analysis of sequence from tem35 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ >gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSKFVCNTEQPGCENVCYDAFAP LSHVRFWVFQIILVATPSVMYLGYAIHKIAKMEHGEADKKAARSKPYAMRWKQHRALEETEEDNEEDPMM YPEMELESDKENKEQSQPKPKHDGRRRIREDGLMKIYVLQLLARTVFEVGFLIGQYFLYGFQVHPFYVCS RLPCPHKIDCFISRPTEKTIFLLIMYGVTGLCLLLNIWEMLHLGFGTIRDSLNSKRRELEDPGAYNYPFT WNTPSAPPGYNIAVKPDQIQYTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLD LAVQAYSHQNNPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ sec.str. with predator > gi|4885169|ref|NP_005488.1| . . . . . 1 MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSK 50 ___HHHHHHHHHHH_____HHHHHHHHHHHHHHHHHH_____EEE_____ . . . . . 51 FVCNTEQPGCENVCYDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIA 100 _______________________EEEHHHHHHHH____EEEEHHHHHHHH . . . . . 101 KMEHGEADKKAARSKPYAMRWKQHRALEETEEDNEEDPMMYPEMELESDK 150 HHH_____HHHHHHHHHHHHHHHHHHHHHHHH_________HHHHHHHHH . . . . . 151 ENKEQSQPKPKHDGRRRIREDGLMKIYVLQLLARTVFEVGFLIGQYFLYG 200 HHHHH__________EEEE____HHHHHHHHHHHHHHHHHHHHHHEEEEE . . . . . 201 FQVHPFYVCSRLPCPHKIDCFISRPTEKTIFLLIMYGVTGLCLLLNIWEM 250 EE_____EEE________EEEE_____HHHHHHHHH_____HHHHHHHHH . . . . . 251 LHLGFGTIRDSLNSKRRELEDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ 300 HH__________HHHHHHH_____________________EEEE____EE . . . . . 301 YTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLD 350 EEE__HHHHHHHH___HHHHHHHH__________HHHHHHHHHHHHHHHH . . . . 351 LAVQAYSHQNNPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI 396 HHHHHHH__________HHHHHH_______________________ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ method : 1 alpha-contents : 47.6 % beta-contents : 14.5 % coil-contents : 37.9 % class : mixed method : 2 alpha-contents : 36.4 % beta-contents : 12.9 % coil-contents : 50.7 % class : mixed ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ GPI: learning from metazoa -29.22 -1.21 -0.14 0.00 -4.00 0.00 0.00 -0.56 -0.13 -7.81 -2.74 -12.00 -12.00 -12.00 -12.00 0.00 -93.81 -23.63 -0.96 -1.41 -1.27 -4.00 0.00 0.00 0.00 -0.57 -9.26 -2.74 -12.00 -12.00 -12.00 -12.00 0.00 -91.84 ID: gi|4885169|ref|NP_005488.1| AC: xxx Len: 350 1:I 333 Sc: -91.84 Pv: 9.521474e-01 NO_GPI_SITE GPI: learning from protozoa -35.28 -1.02 -0.74 -0.49 -4.00 0.00 0.00 -1.18 -0.24 -5.77 -9.80 -12.00 -12.00 -12.00 -12.00 0.00 -106.53 -14.54 -1.02 -0.03 -0.21 0.00 0.00 0.00 0.00 -0.11 -7.90 -9.80 -12.00 -12.00 -12.00 -12.00 0.00 -81.62 ID: gi|4885169|ref|NP_005488.1| AC: xxx Len: 350 1:I 333 Sc: -81.62 Pv: 5.383399e-01 NO_GPI_SITE ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ # SignalP euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? gi|4885169| 0.727 41 Y 0.774 41 Y 0.956 29 Y 0.549 Y # SignalP gram- predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? gi|4885169| 0.347 346 N 0.318 40 N 0.927 31 Y 0.395 N # SignalP gram+ predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? gi|4885169| 0.389 96 N 0.401 40 Y 0.992 28 Y 0.517 N ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ low complexity regions: SEG 12 2.2 2.5 >gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] 1-127 MSWSFLTRLLEEIHNHSTFVGKIWLTVLIV FRIVLTAVGGESIYYDEQSKFVCNTEQPGC ENVCYDAFAPLSHVRFWVFQIILVATPSVM YLGYAIHKIAKMEHGEADKKAARSKPYAMR WKQHRAL eeteedneed 128-137 138-396 PMMYPEMELESDKENKEQSQPKPKHDGRRR IREDGLMKIYVLQLLARTVFEVGFLIGQYF LYGFQVHPFYVCSRLPCPHKIDCFISRPTE KTIFLLIMYGVTGLCLLLNIWEMLHLGFGT IRDSLNSKRRELEDPGAYNYPFTWNTPSAP PGYNIAVKPDQIQYTELSNAKIAYKQNKAN TAQEQQYGSHEENLPADLEALQREIRMAQE RLDLAVQAYSHQNNPHGPREKKAKVGSKAG SNKSTASSKSGDGKNSVWI low complexity regions: SEG 25 3.0 3.3 >gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] 1-126 MSWSFLTRLLEEIHNHSTFVGKIWLTVLIV FRIVLTAVGGESIYYDEQSKFVCNTEQPGC ENVCYDAFAPLSHVRFWVFQIILVATPSVM YLGYAIHKIAKMEHGEADKKAARSKPYAMR WKQHRA leeteedneedpmmypemelesdkenkeqs 127-159 qpk 160-367 PKHDGRRRIREDGLMKIYVLQLLARTVFEV GFLIGQYFLYGFQVHPFYVCSRLPCPHKID CFISRPTEKTIFLLIMYGVTGLCLLLNIWE MLHLGFGTIRDSLNSKRRELEDPGAYNYPF TWNTPSAPPGYNIAVKPDQIQYTELSNAKI AYKQNKANTAQEQQYGSHEENLPADLEALQ REIRMAQERLDLAVQAYSHQNNPHGPRE kkakvgskagsnkstassksgdgkns 368-393 394-396 VWI low complexity regions: SEG 45 3.4 3.75 >gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] 1-396 MSWSFLTRLLEEIHNHSTFVGKIWLTVLIV FRIVLTAVGGESIYYDEQSKFVCNTEQPGC ENVCYDAFAPLSHVRFWVFQIILVATPSVM YLGYAIHKIAKMEHGEADKKAARSKPYAMR WKQHRALEETEEDNEEDPMMYPEMELESDK ENKEQSQPKPKHDGRRRIREDGLMKIYVLQ LLARTVFEVGFLIGQYFLYGFQVHPFYVCS RLPCPHKIDCFISRPTEKTIFLLIMYGVTG LCLLLNIWEMLHLGFGTIRDSLNSKRRELE DPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ YTELSNAKIAYKQNKANTAQEQQYGSHEEN LPADLEALQREIRMAQERLDLAVQAYSHQN NPHGPREKKAKVGSKAGSNKSTASSKSGDG KNSVWI 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 >gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSKFVCNTEQPGC ENVCYDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIAKMEHGEADKKAARSKPYAMR WKQHRALeeteedneedpmmYPemelesdkenkeqsqpkpkHDGRRRIREDGLMKIYVLQ LLARTVFEVGFLIGQYFLYGFQVHPFYVCSRLPCPHKIDCFISRPTEKTIFLLIMYGVTG LCLLLNIWEMLHLGFGTIRDSLNSKRRELEDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ YTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLDLAVQAYSHQN NPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI 1 - 127 MSWSFLTRLL EEIHNHSTFV GKIWLTVLIV FRIVLTAVGG ESIYYDEQSK FVCNTEQPGC ENVCYDAFAP LSHVRFWVFQ IILVATPSVM YLGYAIHKIA KMEHGEADKK AARSKPYAMR WKQHRAL 128 - 140 eet eedneedpmm 141 - 142 YP 143 - 161 emelesdk enkeqsqpkp k 162 - 396 HDGRRRIRE DGLMKIYVLQ LLARTVFEVG FLIGQYFLYG FQVHPFYVCS RLPCPHKIDC F ISRPTEKTI FLLIMYGVTG LCLLLNIWEM LHLGFGTIRD SLNSKRRELE DPGAYNYPFT W NTPSAPPGY NIAVKPDQIQ YTELSNAKIA YKQNKANTAQ EQQYGSHEEN LPADLEALQR E IRMAQERLD LAVQAYSHQN NPHGPREKKA KVGSKAGSNK STASSKSGDG KNSVWI low complexity regions: DUST >gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSKFVCNTEQPGC ENVCYDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIAKMEHGEADKKAARSKPYAMR WKQHRALEETEEDNEEDPMMYPEMELESDKENKEQSQPKPKHDGRRRIREDGLMKIYVLQ LLARTVFEVGFLIGQYFLYGFQVHPFYVCSRLPCPHKIDCFISRPTEKTIFLLIMYGVTG LCLLLNIWEMLHLGFGTIRDSLNSKRRELEDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ YTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLDLAVQAYSHQN NPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ coiled coil prediction for gi|4885169|ref|NP_005488.1| sequence: 350 amino acids, 23 residue(s) in coiled coil state Coil 1 * 327* 0* . | . | . | . | . | . 60 MSWSFLTRLL EEIHNHSTFV GKIWLTVLIV FRIVLTAVGG ESIYYDEQSK FVCNTEQPGC ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 ENVCYDAFAP LSHVRFWVFQ IILVATPSVM YLGYAIHKIA KMEHGEADKK AARSKPYAMR ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 WKQHRALEET EEDNEEDPMM YPEMELESDK ENKEQSQPKP KHDGRRRIRE DGLMKIYVLQ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- ---------- * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~677777777 7777773~~~ ~~44444444 4444442~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | . 240 LLARTVFEVG FLIGQYFLYG FQVHPFYVCS RLPCPHKIDC FISRPTEKTI FLLIMYGVTG ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 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 LCLLLNIWEM LHLGFGTIRD SLNSKRRELE DPGAYNYPFT WNTPSAPPGY NIAVKPDQIQ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~111 * 21 M'95 -w border ---------- ---------- ---------- ---------- ---------- -------efg * 21 M'95 -w register ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 M'95 +w polar ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 21 MTK -w class ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 28 M'95 -w signif. ~~~~~~~~~~ ~~~~~~2444 4444444444 4~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ * 14 M'95 -w local . | . | . | . | . | YTELSNAKIA YKQNKANTAQ EQQYGSHEEN LPADLEALQR EIRMAQERLD 1111111111 1111111111 111~~~2799 9999999999 9999999999 abgabcdefg abcdefgabc def---gabc defgabcdef gabcdefgab ~~~~~~~~~~ ~~~~~~~~~~ ~111136899 9999999999 9999999999 ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~399 9999999999 9999999998 ~~~~~~~~~~ ~~~~~~~~~~ ~444444444 4444444444 4444444444 ~~~~~~~~~~ ~~~~~~~111 1111111155 5599999999 9999999999 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ prediction of transmembrane regions with toppred2 *********************************** *TOPPREDM with eukaryotic function* *********************************** tem35.___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: tem35.___inter___ (1 sequences) MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSK FVCNTEQPGCENVCYDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIA KMEHGEADKKAARSKPYAMRWKQHRALEETEEDNEEDPMMYPEMELESDK ENKEQSQPKPKHDGRRRIREDGLMKIYVLQLLARTVFEVGFLIGQYFLYG FQVHPFYVCSRLPCPHKIDCFISRPTEKTIFLLIMYGVTGLCLLLNIWEM LHLGFGTIRDSLNSKRRELEDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ YTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLD LAVQAYSHQNNPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI (p)rokaryotic or (e)ukaryotic: e Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 20 40 1.180 Certain 2 76 96 1.653 Certain 3 185 205 0.952 Putative 4 228 248 1.946 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 4 Loop length 19 35 88 22 148 K+R profile 3.00 + + 2.00 4.00 CYT-EXT prof - -0.82 0.70 - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -3.00 Tm probability: 0.88 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): 0.0000 NEG: 2.0000 POS: 2.0000 -> Orientation: N-in CYT-EXT difference: -0.12 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 2 4 Loop length 19 35 131 148 K+R profile 3.00 + 2.00 + CYT-EXT prof - -0.42 - 0.70 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 1.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): 0.0000 NEG: 2.0000 POS: 2.0000 -> Orientation: N-in CYT-EXT difference: -1.12 -> Orientation: N-in ---------------------------------------------------------------------- "tem35" 396 20 40 #t 1.18021 76 96 #t 1.65313 185 205 #f 0.952083 228 248 #t 1.94583 ************************************ *TOPPREDM with prokaryotic function* ************************************ tem35.___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: tem35.___inter___ (1 sequences) MSWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSK FVCNTEQPGCENVCYDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIA KMEHGEADKKAARSKPYAMRWKQHRALEETEEDNEEDPMMYPEMELESDK ENKEQSQPKPKHDGRRRIREDGLMKIYVLQLLARTVFEVGFLIGQYFLYG FQVHPFYVCSRLPCPHKIDCFISRPTEKTIFLLIMYGVTGLCLLLNIWEM LHLGFGTIRDSLNSKRRELEDPGAYNYPFTWNTPSAPPGYNIAVKPDQIQ YTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEALQREIRMAQERLD LAVQAYSHQNNPHGPREKKAKVGSKAGSNKSTASSKSGDGKNSVWI (p)rokaryotic or (e)ukaryotic: p Charge-pair energy: 0 Length of full window (odd number!): 21 Length of core window (odd number!): 11 Number of residues to add to each end of helix: 1 Critical length: 60 Upper cutoff for candidates: 1 Lower cutoff for candidates: 0.6 Total of 2 structures are to be tested Candidate membrane-spanning segments: Helix Begin End Score Certainity 1 20 40 1.180 Certain 2 76 96 1.653 Certain 3 185 205 0.952 Putative 4 228 248 1.946 Certain ---------------------------------------------------------------------- Structure 1 Transmembrane segments included in this structure: Segment 1 2 3 4 Loop length 19 35 88 22 148 K+R profile 3.00 + + 2.00 4.00 CYT-EXT prof - -0.82 0.70 - - For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: -3.00 Tm probability: 0.88 -> Orientation: N-out Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): 0.0000 NEG: 2.0000 POS: 2.0000 -> Orientation: N-in CYT-EXT difference: -0.12 -> Orientation: N-in ---------------------------------------------------------------------- Structure 2 Transmembrane segments included in this structure: Segment 1 2 4 Loop length 19 35 131 148 K+R profile 3.00 + 2.00 + CYT-EXT prof - -0.42 - 0.70 For CYT-EXT profile neg. values indicate cytoplasmic preference. K+R difference: 1.00 Tm probability: 1.00 -> Orientation: N-in Charge-difference over N-terminal Tm (+-15 residues): 2.00 (NEG-POS)/(NEG+POS): 0.0000 NEG: 2.0000 POS: 2.0000 -> Orientation: N-in CYT-EXT difference: -1.12 -> Orientation: N-in ---------------------------------------------------------------------- "tem35" 396 20 40 #t 1.18021 76 96 #t 1.65313 185 205 #f 0.952083 228 248 #t 1.94583 ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ NOW EXECUTING: /bio_software/1D/stat/saps/saps-stroh/SAPS.SSPA/saps /people/maria/tem35.___saps___ SAPS. Version of April 11, 1996. Date run: Thu Dec 21 12:12:35 2000 File: /people/maria/tem35.___saps___ ID gi|4885169|ref|NP_005488.1| DE gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] number of residues: 396; molecular weight: 45.5 kdal 1 MSWSFLTRLL EEIHNHSTFV GKIWLTVLIV FRIVLTAVGG ESIYYDEQSK FVCNTEQPGC 61 ENVCYDAFAP LSHVRFWVFQ IILVATPSVM YLGYAIHKIA KMEHGEADKK AARSKPYAMR 121 WKQHRALEET EEDNEEDPMM YPEMELESDK ENKEQSQPKP KHDGRRRIRE DGLMKIYVLQ 181 LLARTVFEVG FLIGQYFLYG FQVHPFYVCS RLPCPHKIDC FISRPTEKTI FLLIMYGVTG 241 LCLLLNIWEM LHLGFGTIRD SLNSKRRELE DPGAYNYPFT WNTPSAPPGY NIAVKPDQIQ 301 YTELSNAKIA YKQNKANTAQ EQQYGSHEEN LPADLEALQR EIRMAQERLD LAVQAYSHQN 361 NPHGPREKKA KVGSKAGSNK STASSKSGDG KNSVWI -------------------------------------------------------------------------------- COMPOSITIONAL ANALYSIS (extremes relative to: swp23s) A : 27( 6.8%); C : 7( 1.8%); D : 15( 3.8%); E : 33( 8.3%); F : 16( 4.0%) G : 23( 5.8%); H : 13( 3.3%); I : 23( 5.8%); K : 27( 6.8%); L : 34( 8.6%) M : 11( 2.8%); N : 18( 4.5%); P : 21( 5.3%); Q : 19( 4.8%); R : 20( 5.1%) S : 25( 6.3%); T : 17( 4.3%); V : 21( 5.3%); W : 7( 1.8%); Y : 19( 4.8%) KR : 47 ( 11.9%); ED : 48 ( 12.1%); AGP : 71 ( 17.9%); KRED : 95 ( 24.0%); KR-ED : -1 ( -0.3%); FIKMNY : 114 ( 28.8%); LVIFM : 105 ( 26.5%); ST : 42 ( 10.6%). -------------------------------------------------------------------------------- CHARGE DISTRIBUTIONAL ANALYSIS 1 0000000+00 --00000000 0+00000000 0+00000000 -0000--00+ 00000-0000 61 -0000-0000 0000+00000 0000000000 0000000+00 +0-00-0-++ 00+0+0000+ 121 0+00+00--0 ---0---000 00-0-0-0-+ -0+-0000+0 +0-0+++0+- -000+00000 181 000+000-00 0000000000 0000000000 +00000+0-0 000+00-+00 0000000000 241 00000000-0 00000000+- 0000+++-0- -000000000 0000000000 0000+0-000 301 00-0000+00 0+00+00000 -000000--0 000-0-000+ -0+000-+0- 0000000000 361 00000+-++0 +000+0000+ 00000+00-0 +00000 A. CHARGE CLUSTERS. Positive charge clusters (cmin = 10/30 or 14/45 or 17/60): none Negative charge clusters (cmin = 10/30 or 14/45 or 17/60): 1)*From 128 to 149: EETEEDNEEDPMMYPEMELESD --0---0---00000-0-0-0- quartile: 2; size: 22, +count: 0, -count: 12, 0count: 10; t-value: 6.10 * E: 9 (40.9%); D: 3 (13.6%); M: 3 (13.6%); Mixed charge clusters (cmin = 16/30 or 22/45 or 27/60): 1)*From 98 to 171: see sequence above see sequence above quartile: 1; size: 74, +count: 17, -count: 20, 0count: 37; t-value: 5.24 * K: 10 (13.5%); E: 14 (18.9%); B. HIGH SCORING (UN)CHARGED SEGMENTS. There are no high scoring positive charge segments. ______________________________________ High scoring negative charge segments: score= 2.00 frequency= 0.121 ( ED ) score= 0.00 frequency= 0.000 ( BZX ) score= -1.00 frequency= 0.760 ( LAGSVTIPNFQYHMCW ) score= -2.00 frequency= 0.119 ( KR ) Expected score/letter: -0.755 M_0.01= 11.19; M_0.05= 9.25 1) From 128 to 147: length= 20, score=13.00 ** (pocket at 138 to 142: length= 5, score=-5.00) 128 EETEEDNEED |PMMYP| EMELE E: 9(45.0%); D: 2(10.0%); P: 2(10.0%); M: 3(15.0%); 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 | 7 | 33 | 9 | 10 | 13 | 11 | 11 | 15 | 7 | 9 | lmin1 6 | 6 | 9 | 40 | 12 | 12 | 16 | 14 | 14 | 18 | 9 | 11 | lmin2 7 | 7 | 10 | 45 | 13 | 13 | 17 | 15 | 16 | 20 | 10 | 13 | (Significance level: 0.010000; Minimal displayed length: 6) (-) 8(2,0,0); at 128- 137: EETEEDNEED (2. quartile) --0---0--- Run count statistics: + runs >= 3: 2, at 165; 265; - runs >= 3: 2, at 131; 135; * runs >= 5: 0 0 runs >= 22: 3, at 76; 189; 272; -------------------------------------------------------------------------------- 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: -2.149 M_0.01= 23.07; M_0.05= 19.07 1) From 230 to 245: length= 16, score=22.00 * 230 IFLLIMYGVT GLCLLL L: 6(37.5%); G: 2(12.5%); I: 2(12.5%); ____________________________________ 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: -4.275 M_0.01= 51.17; M_0.05= 42.08; M_0.30= 31.26 1) From 23 to 40: length= 18, score=40.00 (pocket at 32 to 32: length= 1, score=-16.00) 23 IWLTVLIVF |R| IVLTAVGG L: 3(16.7%); G: 2(11.1%); V: 4(22.2%); T: 2(11.1%); I: 3(16.7%); 2) From 76 to 96: length= 21, score=35.00 (pocket at 86 to 88: length= 3, score=-10.00) (pocket at 80 to 80: length= 1, score=-10.00) 76 FWVF |Q| IILVA |TPS| VMYLGYA I V: 3(14.3%); I: 3(14.3%); 3) From 230 to 245: length= 16, score=52.00 ** 230 IFLLIMYGVT GLCLLL L: 6(37.5%); G: 2(12.5%); I: 2(12.5%); 2. SPACINGS OF C. H2N-52-C-6-C-3-C-144-C-4-C-5-C-21-C-154-COOH 2*. SPACINGS OF C and H. (additional deluxe function for ALEX) H2N-13-H-1-H-36-C-6-C-3-C-8-H-23-H-6-H-19-H-37-H-41-H-4-C-4-C-1-H-3-C-21-C-9-H-74-H-30-H-4-H-33-COOH -------------------------------------------------------------------------------- REPETITIVE STRUCTURES. A. SEPARATED, TANDEM, AND PERIODIC REPEATS: amino acid alphabet. Repeat core block length: 4 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 Aligned matching blocks: [ 22- 31] +iaioiiiii [ 75- 84] +iaiiniiii with superset: [ 22- 29] +iaioiii [ 75- 82] +iaiinii [ 175- 182] +iaiinii -------------------------------------------------------------------------------- MULTIPLETS. A. AMINO ACID ALPHABET. 1. Total number of amino acid multiplets: 22 (Expected range: 7-- 35) 2. Histogram of spacings between consecutive amino acid multiplets: (1-5) 7 (6-10) 3 (11-20) 5 (>=21) 8 3. Clusters of amino acid multiplets (cmin = 10/30 or 13/45 or 16/60): none B. CHARGE ALPHABET. 1. Total number of charge multiplets: 12 (Expected range: 0-- 20) 4 +plets (f+: 11.9%), 8 -plets (f-: 12.1%) Total number of charge altplets: 10 (Critical number: 23) 2. Histogram of spacings between consecutive charge multiplets: (1-5) 4 (6-10) 0 (11-20) 2 (>=21) 7 -------------------------------------------------------------------------------- PERIODICITY ANALYSIS. A. AMINO ACID ALPHABET (core: 4; !-core: 5) Location Period Element Copies Core Errors 13- 52 10 I......... 4 4 0 378- 389 3 S.. 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 23- 36 2 i. 7 7 0 101- 156 7 *...... 8 8 0 129- 138 2 -. 5 5 0 129- 176 8 *.*0..*. 6 6 /0/./2/2/././0/./ 143- 152 2 -0 5 5 /0/1/ 159- 172 2 *. 7 7 0 230- 235 1 i 6 6 0 232- 255 3 i.. 8 8 0 -------------------------------------------------------------------------------- SPACING ANALYSIS. There are no unusual spacings. ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ 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: tem35 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- connexin Connexin 510.0 1.7e-149 1 cytochr_b559 Cytochrome b559, alpha (gene psbE) and b 0.9 89 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- cytochr_b559 1/1 59 93 .. 1 33 [] 0.9 89 connexin 1/1 1 253 [. 1 246 [] 510.0 1.7e-149 Alignments of top-scoring domains: cytochr_b559: domain 1 of 1, from 59 to 93: score 0.9, E = 89 *->ttntserpvtypIftvRwla..iHalaiPtvFflG<-* + ++ + p vR+++ +i +a P+v lG gi|4885169 59 GCENVCYDAFAPLSHVRFWVfqIILVATPSVMYLG 93 connexin: domain 1 of 1, from 1 to 253: score 510.0, E = 1.7e-149 *->MGDWsfLgrLLegVnkHSTviGKvWLtVLFIFRILvLgvAAEsVWGD M +WsfL+rLLe++++HST++GK+WLtVL++FRI++++v++Es+++D gi|4885169 1 M-SWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYD 46 EQsdFvCNTqQPGCeNVCYDqaFPISHvRlWvLQiIFVSTPsLlYlgHVa EQs+FvCNT+QPGCeNVCYD+++P+SHvR+Wv+QiI+V+TPs++Ylg gi|4885169 47 EQSKFVCNTEQPGCENVCYDAFAPLSHVRFWVFQIILVATPSVMYLG--- 93 YrvrreeKrkekeeelrrl.ask.lsveeakkqgaeeae.ekeedpplva Y++++++K+ e+ e +++ +sk+ +++++++ +ee e+++eedp++++ gi|4885169 94 YAIHKIAKM-EHGEADKKAaRSKpYAMRWKQHRALEETEeDNEEDPMMYP 142 ek.........qklkikde.dGkvrir.GgLlwTYvlSilFKtifEvgFL e + +++++++++ k+++dG++rir++gL+ +Yvl++l +t+fEvgFL gi|4885169 143 EMelesdkenkEQSQPKPKhDGRRRIReDGLMKIYVLQLLARTVFEVGFL 192 ygQYlLYpGFtlsplyvCerayPCPhtVDCFvSRPTEKTIFiiFMLvVsa +gQY+LY GF++ p yvC+r PCPh++DCF+SRPTEKTIF+++M++V + gi|4885169 193 IGQYFLY-GFQVHPFYVCSRL-PCPHKIDCFISRPTEKTIFLLIMYGVTG 240 isLlLNlaElvhL<-* ++LlLN++E++hL gi|4885169 241 LCLLLNIWEMLHL 253 // 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: tem35 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- connexin Connexin 508.1 6.5e-149 1 NifU_N NifU-like N terminal domain 1.9 38 1 cytochr_b559 Cytochrome b559, alpha (gene psbE) and 0.9 89 1 MOZ_SAS MOZ/SAS family 0.6 37 1 AAA ATPases associated with various cellula -0.9 1e+02 1 Synaptophysin Synaptophysin / synaptoporin -1.2 66 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Synaptophysin 1/1 63 86 .. 1 26 [. -1.2 66 cytochr_b559 1/1 59 93 .. 1 33 [] 0.9 89 MOZ_SAS 1/1 168 180 .. 192 204 .] 0.6 37 connexin 1/1 1 253 [. 1 246 [] 508.1 6.5e-149 AAA 1/1 333 348 .. 201 216 .] -0.9 1e+02 NifU_N 1/1 344 363 .. 110 129 .] 1.9 38 Alignments of top-scoring domains: Synaptophysin: domain 1 of 1, from 63 to 86: score -1.2, E = 66 *->qfrvvkePLgfvkvlqwvFAiFAFAt<-* + ++PL +v wvF i At gi|4885169 63 VCYDAFAPL--SHVRFWVFQIILVAT 86 cytochr_b559: domain 1 of 1, from 59 to 93: score 0.9, E = 89 *->ttntserpvtypIftvRwla..iHalaiPtvFflG<-* + ++ + p vR+++ +i +a P+v lG gi|4885169 59 GCENVCYDAFAPLSHVRFWVfqIILVATPSVMYLG 93 MOZ_SAS: domain 1 of 1, from 168 to 180: score 0.6, E = 37 *->ikyykgqylqvLn<-* i+++++ +++vL+ gi|4885169 168 IREDGLMKIYVLQ 180 connexin: domain 1 of 1, from 1 to 253: score 508.1, E = 6.5e-149 *->MGDWsfLgrLLegVnkHSTviGKvWLtVLFIFRILvLgvAAEsVWGD M +WsfL+rLLe++++HST++GK+WLtVL++FRI++++v++Es+++D gi|4885169 1 M-SWSFLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYD 46 EQsdFvCNTqQPGCeNVCYDqaFPISHvRlWvLQiIFVSTPsLlYlgHVa EQs+FvCNT+QPGCeNVCYD+++P+SHvR+Wv+QiI+V+TPs++Ylg gi|4885169 47 EQSKFVCNTEQPGCENVCYDAFAPLSHVRFWVFQIILVATPSVMYLG--- 93 YrvrreeKrkekeeelrrl.ask.lsveeakkqgaeeae.ekeedpplva Y++++++K+ e+ e +++ +sk+ +++++++ +ee e+++eedp++++ gi|4885169 94 YAIHKIAKM-EHGEADKKAaRSKpYAMRWKQHRALEETEeDNEEDPMMYP 142 ek.........qklkikde.dGkvrir.GgLlwTYvlSilFKtifEvgFL e + +++++++++ k+++dG++rir++gL+ +Yvl++l +t+fEvgFL gi|4885169 143 EMelesdkenkEQSQPKPKhDGRRRIReDGLMKIYVLQLLARTVFEVGFL 192 ygQYlLYpGFtlsplyvCerayPCPhtVDCFvSRPTEKTIFiiFMLvVsa +gQY+LY GF++ p yvC+r PCPh++DCF+SRPTEKTIF+++M++V + gi|4885169 193 IGQYFLY-GFQVHPFYVCSRL-PCPHKIDCFISRPTEKTIFLLIMYGVTG 240 isLlLNlaElvhL<-* ++LlLN++E++hL gi|4885169 241 LCLLLNIWEMLHL 253 AAA: domain 1 of 1, from 333 to 348: score -0.9, E = 1e+02 *->adlaalcreAalralr<-* adl+al re +++ r gi|4885169 333 ADLEALQREIRMAQER 348 NifU_N: domain 1 of 1, from 344 to 363: score 1.9, E = 38 *->LgqdalkaAiadYkgknlka<-* ++q++l A+ +Y + n+ + gi|4885169 344 MAQERLDLAVQAYSHQNNPH 363 // 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: tem35 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [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: Thu Dec 21 12:14:34 2000 Sequence file: tem35 ---------------------------------------- Sequence gi|4885169|ref|NP_005488.1| (396 residues): Matching pattern PS00001 ASN_GLYCOSYLATION: 15: NHST 379: NKST Total matches: 2 Matching pattern PS00005 PKC_PHOSPHO_SITE: 148: SDK 226: TEK 257: TIR 264: SKR 378: SNK 384: SSK Total matches: 6 Matching pattern PS00006 CK2_PHOSPHO_SITE: 130: TEED 148: SDKE 185: TVFE 257: TIRD 318: TAQE 326: SHEE Total matches: 6 Matching pattern PS00007 TYR_PHOSPHO_SITE: 267: RELEDPGAY Total matches: 1 Matching pattern PS00008 MYRISTYL: 373: GSKAGS 377: GSNKST Total matches: 2 Matching pattern PS00009 AMIDATION: 163: DGRR Total matches: 1 Matching pattern PS00407 CONNEXINS_1: 53: CNTEQPGCENVCYD Total matches: 1 Matching pattern PS00408 CONNEXINS_2: 209: CSRLPCPHKIDCFISRP Total matches: 1 Total no of hits in this sequence: 20 ======================================== 1314 pattern(s) searched in 1 sequence(s), 396 residues. Total no of hits in all sequences: 20. Search time: 00:00 min ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with Profile Search ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ ~~~~~ Start with motif search against own library ***** bioMotif : Version V41a DB, 1999 Nov 11 ***** argv[1]=P argv[2]=-m /data/patterns/own/motif.fa argv[4]=-seq tem35 ***** 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, 396 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: tem35 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [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: tem35 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [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= gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] (396 letters) Searching..................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value CHROMO Chromodomain- A chromatin associated domain 26 0.12 KIN Protein kinase domain 22 1.6 ARR Arrestin domain 21 2.5 TBC Probable RAB-type GTPase GTP hydrolysis activating prote... 21 2.6 DHHC Novel zinc finger domain with DHHC signature 21 3.5 CALC Calcineurin like Phosphoesterase domain 21 3.6 UBA Ubiquitin pathway associated domain 20 4.0 ARM Armadillo repeat 20 6.5 S1 S1 RNA binding domain 19 7.9 KELCH Kelch repeat- beta propeller like domain 20 8.8 >CHROMO Chromodomain- A chromatin associated domain Length = 66 Score = 25.6 bits (56), Expect = 0.12 Identities = 14/71 (19%), Positives = 14/71 (19%), Gaps = 9/71 (12%) Query: 94 YAIHKIAKMEHGEADKKAARSKPYAMRWKQHRALEETEE--DNEEDPMMYPEMELESDKE 151 Sbjct: 2 FVVEKV------LDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFL-NSQKA 54 Query: 152 NKEQSQPKPKH 162 Sbjct: 55 GKEKDGTKRKS 65 >KIN Protein kinase domain Length = 313 Score = 22.0 bits (46), Expect = 1.6 Identities = 14/58 (24%), Positives = 14/58 (24%), Gaps = 5/58 (8%) Query: 94 YAIHKIAKMEHGEADKKAARSKPYAMRWKQHRALEE-----TEEDNEEDPMMYPEMEL 146 Sbjct: 57 VAIKKISKAFDNLKDTKRTLREIHLLRHFKHENLISIKDILKPNSKEQFEDVYIVSEL 114 >ARR Arrestin domain Length = 454 Score = 21.4 bits (45), Expect = 2.5 Identities = 5/27 (18%), Positives = 5/27 (18%), Gaps = 1/27 (3%) Query: 265 KRRELEDPGAYNYPFTWNTP-SAPPGY 290 Sbjct: 126 QERLKRKLGANAFPFWFEVAPKSASSV 152 >TBC Probable RAB-type GTPase GTP hydrolysis activating protein Length = 225 Score = 21.0 bits (44), Expect = 2.6 Identities = 10/122 (8%), Positives = 10/122 (8%), Gaps = 30/122 (24%) Query: 109 KKAARSKPYAMRWKQHRALEETEEDNEED-PMMYPEMELESDKENKEQSQPKPKHDGRRR 167 Sbjct: 21 SMEASTQRYLALLKLGPPSTTIYQKIKNDTSRTFQTDPNFRNRVSEDAL---------IR 71 Query: 168 IREDGLMKIY-------VLQLLARTVFEVGFLIGQYFLYGFQVHPFYVCSRLPCPHKIDC 220 Sbjct: 72 C-----LSCFAWQTQQRRQKTRFGRIPVSTYVQGMNVL----LAPLL----YSCPSEPMA 118 Query: 221 FI 222 Sbjct: 119 YQ 120 >DHHC Novel zinc finger domain with DHHC signature Length = 217 Score = 20.9 bits (43), Expect = 3.5 Identities = 13/55 (23%), Positives = 13/55 (23%) Query: 154 EQSQPKPKHDGRRRIREDGLMKIYVLQLLARTVFEVGFLIGQYFLYGFQVHPFYV 208 Sbjct: 26 QPSGPSPELQGQRSRRNGWSWPPHPLQIVAWLLYLFFAVIGFGILVPLLPHHWVP 80 >CALC Calcineurin like Phosphoesterase domain Length = 274 Score = 20.5 bits (42), Expect = 3.6 Identities = 3/40 (7%), Positives = 3/40 (7%) Query: 339 QREIRMAQERLDLAVQAYSHQNNPHGPREKKAKVGSKAGS 378 Sbjct: 183 HELAEVLAPFTNVKAILYGHIHQEVNSEWNGYQVMATPAT 222 >UBA Ubiquitin pathway associated domain Length = 255 Score = 20.4 bits (42), Expect = 4.0 Identities = 14/42 (33%), Positives = 14/42 (33%), Gaps = 2/42 (4%) Query: 316 ANTAQEQQYGSHEENL-PADLEALQREIRMAQERLDLAVQAY 356 Sbjct: 211 AGLGQGEGEGSFQVDYTPEDDQAISRLCELGFER-DLVIQVY 251 >ARM Armadillo repeat Length = 532 Score = 19.9 bits (41), Expect = 6.5 Identities = 5/19 (26%), Positives = 5/19 (26%) Query: 271 DPGAYNYPFTWNTPSAPPG 289 Sbjct: 509 DGSQAGFQFGGNQAPVPSG 527 >S1 S1 RNA binding domain Length = 305 Score = 19.5 bits (40), Expect = 7.9 Identities = 7/51 (13%), Positives = 7/51 (13%), Gaps = 1/51 (1%) Query: 288 PGYNIAVKPD-QIQYTELSNAKIAYKQNKANTAQEQQYGSHEENLPADLEA 337 Sbjct: 143 PRSHLMHKDNMDALVGQVLKAHILEANQDNNKLVLTQRRIQQAESMGKIAA 193 >KELCH Kelch repeat- beta propeller like domain Length = 319 Score = 19.5 bits (40), Expect = 8.8 Identities = 5/25 (20%), Positives = 5/25 (20%), Gaps = 2/25 (8%) Query: 3 WSFLTRLLEEIHNHSTFV--GKIWL 25 Sbjct: 154 WTMVAPLREGVSNAAVVSAKLKLFA 178 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: 396 Total length of test sequences: 20182 Effective length of test sequences: 16637.0 Effective search space size: 6025420.2 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= gi|4885169|ref|NP_005488.1| gap junction protein, alpha 7, 45kD (connexin 45) [Homo sapiens] (396 letters) Searching.................................................done Results from profile search Score E Sequences producing significant alignments: (bits) Value gi|1817676 [157..389] Protein kinases (PK), catalytic core 26 1.1 gi|2493387 [94..456] Cytochrome P450 25 2.1 gi|1127061 [6..559] Single-stranded right-handed beta-helix 24 5.0 gi|730275 [335..617] beta-Lactamase/D-ala carboxypeptidase 23 6.1 >gi|1817676 [157..389] Protein kinases (PK), catalytic core Length = 233 Score = 25.8 bits (55), Expect = 1.1 Identities = 4/55 (7%), Positives = 4/55 (7%) Query: 94 YAIHKIAKMEHGEADKKAARSKPYAMRWKQHRALEETEEDNEEDPMMYPEMELES 148 Sbjct: 21 PVVLKGLVHSGDAEAQAMAMAERQFLAEVVHPSIVQIFNFVEHTDRHGDPVGYIV 75 >gi|2493387 [94..456] Cytochrome P450 Length = 363 Score = 25.1 bits (54), Expect = 2.1 Identities = 9/151 (5%), Positives = 9/151 (5%), Gaps = 9/151 (5%) Query: 5 FLTRLLEEIHNHSTFVGKIWLTVLIVFRIVLTAVGGESIYYDEQSKFVCNTEQPGCENVC 64 Sbjct: 35 FCEQLRQKARTGTVFQLEPLTLRL-TVDTICSVTLYVVTPVGRWPFLTPDLEI---HSST 90 Query: 65 YDAFAPLSHVRFWVFQIILVATPSVMYLGYAIHKIAKMEHGEADKKAARSKPYAMRWKQH 124 Sbjct: 91 TKLRTTPLPQRCNGRSN----GPRLELPSTPLRRYLTVRPLVMWYNNRLMNRFIDQEVDR 146 Query: 125 RALEETEEDNEEDPMMYPEMELESDKENKEQ 155 Sbjct: 147 A-YREQSGRQSKSVISLALRDYMKEKDGSLE 176 >gi|1127061 [6..559] Single-stranded right-handed beta-helix Length = 554 Score = 24.0 bits (51), Expect = 5.0 Identities = 19/73 (26%), Positives = 19/73 (26%), Gaps = 1/73 (1%) Query: 314 NKANTAQEQQYGSHEENLPADLEALQREIRMAQERLDLAVQAYSHQNNPHGPREKKAKVG 373 Sbjct: 424 NVANLAEEGLGNIRANSFGYDSAAIKLRIHKLSKTLDSGA-LYSHINGGAGSGSAYTQLT 482 Query: 374 SKAGSNKSTASSK 386 Sbjct: 483 AISGSTPDAVSLK 495 >gi|730275 [335..617] beta-Lactamase/D-ala carboxypeptidase Length = 283 Score = 23.4 bits (50), Expect = 6.1 Identities = 5/31 (16%), Positives = 5/31 (16%) Query: 286 APPGYNIAVKPDQIQYTELSNAKIAYKQNKA 316 Sbjct: 230 QVPGVEVAGKTGTTNFDDNEVKRYNIASGGA 260 Underlying Matrix: BLOSUM62 Number of sequences tested against query: 1187 Number of sequences better than 10.0: 4 Number of calls to ALIGN: 4 Length of query: 396 Total length of test sequences: 256703 Effective length of test sequences: 208388.0 Effective search space size: 74181392.3 Initial X dropoff for ALIGN: 25.0 bits