFVEKAAAVSLENVLLDVKELGRGMELI RRECSIHDNSVLRNFLSTNEGKLDKLQRDA KTAEEAYNAVVRYFGESPKTTPPSVFFPVF VRFIRSY keaeqenearkkqeevmrekqlaqeakkld 398-455 aktpsqrnkwqqqeliaelrrrqakehr 456-500 PVYEGKDGTIEDIITVLKSVPFTARTAKRG SRFFCDAAHHDESNC 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 >Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFNWTALKPNQIP SGTVFSELDDEKILEDKFEELFKTKAQGPALDLICSKNKTAQKAASKVTLLEANRAKNLA ITLRKAGRSAEEICRAIHTFDLQTLPVDFVECLMRFLPTEAEVKLLRQYERERQPLEELA AEDRFMLLFSKVERLTQRMAGMAflgnfqdnlqmltpqlnaiiaasasvkssqklkqmle iilalGNYMNSSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWH ELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNEGKLDKLQRDA KTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEAEQENEARKKQEEVMREKQLA QEAKKLDAKTPSQRNKWQQQELIAELRRRQAKEHRPVYEGKDGTIEDIITVLKSVPFTAR TAKRGSRFFCDAAHHDESNC 1 - 203 LPPPPDKCPP APPLPGAAPS VVLTVPPGLS AIRIKKPPPI KTKFRLPVFN WTALKPNQIP SGTVFSELDD EKILEDKFEE LFKTKAQGPA LDLICSKNKT AQKAASKVTL LEANRAKNLA ITLRKAGRSA EEICRAIHTF DLQTLPVDFV ECLMRFLPTE AEVKLLRQYE RERQPLEELA AEDRFMLLFS KVERLTQRMA GMA 204 - 245 flgnfqd nlqmltpqln aiiaasasvk ssqklkqmle iilal 246 - 500 GNYMN SSKRGAVYGF KLQSLDLLLD TKSTDRKMTL LHFIALTVKE KYPDLANFWH ELHFV EKAAA VSLENVLLDV KELGRGMELI RRECSIHDNS VLRNFLSTNE GKLDKLQRDA KTAEE AYNAV VRYFGESPKT TPPSVFFPVF VRFIRSYKEA EQENEARKKQ EEVMREKQLA QEAKK LDAKT PSQRNKWQQQ ELIAELRRRQ AKEHRPVYEG KDGTIEDIIT VLKSVPFTAR TAKRG SRFFC DAAHHDESNC low complexity regions: DUST >Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFNWTALKPNQIP SGTVFSELDDEKILEDKFEELFKTKAQGPALDLICSKNKTAQKAASKVTLLEANRAKNLA ITLRKAGRSAEEICRAIHTFDLQTLPVDFVECLMRFLPTEAEVKLLRQYERERQPLEELA AEDRFMLLFSKVERLTQRMAGMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLE IILALGNYMNSSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWH ELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNEGKLDKLQRDA KTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEAEQENEARKKQEEVMREKQLA QEAKKLDAKTPSQRNKWQQQELIAELRRRQAKEHRPVYEGKDGTIEDIITVLKSVPFTAR TAKRGSRFFCDAAHHDESNC ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for Tem21.2_gi|7328133|emb|CAB82400.1| sequence: 490 amino acids, 59 residue(s) in coiled coil state Coil 1 * 345* 372* LSTNEGKLDKLQRDAKTAEEAYNAVVRY Coil 2 * 394* 426* RSYKEAEQENEARKKQEEVMREKQLAQEAKKLD . | . | . | . | . | . 60 LPPPPDKCPP APPLPGAAPS VVLTVPPGLS AIRIKKPPPI KTKFRLPVFN WTALKPNQIP ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 SGTVFSELDD EKILEDKFEE LFKTKAQGPA LDLICSKNKT AQKAASKVTL LEANRAKNLA ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~1111 1111111111 1111111111 * 21 M'95 -w border ---------- ---------- ---------- ------defg abcdefgabc dgabcdefga * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~122222222 * 21 M'95 +w polar ~~~~~11111 1111111111 1111111~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~111 1114444444 4444444~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~111111111 * 14 M'95 -w local . | . | . | . | . | . 180 ITLRKAGRSA EEICRAIHTF DLQTLPVDFV ECLMRFLPTE AEVKLLRQYE RERQPLEELA 1111111111 11~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~1 1112222222 2222222222 * 21 M'95 -w border bcdefgabcd ef-------- ---------- ---------b cdefgabcde fgabcdefgc * 21 M'95 -w register 2222222222 2221111~~~ ~~~~~~~~~~ ~~~~~~~~~1 1111111111 1111111125 * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~2 * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. 11111~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~2 2222444444 4444444442 * 14 M'95 -w local . | . | . | . | . | . 240 AEDRFMLLFS KVERLTQRMA GMAFLGNFQD NLQMLTPQLN AIIAASASVK SSQKLKQMLE 2222222222 2222222222 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border defgabcdef gabcdefgab ---------- ---------- ---------- ---------- * 21 M'95 -w register 5555555555 5555555555 31~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar 2222222222 2222222222 11~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. 22~~~~~~~1 1111111111 111~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 300 IILALGNYMN SSKRGAVYGF KLQSLDLLLD TKSTDRKMTL LHFIALTVKE KYPDLANFWH ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 ELHFVEKAAA VSLENVLLDV KELGRGMELI RRECSIHDNS VLRNFLSTNE GKLDKLQRDA ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~1199999 9999999999 * 21 M'95 -w border ---------- ---------- ---------- ---------- ---fgabcde fgabcdefga * 21 M'95 -w register ~~~~~~~~~~ ~~11111111 1111111111 111~~~~~~~ 1111177779 9999999999 * 21 M'95 +w polar ~~~~~~~~~~ ~~11111111 1111111111 111~~~~~~~ ~~~~~88889 9999999999 * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~444 5888888888 8888888888 * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~22229 9999999999 * 14 M'95 -w local . | . | . | . | . | . 420 KTAEEAYNAV VRYFGESPKT TPPSVFFPVF VRFIRSYKEA EQENEARKKQ EEVMREKQLA 9999999999 993~~~~~~~ ~~~~~~~~~~ ~333569999 9999999999 9999999999 * 21 M'95 -w border bcdefgabcd efg------- ---------- -cdefgafga cdefgabcde fgabcdefga * 21 M'95 -w register 9999999999 995~~~~~~~ ~~~~~~~~~~ ~~~~~~~111 1166666666 6666666666 * 21 M'95 +w polar 9999999999 9951~~~~~~ ~~~~~~~~~~ ~~~~124666 6677888888 8888888888 * 21 MTK -w class 8888888884 111~~~~~~~ ~~~~~~~~~1 1113489999 9999999999 9999999999 * 28 M'95 -w signif. 9999999984 ~~~~~~~~~~ ~~~~~~~~~~ 1666668899 9999999999 9999887777 * 14 M'95 -w local . | . | . | . | . | . 480 QEAKKLDAKT PSQRNKWQQQ ELIAELRRRQ AKEHRPVYEG KDGTIEDIIT VLKSVPFTAR 999997322~ ~122222222 2222222222 222~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border bcdefgefg- -dgabcdefg abcdefgabc def------- ---------- ---------- * 21 M'95 -w register 666431~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar 888884322~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class 9999999999 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. 7776555553 ~~11111444 4444444444 433~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | TAKRGSRFFC ~~~~~~~~~~ ---------- ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** tem21_2hypoth.___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: tem21_2hypoth.___inter___ (1 sequences) LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFN WTALKPNQIPSGTVFSELDDEKILEDKFEELFKTKAQGPALDLICSKNKT AQKAASKVTLLEANRAKNLAITLRKAGRSAEEICRAIHTFDLQTLPVDFV ECLMRFLPTEAEVKLLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMA GMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGNYMN SSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWH ELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNE GKLDKLQRDAKTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEA EQENEARKKQEEVMREKQLAQEAKKLDAKTPSQRNKWQQQELIAELRRRQ AKEHRPVYEGKDGTIEDIITVLKSVPFTARTAKRGSRFFCDAAHHDESNC (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 12 32 1.316 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 11 468 K+R profile 2.00 + CYT-EXT prof - -0.55 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): -6.00 (NEG-POS)/(NEG+POS): 0.0000 NEG: 1.0000 POS: 1.0000 -> Orientation: N-out CYT-EXT difference: 0.55 -> Orientation: N-out ---------------------------------------------------------------------- "tem21_2hypoth" 500 12 32 #t 1.31563 ************************************ *TOPPREDM with prokaryotic function* ************************************ tem21_2hypoth.___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: tem21_2hypoth.___inter___ (1 sequences) LPPPPDKCPPAPPLPGAAPSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFN WTALKPNQIPSGTVFSELDDEKILEDKFEELFKTKAQGPALDLICSKNKT AQKAASKVTLLEANRAKNLAITLRKAGRSAEEICRAIHTFDLQTLPVDFV ECLMRFLPTEAEVKLLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMA GMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGNYMN SSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWH ELHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNE GKLDKLQRDAKTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEA EQENEARKKQEEVMREKQLAQEAKKLDAKTPSQRNKWQQQELIAELRRRQ AKEHRPVYEGKDGTIEDIITVLKSVPFTARTAKRGSRFFCDAAHHDESNC (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 12 32 1.316 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 Loop length 11 468 K+R profile 2.00 + CYT-EXT prof - -0.55 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): -6.00 (NEG-POS)/(NEG+POS): 0.0000 NEG: 1.0000 POS: 1.0000 -> Orientation: N-out CYT-EXT difference: 0.55 -> Orientation: N-out ---------------------------------------------------------------------- "tem21_2hypoth" 500 12 32 #t 1.31563 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ SAPS. Version of April 11, 1996. Date run: Fri Jan 19 18:07:46 2001 File: /people/maria/tem21_2hypoth.___saps___ ID Tem21.2_gi|7328133|emb|CAB82400.1| DE hypothetical protein [Homo sapiens] number of residues: 500; molecular weight: 56.7 kdal 1 LPPPPDKCPP APPLPGAAPS VVLTVPPGLS AIRIKKPPPI KTKFRLPVFN WTALKPNQIP 61 SGTVFSELDD EKILEDKFEE LFKTKAQGPA LDLICSKNKT AQKAASKVTL LEANRAKNLA 121 ITLRKAGRSA EEICRAIHTF DLQTLPVDFV ECLMRFLPTE AEVKLLRQYE RERQPLEELA 181 AEDRFMLLFS KVERLTQRMA GMAFLGNFQD NLQMLTPQLN AIIAASASVK SSQKLKQMLE 241 IILALGNYMN SSKRGAVYGF KLQSLDLLLD TKSTDRKMTL LHFIALTVKE KYPDLANFWH 301 ELHFVEKAAA VSLENVLLDV KELGRGMELI RRECSIHDNS VLRNFLSTNE GKLDKLQRDA 361 KTAEEAYNAV VRYFGESPKT TPPSVFFPVF VRFIRSYKEA EQENEARKKQ EEVMREKQLA 421 QEAKKLDAKT PSQRNKWQQQ ELIAELRRRQ AKEHRPVYEG KDGTIEDIIT VLKSVPFTAR 481 TAKRGSRFFC DAAHHDESNC -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 47( 9.4%); C : 7( 1.4%); D : 22( 4.4%); E : 43( 8.6%); F : 25( 5.0%) G : 17( 3.4%); H : 8( 1.6%); I : 21( 4.2%); K : 45( 9.0%); L : 58(11.6%) M : 10( 2.0%); N : 19( 3.8%); P : 31( 6.2%); Q : 23( 4.6%); R : 33( 6.6%) S : 27( 5.4%); T : 26( 5.2%); V : 27( 5.4%); W : 3( 0.6%); Y : 8( 1.6%) KR : 78 ( 15.6%); ED : 65 ( 13.0%); AGP : 95 ( 19.0%); KRED : 143 ( 28.6%); KR-ED : 13 ( 2.6%); FIKMNY : 128 ( 25.6%); LVIFM : 141 ( 28.2%); ST : 53 ( 10.6%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 00000-+000 0000000000 0000000000 00+0++0000 +0+0+00000 0000+00000 61 000000-0-- -+00--+0-- 00+0+00000 0-0000+0+0 00+000+000 0-00+0+000 121 000++00+00 --00+00000 -000000-00 -000+0000- 0-0+00+00- +-+000--00 181 0--+000000 +0-+000+00 000000000- 0000000000 000000000+ 000+0+000- 241 0000000000 00++000000 +0000-000- 0+00-++000 00000000+- +00-000000 301 -0000-+000 000-0000-0 +-00+00-00 ++-0000-00 00+000000- 0+0-+00+-0 361 +00--00000 0+000-00+0 0000000000 0+00+00+-0 -0-0-0+++0 --00+-+000 421 0-0++0-0+0 000+0+0000 -000-0+++0 0+-0+000-0 +-000--000 00+000000+ 481 00++00+000 -0000--000 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 12/30 or 16/45 or 20/60): none Negative charge clusters (cmin = 11/30 or 14/45 or 18/60): none Mixed charge clusters (cmin = 18/30 or 24/45 or 31/60): 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. ________________________________ High scoring uncharged segments: score= 1.00 frequency= 0.714 ( LAGSVTIPNFQYHMCW ) score= 0.00 frequency= 0.000 ( BZX ) score= -8.00 frequency= 0.286 ( KEDR ) Expected score/letter: -1.574 M_0.01= 29.58; M_0.05= 24.38 1) From 8 to 32: length= 25, score=25.00 * 8 CPPAPPLPGA APSVVLTVPP GLSAI L: 3(12.0%); A: 4(16.0%); V: 3(12.0%); P: 8(32.0%); C. CHARGE RUNS AND PATTERNS. pattern (+)| (-)| (*)| (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)| (H.)|(H..)| lmin0 6 | 5 | 8 | 28 | 10 | 10 | 14 | 12 | 11 | 16 | 6 | 8 | lmin1 7 | 7 | 10 | 34 | 13 | 12 | 17 | 15 | 14 | 19 | 8 | 10 | lmin2 8 | 8 | 12 | 38 | 14 | 13 | 19 | 17 | 16 | 21 | 9 | 11 | (Significance level: 0.010000; Minimal displayed length: 6) There are no charge runs or patterns exceeding the given minimal lengths. Run count statistics: + runs >= 4: 0 - runs >= 3: 1, at 69; * runs >= 6: 0 0 runs >= 19: 2, at 8; 211; -------------------------------------------------------------------------------- DISTRIBUTION OF OTHER AMINO ACID TYPES 1. HIGH SCORING SEGMENTS. There are no high scoring hydrophobic segments. There are no high scoring transmembrane segments. 2. SPACINGS OF C. H2N-7-C-86-C-38-C-17-C-181-C-155-C-9-C-0-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-7-C-86-C-38-C-3-H-13-C-129-H-17-H-2-H-30-C-2-H-116-H-35-C-3-H-H-4-C-0-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 4 Aligned matching blocks: [ 355- 362] KLQRDAKT [ 425- 430] KL__DAKT 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: 41 (Expected range: 14-- 47) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 16 (6-10) 10 (11-20) 9 (>=21) 7 3. Clusters of amino acid multiplets (cmin = 13/30 or 17/45 or 21/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 19 (Expected range: 5-- 30) 9 +plets (f+: 15.6%), 10 -plets (f-: 13.0%) Total number of charge altplets: 17 (Critical number: 34) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 5 (6-10) 1 (11-20) 4 (>=21) 10 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 2- 5 1 P 4 4 0 5- 32 7 P...... 4 4 0 67- 82 4 E... 4 4 0 360- 371 3 A.. 4 4 0 399- 406 2 E. 4 4 0 B. CHARGE ALPHABET ({+= KR; -= ED; 0}; core: 5; !-core: 7) and HYDROPHOBICITY ALPHABET ({*= KRED; i= LVIF; 0}; core: 6; !-core:10) Location Period Element Copies Core Errors 399- 418 2 *. 9 7 1 401- 442 7 *0.0... 6 6 /0/2/./2/./././ 427- 468 7 *0.0*.. 6 6 /0/2/./1/2/././ 445- 493 7 *....00 7 7 /0/././././2/2/ -------------------------------------------------------------------------------- SPACING ANALYSIS. Location (Quartile) Spacing Rank P-value Interpretation 6- 67 (1.) -( 61)- 1 of 66 0.0074 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: tem21_2hypoth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- FH2 Formin Homology 2 Domain 487.7 8.9e-143 1 SMC_C SMC family, C-terminal domain -146.8 66 1 IPT Isopentenyl transferase -163.9 13 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- SMC_C 1/1 130 262 .. 1 210 [] -146.8 66 IPT 1/1 121 303 .. 1 240 [] -163.9 13 FH2 1/1 36 467 .. 1 503 [] 487.7 8.9e-143 Alignments of top-scoring domains: SMC_C: domain 1 of 1, from 130 to 262: score -146.8, E = 66 *->lekeikeLgpVlnElqvNlkAi.eEYaeveeRyeelvekledleeer +e+ ++ + +l ++ ++ e+ R+ ++++ l + + Tem21.2_gi 130 AEEICRAIHTF------DLQTLpVDFVECLMRFLPTEAEVKLLRQYE 170 kkllevieeldkkrleeFmeaFnkInknfkevFqeLtgGGdAeLrLtDpd ++ ++ +eel ++Fm F k+++ ++++ + + G + D + Tem21.2_gi 171 RE-RQPLEEL--AAEDRFMLLFSKVERLTQRMAGMAFLGN-----FQDNL 212 DPFssGieisArPPgKkwknlelLSGGEKtLtALALlFAIhkykPsPFYv +++ +l+ A + A ++k s Tem21.2_gi 213 QMLTP--------------QLN------------AIIAASASVKSS---- 232 lDEvDAALDeaNVsRvAnyIkrersknaQFIVIsLRnnmmekADaLvGVy +++ ++++ I+ L n m + + Tem21.2_gi 233 -------------QKLKQMLE---------IILALGNYMNS--------S 252 mqddgvskVislkL<-* +++ V + kL Tem21.2_gi 253 KRG----AVYGFKL 262 IPT: domain 1 of 1, from 121 to 303: score -163.9, E = 13 *->mklYLIwGATcTGKTaeAiaLAksT....GwPVivLDRvQCcsqLat + l+ G +ae i A T + + +PV D v C + Tem21.2_gi 121 ITLR------KAGRSAEEICRAIHTfdlqTLPV---DFVECLMRFL- 157 GSGRPlpaELqgTrRiYLdPnR.slseGvIdAeeAndrLiaeVtshkdre P++aE+ ++ R Y +R++l e + Ae+ + +L+++V+++ Tem21.2_gi 158 ----PTEAEV-KLLRQYER-ERqPLEE--LAAEDRFMLLFSKVERLTQ-- 197 gglILEGGSISLLkrMaqdpyWnadFeWhvkrlrLpdrdvFlaqAKkRvr rMa ++ F+ + Tem21.2_gi 198 --------------RMAGMAFL-GNFQDNL-------------------- 212 qMLrpdsggpSlLdELvelWkepaaraiLEdIDGYRyiidyArahqltid qML p + + ++ +++ + +++ LE I + ++ + Tem21.2_gi 213 QMLTP--QLNAIIAASASVKSSQKLKQMLEIILALGNYMNSSKRGAVYGF 260 qLtnldt.....tTdqeeeLiegIAqEYleHAlwQEqeFPltPAtalewg +L +ld+ +++ Td++ +L + I Al ++ P a +w Tem21.2_gi 261 KLQSLDLlldtkSTDRKMTLLHFI-------ALTVKEKYPDL---ANFWH 300 rgp<-* + Tem21.2_gi 301 ELH 303 FH2: domain 1 of 1, from 36 to 467: score 487.7, E = 8.9e-143 *->pkkvpkpkkpLKqLhWdkletlkqpdapPsekskgtvWgttlndeld ++ ++k+k++L+ ++W++l+ P+++++gtv+ eld Tem21.2_gi 36 KPPPIKTKFRLPVFNWTALK--------PNQIPSGTVF-----SELD 69 etklLenegdldeleelFatkektksakkgdvsetksklmkkkvkknlki ++k+ + d++eelF k+k++++ d+ ++k k ++k+++k +++ Tem21.2_gi 70 DEKI-----LEDKFEELF--KTKAQGPAL-DLICSKNKTAQKAASK-VTL 110 ldpkrsqnppleIllrslhcdmsieetvikvailevDevkvlsedlleqL l ++r++n l+I+lr+ s+ee i+ ai+++D ++l++d++e+L Tem21.2_gi 111 LEANRAKN--LAITLRKA--GRSAEE--ICRAIHTFDL-QTLPVDFVECL 153 lkfaPYsktkeelkklrevkedkekdleeLsraeqiFllllsnLipylee ++f+P t+ e+k+lr+++++ + +leeL+ +++ F+ll+s+ + +l + Tem21.2_gi 154 MRFLP---TEAEVKLLRQYERE-RQPLEELAAEDR-FMLLFSK-VERLTQ 197 RlkallfklnfeeevedLkpklekvtaAseeLreSkkFkklLeliLaiGN R+ + f++nf +++++L p+l++++aAs ++++S k+k++Le+iLa+GN Tem21.2_gi 198 RMAGMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGN 247 yMNggsrrrgqAkGFkLssLtkLsdvKsadnktTLLHylvkiirekypel yMN +s+r g+++GFkL+sL+ L+d+Ks+d+k+TLLH+++ +++ekyp+l Tem21.2_gi 248 YMN-SSKR-GAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDL 295 ldFysdlhhvdeaSsrkvnleelekdvkslekqiknlEtsldlgnlsdpe ++F +lh+v++a+ v+le+++ dvk+l++ ++E l +++s+ Tem21.2_gi 296 ANFWHELHFVEKAA--AVSLENVLLDVKELGR---GME--LIRRECSI-- 336 lhpdDkflevmrpFlkaAkekfdkLqkdlkdmktrleslveyygedpkdd h+ v+r Fl + k+dkLq d+k+++++++ +v+y+ge+pk+ Tem21.2_gi 337 -HD----NSVLRNFLSTNEGKLDKLQRDAKTAEEAYNAVVRYFGESPKT- 380 lspneFFkdfneFleefkkarkenlAEeqrkekeeelkrrrklalkalsk ++p FF f++F+ ++k+a +en + ++k+ee +r ++la + Tem21.2_gi 381 TPPSVFFPVFVRFIRSYKEAEQEN----EARKKQEEVMREKQLA-----Q 421 eklereqgkskqkentlerrkernplmdgeaekeqdfkgvldsllkalrt e ++ ++++ q + + ++++++a e+ +++++ + + ++++ Tem21.2_gi 422 EAKKLDAKTPSQRN--------KWQQQELIA--ELRRRQAKEHRPVYEGK 461 dssfrr<-* d+ +++ Tem21.2_gi 462 DGTIED 467 // 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: tem21_2hypoth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- FH2 Formin Homology 2 Domain 485.9 3.3e-142 1 cofilin_ADF Cofilin/tropomyosin-type actin-bindin 4.3 7.7 1 HNH HNH endonuclease 2.1 77 1 Auxin_BP Auxin binding protein -0.8 54 1 GTP_cyclohydroI GTP cyclohydrolase I -0.9 90 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- cofilin_ADF 1/1 63 79 .. 134 150 .] 4.3 7.7 HNH 1/1 210 227 .. 35 52 .] 2.1 77 Auxin_BP 1/1 332 344 .. 1 14 [. -0.8 54 GTP_cyclohydroI 1/1 357 372 .. 169 184 .] -0.9 90 FH2 1/1 36 467 .. 1 503 [] 485.9 3.3e-142 Alignments of top-scoring domains: cofilin_ADF: domain 1 of 1, from 63 to 79: score 4.3, E = 7.7 *->gDaselsDeealleklk<-* +++sel+De++l++k Tem21.2_gi 63 TVFSELDDEKILEDKFE 79 HNH: domain 1 of 1, from 210 to 227: score 2.1, E = 77 *->dNLvlltpkeNsrkhatk<-* dNL++ltp+ N +++a Tem21.2_gi 210 DNLQMLTPQLNAIIAASA 227 Auxin_BP: domain 1 of 1, from 332 to 344: score -0.8, E = 54 *->askcsikglplvRn<-* +csi+++++ Rn Tem21.2_gi 332 -RECSIHDNSVLRN 344 GTP_cyclohydroI: domain 1 of 1, from 357 to 372: score -0.9, E = 90 *->redqkTReEfLrlirk<-* + d+kT eE+++++ + Tem21.2_gi 357 QRDAKTAEEAYNAVVR 372 FH2: domain 1 of 1, from 36 to 467: score 485.9, E = 3.3e-142 *->pkkvpkpkkpLKqLhWdkletlkqpdapPsekskgtvWgttlndeld ++ ++k+k++L+ ++W++l+ P+++++gtv+ eld Tem21.2_gi 36 KPPPIKTKFRLPVFNWTALK--------PNQIPSGTVF-----SELD 69 etklLenegdldeleelFatkektksakkgdvsetksklmkkkvkknlki ++k+ + d++eelF k+k++++ d+ ++k k ++k+++k +++ Tem21.2_gi 70 DEKI-----LEDKFEELF--KTKAQGPAL-DLICSKNKTAQKAASK-VTL 110 ldpkrsqnppleIllrslhcdmsieetvikvailevDevkvlsedlleqL l ++r++n l+I+lr+ s+ee i+ ai+++D ++l++d++e+L Tem21.2_gi 111 LEANRAKN--LAITLRKA--GRSAEE--ICRAIHTFDL-QTLPVDFVECL 153 lkfaPYsktkeelkklrevkedkekdleeLsraeqiFllllsnLipylee ++f+P t+ e+k+lr+++++ + +leeL+ +++ F+ll+s+ + +l + Tem21.2_gi 154 MRFLP---TEAEVKLLRQYERE-RQPLEELAAEDR-FMLLFSK-VERLTQ 197 RlkallfklnfeeevedLkpklekvtaAseeLreSkkFkklLeliLaiGN R+ + f++nf +++++L p+l++++aAs ++++S k+k++Le+iLa+GN Tem21.2_gi 198 RMAGMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGN 247 yMNggsrrrgqAkGFkLssLtkLsdvKsadnktTLLHylvkiirekypel yMN +s+r g+++GFkL+sL+ L+d+Ks+d+k+TLLH+++ +++ekyp+l Tem21.2_gi 248 YMN-SSKR-GAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDL 295 ldFysdlhhvdeaSsrkvnleelekdvkslekqiknlEtsldlgnlsdpe ++F +lh+v++a+ v+le+++ dvk+l++ ++E l +++s+ Tem21.2_gi 296 ANFWHELHFVEKAA--AVSLENVLLDVKELGR---GME--LIRRECSI-- 336 lhpdDkflevmrpFlkaAkekfdkLqkdlkdmktrleslveyygedpkdd h+ v+r Fl + k+dkLq d+k+++++++ +v+y+ge+pk+ Tem21.2_gi 337 -HD----NSVLRNFLSTNEGKLDKLQRDAKTAEEAYNAVVRYFGESPKT- 380 lspneFFkdfneFleefkkarkenlAEeqrkekeeelkrrrklalkalsk ++p FF f++F+ ++k+a +en + ++k+ee +r ++la + Tem21.2_gi 381 TPPSVFFPVFVRFIRSYKEAEQEN----EARKKQEEVMREKQLA-----Q 421 eklereqgkskqkentlerrkernplmdgeaekeqdfkgvldsllkalrt e ++ ++++ q + + ++++++a e+ +++++ + + ++++ Tem21.2_gi 422 EAKKLDAKTPSQRN--------KWQQQELIA--ELRRRQAKEHRPVYEGK 461 dssfrr<-* d+ +++ Tem21.2_gi 462 DGTIED 467 // 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: tem21_2hypoth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Prosite --------------------------------------------------------- | ppsearch (c) 1994 EMBL Data Library | | based on MacPattern (c) 1990-1994 R. Fuchs | --------------------------------------------------------- PROSITE pattern search started: Fri Jan 19 18:09:57 2001 Sequence file: tem21_2hypoth ---------------------------------------- Sequence Tem21.2_gi|7328133|emb|CAB82400.1| (500 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 50: NWTA 98: NKTA 250: NSSK Total matches: 3 Matching pattern PS00004 CAMP_PHOSPHO_SITE: 276: RKMT 483: KRGS Total matches: 2 Matching pattern PS00005 PKC_PHOSPHO_SITE: 122: TLR 196: TQR 228: SVK 232: SQK 251: SSK 252: SKR 274: TDR 287: TVK 377: SPK 396: SYK 432: SQR 478: TAR 481: TAK Total matches: 13 Matching pattern PS00006 CK2_PHOSPHO_SITE: 66: SELD 109: TLLE 129: SAEE 159: TEAE 190: SKVE 287: TVKE 335: SIHD 347: STNE 362: TAEE 396: SYKE 464: TIED Total matches: 11 Matching pattern PS00008 MYRISTYL: 16: GAAPSV 62: GTVFSE 246: GNYMNS 255: GAVYGF Total matches: 4 Matching pattern PS00290 IG_MHC: 488: FFCDAAH Total matches: 1 Total no of hits in this sequence: 34 ======================================== 1314 pattern(s) searched in 1 sequence(s), 500 residues. Total no of hits in all sequences: 34. Search time: 00:00 min ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Profile Search ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with motif search against own library ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** SeqTyp=2 : PROTEIN search; >APC D-Box is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 500 units >ER-GOLGI-traffic signal is the MOTIF name >STATISTICS Total : 0 solutions in 0 sequences, 0 units; out of 1 sequences, 500 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: tem21_2hypoth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] 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: tem21_2hypoth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] 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= Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] (500 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value ARM Armadillo repeat 26 0.10 ARR Arrestin domain 24 0.34 PDE cyclic NMP phosphodiesterase domain 23 0.75 PAIRED Paired domain (A HTH domain) 22 1.6 KIN Protein kinase domain 22 2.2 SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chrom... 21 2.3 CALC Calcineurin like Phosphoesterase domain 21 2.8 INSL Insulinase like Metallo protease domain 21 3.1 UBHYD Ubiquitin C-terminal hydrolase domain 21 3.8 SH3 Src Homology domain 3 21 4.6 14-3-3 14-3-3 protein alpha Helical domain 20 6.4 CYCLIN Cyclin/TFIIB domain 20 7.9 RHOGAP RHO-type GTPase GTP hydrolysis activating protein 19 9.5 >ARM Armadillo repeat Length = 532 Score = 26.1 bits (57), Expect = 0.10 Identities = 14/81 (17%), Positives = 14/81 (17%), Gaps = 10/81 (12%) Query: 394 IRSYKEAEQENEARKKQEEVMREKQLAQEAKKLDAKTPSQRNKWQQQELIAELRRRQAKE 453 Sbjct: 13 RNRYKVAVDAEEGRRRREDNMVEIRKSKREESLMKK----RREGMQALQGFPSASAASVD 68 Query: 454 HRPVYEGKDGTIEDIITVLKS 474 Sbjct: 69 KKL------DSLKDMVAGVWS 83 Score = 23.4 bits (50), Expect = 0.66 Identities = 15/74 (20%), Positives = 15/74 (20%), Gaps = 11/74 (14%) Query: 307 KAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNEG--KLDKLQR--DAKT 362 Sbjct: 430 TVCLEGLENILKV----GEAEKNLGHT---GDMNYYAQLIDDAEGLEKIENLQSHDNNEI 482 Query: 363 AEEAYNAVVRYFGE 376 Sbjct: 483 YEKAVKILETYWLE 496 Score = 19.5 bits (40), Expect = 9.5 Identities = 11/86 (12%), Positives = 11/86 (12%), Gaps = 4/86 (4%) Query: 165 LLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMAGMAFLGN---FQDNLQMLTPQLNA 221 Sbjct: 269 LSDGTNDKIQTVIQAGVVPKLVELLLHHSPSVLIPALRT-VGNIVTGDDIQTQCVINSGA 327 Query: 222 IIAASASVKSSQKLKQMLEIILALGN 247 Sbjct: 328 LPCLANLLTQNHKKSIKKEACWTISN 353 >ARR Arrestin domain Length = 454 Score = 24.5 bits (53), Expect = 0.34 Identities = 11/74 (14%), Positives = 11/74 (14%), Gaps = 15/74 (20%) Query: 19 PSVVLTVPPGLSAIRIKKPPPIKTKFRLPVFNWTALKPNQIPSGTVFSELDDEKILEDK- 77 Sbjct: 374 PFTLTHSKPPESPERTDRGLPSIEAT-----------NGSEPVDIDLIQLHEELEPRYDD 422 Query: 78 ---FEELFKTKAQG 88 Sbjct: 423 DLIFEDFARMRLHG 436 Score = 19.8 bits (41), Expect = 7.7 Identities = 5/22 (22%), Positives = 5/22 (22%) Query: 3 PPPDKCPPAPPLPGAAPSVVLT 24 Sbjct: 197 LAIRKLTYAPFESRPQPMVDVS 218 >PDE cyclic NMP phosphodiesterase domain Length = 350 Score = 23.2 bits (49), Expect = 0.75 Identities = 28/149 (18%), Positives = 28/149 (18%), Gaps = 7/149 (4%) Query: 168 QYERERQPLEELAAEDRFMLLFSKVERLTQRMAGMAFLGNFQDNLQMLTPQLNAIIAASA 227 Sbjct: 163 QYKELRRSVVQLILATDMQNHFEHTNKFQHHLNNLPFDRNKKEDRQMI---LNFLIKCGD 219 Query: 228 SVKSSQKLKQMLEIILALGN-YMNSSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIAL 286 Sbjct: 220 ISNIARPWHLNFEWSLRVSDEFFQQSHYETICGYPVTP---FMDKTKTTRARIAADFIDF 276 Query: 287 TVKEKYPDLANFWHELHFVEKAAAVSLEN 315 Sbjct: 277 VASPLFQSMAKFLKESQFLLKVISKNREN 305 >PAIRED Paired domain (A HTH domain) Length = 127 Score = 22.4 bits (47), Expect = 1.6 Identities = 10/27 (37%), Positives = 10/27 (37%), Gaps = 5/27 (18%) Query: 375 GESPKTTPPSVFFPVFVRFIRSYKEAE 401 Sbjct: 70 GSKPRVTTPTV-----VKHIRTYKQRD 91 >KIN Protein kinase domain Length = 313 Score = 21.6 bits (45), Expect = 2.2 Identities = 10/53 (18%), Positives = 10/53 (18%), Gaps = 1/53 (1%) Query: 300 HELH-FVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNEG 351 Sbjct: 117 TDLHQIITSPQPLSDDHCQYFVYQMLRGLKHIHSANVLHRDLKPSNLLINEDC 169 >SET Su(var)3-9, Enhancer of Zeste, trithorax domain (A chromatin associated domain) Length = 219 Score = 21.5 bits (45), Expect = 2.3 Identities = 5/20 (25%), Positives = 5/20 (25%) Query: 393 FIRSYKEAEQENEARKKQEE 412 Sbjct: 200 YGPLYWKHRKKREEFVPQEE 219 >CALC Calcineurin like Phosphoesterase domain Length = 274 Score = 21.3 bits (44), Expect = 2.8 Identities = 18/103 (17%), Positives = 18/103 (17%), Gaps = 6/103 (5%) Query: 242 ILALGNYMNSSKRGAVYGFKLQSLDLLLDTKSTDRKMTLLHFIALTVKEKYPDLANFWHE 301 Sbjct: 123 ALLLDSQVYGVPHGQLSQHQLDLLKETLGKNPERYTLVVLHHHLLPTNSAWLD----QHN 178 Query: 302 LHFVEKAAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRN 344 Sbjct: 179 LRNSHELAEVLAPF--TNVKAILYGHIHQEVNSEWNGYQVMAT 219 >INSL Insulinase like Metallo protease domain Length = 433 Score = 21.4 bits (45), Expect = 3.1 Identities = 7/25 (28%), Positives = 7/25 (28%) Query: 364 EEAYNAVVRYFGESPKTTPPSVFFP 388 Sbjct: 214 KEVEEEVMKTFGKEEGRPVPKVQIP 238 >UBHYD Ubiquitin C-terminal hydrolase domain Length = 884 Score = 20.7 bits (43), Expect = 3.8 Identities = 26/108 (24%), Positives = 26/108 (24%), Gaps = 26/108 (24%) Query: 388 PVFVRFIRS--YKEAEQENEARKKQEEVMREKQLAQEAKKLDAKTPSQRNKWQQQELIAE 445 Sbjct: 616 PMLLQFFKSQGYRDG-PGNPLRHNYEGTLRD--LLQFFK------PRQPKKLYYQQLKMK 666 Query: 446 L----RRRQAK----------EHRPVYEGKDGTIEDII-TVLKSVPFT 478 Sbjct: 667 ITDFENRRSFKCIWLNSQFREEEITLYPDKHGCVRDLLEECKKAVELG 714 Score = 19.6 bits (40), Expect = 9.8 Identities = 8/35 (22%), Positives = 8/35 (22%) Query: 67 ELDDEKILEDKFEELFKTKAQGPALDLICSKNKTA 101 Sbjct: 261 KFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNA 295 >SH3 Src Homology domain 3 Length = 90 Score = 20.5 bits (43), Expect = 4.6 Identities = 4/16 (25%), Positives = 4/16 (25%) Query: 2 PPPPDKCPPAPPLPGA 17 Sbjct: 1 PRVQAWSPPVRGIPQL 16 >14-3-3 14-3-3 protein alpha Helical domain Length = 270 Score = 20.3 bits (42), Expect = 6.4 Identities = 6/30 (20%), Positives = 6/30 (20%) Query: 399 EAEQENEARKKQEEVMREKQLAQEAKKLDA 428 Sbjct: 241 AAAAGGNTEGAQENAPSNAPEGEAEPKADA 270 >CYCLIN Cyclin/TFIIB domain Length = 317 Score = 19.9 bits (41), Expect = 7.9 Identities = 13/112 (11%), Positives = 13/112 (11%), Gaps = 6/112 (5%) Query: 308 AAAVSLENVLLDVKELGRGMELIRRECSIHDNSVLRNFLSTNEGKLDKLQRDAKTAEEAY 367 Sbjct: 208 LTAILSSASRAGITMESYLSESLMLK----ENRTCLSQLLDIMKSMRNLVKKYEPPRSEE 263 Query: 368 NAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEAEQENEARKKQEEVMREKQL 419 Sbjct: 264 VAVLKQKLERCHSAELALNVI--TKKRKGYEDDDYVSKKSKHEEEEWTDDDL 313 >RHOGAP RHO-type GTPase GTP hydrolysis activating protein Length = 194 Score = 19.4 bits (40), Expect = 9.5 Identities = 9/79 (11%), Positives = 9/79 (11%), Gaps = 9/79 (11%) Query: 384 SVFFPVFVRFIRSYKEA----EQENEARKKQEEVMREKQLAQEAKKLDAKT----PSQRN 435 Sbjct: 95 EQMCKTYSEFCSRHSKALKFYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQR- 153 Query: 436 KWQQQELIAELRRRQAKEH 454 Sbjct: 154 ITKYPLLISRILQHSHGIE 172 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 105 Number of sequences better than 10.0: 13 Number of calls to ALIGN: 17 Length of query: 500 Total length of test sequences: 20182 Effective length of test sequences: 16235.0 Effective search space size: 7512734.8 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= Tem21.2_gi|7328133|emb|CAB82400.1| hypothetical protein [Homo sapiens] (500 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|2131476 [80..370] Zn-dependent exopeptidases 29 0.15 gi|628630 [25..232] Ribosome inactivating proteins (RIP) 28 0.50 gi|1001472 [191..704] N-terminal nucleophile aminohydrolases... 26 1.9 gi|576299 [1..317] alpha/beta-Hydrolases 24 3.7 gi|442637 [1..263] Trypsin-like serine proteases 24 4.2 gi|417068 [395..693] Ribonuclease H-like motif 24 4.3 gi|2809057 [242..451] Metzincin-like 24 7.3 gi|629488 [18..291] Ribosome inactivating proteins (RIP) 23 8.1 >gi|2131476 [80..370] Zn-dependent exopeptidases Length = 291 Score = 29.3 bits (65), Expect = 0.15 Identities = 8/82 (9%), Positives = 8/82 (9%), Gaps = 9/82 (10%) Query: 58 QIPSGTVFSELDDEKILEDKFEELFKTKAQGPALDLI--CSKNKTAQKAASKVTL----L 111 Sbjct: 15 NIDKGSMHKNLAK---FTSFYTRYYKSDHGFESAEWLAATIANITKDIPQDTLTIEHFDH 71 Query: 112 EANRAKNLAITLRKAGRSAEEI 133 Sbjct: 72 KEWKQYSIIVRVTGSTTPEDII 93 >gi|628630 [25..232] Ribosome inactivating proteins (RIP) Length = 208 Score = 27.6 bits (60), Expect = 0.50 Identities = 17/46 (36%), Positives = 17/46 (36%), Gaps = 1/46 (2%) Query: 136 AIHTFDLQTLPVDFVECLMRFLPTEAEVKLLRQYERE-RQPLEELA 180 Sbjct: 140 ALMEFSGNTMTRDASRAVLRFVTVTAEALRFRQIQREFRQALSETA 185 >gi|1001472 [191..704] N-terminal nucleophile aminohydrolases (Ntn hydrolases) Length = 514 Score = 25.7 bits (56), Expect = 1.9 Identities = 27/125 (21%), Positives = 27/125 (21%), Gaps = 19/125 (15%) Query: 203 AFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEIILALGNYMNSSKRGAVYGFKL 262 Sbjct: 294 QFKQKVFDSQMELGDRIVPLLVSAAKVLANPIGIEAAEVLQAWDKQANPDSRGAVL-FML 352 Query: 263 QSLDLLLDT------------------KSTDRKMTLLHFIALTVKEKYPDLANFWHELHF 304 Sbjct: 353 WALTIGADKVLGGQWNPADPLNTPSGMADINKFMAVLEGVAAQVKFLYDDLAISWGEVVQ 412 Query: 305 VEKAA 309 Sbjct: 413 MQVGN 417 >gi|576299 [1..317] alpha/beta-Hydrolases Length = 317 Score = 24.4 bits (52), Expect = 3.7 Identities = 22/171 (12%), Positives = 22/171 (12%), Gaps = 21/171 (12%) Query: 183 DRFMLLFSKVERLTQRMAGMAFLGNFQDNLQMLTPQLNAIIAASASVKSSQKLKQMLEII 242 Sbjct: 145 DALAVSAPSVWQQTTGSALTTALRNAGGLTQIVPTTNLYSATDEIVQPQVSNSPLDSSYL 204 Query: 243 LALGNYMNSSKRGAVYGFKLQSL---------------DLLLDTKSTD---RKMTLLHFI 284 Sbjct: 205 FNGKNVQAQAVCGPLFVIDHAGSLTSQFSYVVGRSALRSTTGQARSADYGITDCNPLPAN 264 Query: 285 ALTVKEKYPDLANFWHELHFVEKAAAVSLENVLLDVKELGRGMELIRRECS 335 Sbjct: 265 DLTPEQKVAAAALLAPAAAAIVAGPKQNCEP---DLMPYARPFAVGKRTCS 312 >gi|442637 [1..263] Trypsin-like serine proteases Length = 263 Score = 24.5 bits (52), Expect = 4.2 Identities = 14/27 (51%), Positives = 14/27 (51%) Query: 101 AQKAASKVTLLEANRAKNLAITLRKAG 127 Sbjct: 107 ATYATSDFTLLELNNAANPAFNLFWAG 133 >gi|417068 [395..693] Ribonuclease H-like motif Length = 299 Score = 24.2 bits (52), Expect = 4.3 Identities = 4/85 (4%), Positives = 4/85 (4%), Gaps = 11/85 (12%) Query: 70 DEKILEDKFEELFKTKAQGPALDLICSKNKTAQKAASKVTLLEANRAKNLAITLRKAGRS 129 Sbjct: 67 VAGAVVQWLRDNLRLIDK----SEDVGPIASTVPDSGGVVFVPAFSGLFAPYWD------ 116 Query: 130 AEEICRAIHTFDLQTLPVDFVECLM 154 Sbjct: 117 -PDARATIMGMSQFTTASHIARAAV 140 >gi|2809057 [242..451] Metzincin-like Length = 210 Score = 23.7 bits (51), Expect = 7.3 Identities = 10/62 (16%), Positives = 10/62 (16%), Gaps = 5/62 (8%) Query: 325 RGMELIRRECSIHDNS----VLRNFLSTNEGKLDKLQRDAKTAEEAYNAVVRYF-GESPK 379 Sbjct: 51 KILVIYEEQKGPEVTSNAALTLRNFCNWQKQHNSPSDRDPEHYDTAILFTRQDLCGSHTC 110 Query: 380 TT 381 Sbjct: 111 DT 112 >gi|629488 [18..291] Ribosome inactivating proteins (RIP) Length = 274 Score = 23.3 bits (50), Expect = 8.1 Identities = 15/94 (15%), Positives = 15/94 (15%), Gaps = 7/94 (7%) Query: 346 LSTNEGKLDKLQRDAKTAEEAYNAVVRYFGESPKTTPPSVFFPVFVRFIRSYKEAEQENE 405 Sbjct: 128 MESKGGARTKLGLGKITLKSRMGKIYGKDATDQKQYQKNEAEFLLI-AVQMVTEA----- 181 Query: 406 ARKKQ-EEVMREKQLAQEAKKLDAKTPSQRNKWQ 438 Sbjct: 182 SRFKYIENKVKAKFDDANGYQPDPKAISLEKNWD 215 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 8 Number of calls to ALIGN: 8 Length of query: 500 Total length of test sequences: 256703 Effective length of test sequences: 204927.0 Effective search space size: 93454301.3 Initial X dropoff for ALIGN: 25.0 bits ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ calculation of internal repeats with prospero ***** PROSPERO v1.3 Fri Jan 19 18:10:42 2001 ***** Copyright 2000, Richard Mott, Wellcome Trust Centre for Human Genetics, University of Oxford For help see http://www.well.ox.ac.uk/ariadne For usage use -help using gap penalty 11+1k using matrix BLOSUM62 printing all alignments with eval < 0.100000 using sequence1 Tem21.2_gi|7328133|emb|CAB82400.1| using self-comparison