BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 040015
(1399 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type Iii
Effector Xcv3220 (Xopl)
Length = 328
Score = 56.2 bits (134), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 60/213 (28%), Positives = 94/213 (44%), Gaps = 31/213 (14%)
Query: 1103 FKELPEKFYELSTLKVLRISNCPSLVAFP-EMGLPSTLVGLEIRSCEALQFLPEKMM--- 1158
ELP+ + + L+ L ++ P L A P + + L L IR+C L LPE +
Sbjct: 116 LXELPDTXQQFAGLETLTLARNP-LRALPASIASLNRLRELSIRACPELTELPEPLASTD 174
Query: 1159 ----HESQKNKDAFLLEYLVIEGCPALVSLPRDKLSGTLKVLEIENCGNLQSLPEQMICS 1214
H+ N + LE+ I PA I N NL+SL ++ S
Sbjct: 175 ASGEHQGLVNLQSLRLEWTGIRSLPA----------------SIANLQNLKSL--KIRNS 216
Query: 1215 SLENLKVAGCLHNLAFLDHLEIDDCPLLQSFPEPCLPTSMLRYARISNCQNLKFLPNGMY 1274
L L A +H+L L+ L++ C L+++P + L+ + +C NL LP ++
Sbjct: 217 PLSALGPA--IHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIH 274
Query: 1275 ILTSLQEFSIHGCSSLMSFPE--GGLPPNLISL 1305
LT L++ + GC +L P LP N I L
Sbjct: 275 RLTQLEKLDLRGCVNLSRLPSLIAQLPANCIIL 307
Score = 45.4 bits (106), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 54/198 (27%), Positives = 78/198 (39%), Gaps = 41/198 (20%)
Query: 1228 LAFLDHLEIDDCPLLQSFPEPCLPTSMLRYARISNC----QNLKFLPNGMYILTSLQEFS 1283
L+ L H ID L + LP + ++A + L+ LP + L L+E S
Sbjct: 103 LSHLQHXTIDAAGLXE------LPDTXQQFAGLETLTLARNPLRALPASIASLNRLRELS 156
Query: 1284 IHGCSSLMSFPE-------GGLPPNLISL---------------SILDCENLK------- 1314
I C L PE G L++L SI + +NLK
Sbjct: 157 IRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNS 216
Query: 1315 PSSEWG--LHRLTCLADFSFGGCQGLVSFPKGWFLPKNLSSLYLERLPNLKSLPNGLKNL 1372
P S G +H L L + GC L ++P + L L L+ NL +LP + L
Sbjct: 217 PLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRL 276
Query: 1373 KYLETLEIWECDNLQTVP 1390
LE L++ C NL +P
Sbjct: 277 TQLEKLDLRGCVNLSRLP 294
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 44/151 (29%), Positives = 65/151 (43%), Gaps = 16/151 (10%)
Query: 1066 LEELQISHLAELMTLSNKIG-------LRSLLSLQRLEISECPYFKELPEKFYELSTLKV 1118
L EL I EL L + + L++LQ L + E + LP L LK
Sbjct: 152 LRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRL-EWTGIRSLPASIANLQNLKS 210
Query: 1119 LRISNCPSLVAFPEMGLPSTLVGLEIRSCEALQFLPEKMMHESQKNKDAFLLEYLVIEGC 1178
L+I N P P + L L++R C AL+ P + L+ L+++ C
Sbjct: 211 LKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAP-------LKRLILKDC 263
Query: 1179 PALVSLPRDKLSGT-LKVLEIENCGNLQSLP 1208
L++LP D T L+ L++ C NL LP
Sbjct: 264 SNLLTLPLDIHRLTQLEKLDLRGCVNLSRLP 294
Score = 37.4 bits (85), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 51/202 (25%), Positives = 82/202 (40%), Gaps = 23/202 (11%)
Query: 828 NLKQLTINDYGGIKFPGWIASPLFCNMTVLVLSNCRNCQFLPSLGRLPMLKDLTIEGMEG 887
+L+ TI+ G + P F + L L+ S+ L L++L+I
Sbjct: 105 HLQHXTIDAAGLXELPDTXQQ--FAGLETLTLARNPLRALPASIASLNRLRELSIRACPE 162
Query: 888 IKSVGAEFYG-DGSFPLLPFPSLETLKFENMSEWEEWTP--SGTEGTEGFLHLQNIEILN 944
+ + D S +L++L+ E WT S +L++++I N
Sbjct: 163 LTELPEPLASTDASGEHQGLVNLQSLRLE-------WTGIRSLPASIANLQNLKSLKIRN 215
Query: 945 CP--KLREFSHHFPSLKKMTIYGCEKLEQ-----GSEFPCLLELSILMCPNLVELP---T 994
P L HH P L+++ + GC L G P L L + C NL+ LP
Sbjct: 216 SPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAP-LKRLILKDCSNLLTLPLDIH 274
Query: 995 FLPSLKTLEIDGCQKLAALPKL 1016
L L+ L++ GC L+ LP L
Sbjct: 275 RLTQLEKLDLRGCVNLSRLPSL 296
Score = 36.6 bits (83), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
Query: 586 LKCLRVLSFSACRITALPDSVGDLKHLRYLDLSR-TAIKQLPDSTGNLCNLQSIILLECY 644
L+ L+ L ++AL ++ L L LDL TA++ P G L+ +IL +C
Sbjct: 205 LQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCS 264
Query: 645 SLSKLPTDLGNLTGLRHLRMSG 666
+L LP D+ LT L L + G
Sbjct: 265 NLLTLPLDIHRLTQLEKLDLRG 286
Score = 36.6 bits (83), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 29/127 (22%), Positives = 52/127 (40%), Gaps = 32/127 (25%)
Query: 591 VLSFSACRITALPDSVGDLKHLRY-----------------------LDLSRTAIKQLPD 627
L + + PD L HL++ L L+R ++ LP
Sbjct: 85 ALELRSVPLPQFPDQAFRLSHLQHXTIDAAGLXELPDTXQQFAGLETLTLARNPLRALPA 144
Query: 628 STGNLCNLQSIILLECYSLSKLPTDLGN---------LTGLRHLRMSGSRLREMPMKMYK 678
S +L L+ + + C L++LP L + L L+ LR+ + +R +P +
Sbjct: 145 SIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIAN 204
Query: 679 LKNLQTL 685
L+NL++L
Sbjct: 205 LQNLKSL 211
Score = 34.7 bits (78), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 46/156 (29%), Positives = 64/156 (41%), Gaps = 11/156 (7%)
Query: 978 LLELSILMCPNLVELPTFLPSLKTLEIDGCQKLAALPKLPSILELELNNCDGKVLHSTGG 1037
L ELSI CP L ELP L S D + L L S L LE + S
Sbjct: 152 LRELSIRACPELTELPEPLAS-----TDASGEHQGLVNLQS-LRLEWTGIRS-LPASIAN 204
Query: 1038 HRSLTYMRICQISKLDCLVEGYFQHFTALEELQISHLAELMTLSNKIGLRSLLSLQRLEI 1097
++L ++I + S L L H LEEL + L G R+ L+RL +
Sbjct: 205 LQNLKSLKI-RNSPLSALGPA-IHHLPKLEELDLRGCTALRNYPPIFGGRA--PLKRLIL 260
Query: 1098 SECPYFKELPEKFYELSTLKVLRISNCPSLVAFPEM 1133
+C LP + L+ L+ L + C +L P +
Sbjct: 261 KDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSL 296
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 53.5 bits (127), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 88/338 (26%), Positives = 148/338 (43%), Gaps = 57/338 (16%)
Query: 205 IVGMGGIGKTTVA-QLVYNDSRVDGRFDLKV-WVCVSDQ-----FDVLRVTTTIL---KS 254
I GM G GK+ +A + V + S ++G F V WV V Q L+ T L +S
Sbjct: 152 IHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDES 211
Query: 255 VTSK-PADVDDDLNLLQVCLREKLAGKKFLLVLDDVWSRRNDDWDLICSPLKAGARGSKI 313
+ + P ++++ + L++ + K + LL+LDDVW D W LKA +I
Sbjct: 212 FSQRLPLNIEEAKDRLRILMLRK--HPRSLLILDDVW----DSW-----VLKAFDSQCQI 260
Query: 314 IITTRDSSIAAS-MGTVAAHHLEC-LAFE---DCSSIFMNQAFENRNTGISPDLETIGAE 368
++TTRD S+ S MG +E L E + S+F+N DL
Sbjct: 261 LLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMK--------KADLPEQAHS 312
Query: 369 IVNKCEGLLLAVKRMGIILRSREDKGEWY--DMLNRNIWDL----PHDESSILQTLGLSY 422
I+ +C+G L V +G +LR ++ E+Y + N+ + +D ++ + + +S
Sbjct: 313 IIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISV 372
Query: 423 HHLPPHLKQCFAYCSVFPAGYEFDKEKLVLLWMAEGFVQQSNAKKKLEEVGREYFHELVS 482
L +K + S+ + + L +LW E EEV + E V+
Sbjct: 373 EMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMET-----------EEV-EDILQEFVN 420
Query: 483 RS-FFRQSVHNSSLYVMHGLMKDLARFVSGEFCFRLED 519
+S F S Y +H L D F++ + C +L+D
Sbjct: 421 KSLLFCDRNGKSFRYYLHDLQVD---FLTEKNCSQLQD 455
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 50.1 bits (118), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 88/338 (26%), Positives = 148/338 (43%), Gaps = 57/338 (16%)
Query: 205 IVGMGGIGKTTVA-QLVYNDSRVDGRFDLKV-WVCVSDQ-----FDVLRVTTTIL---KS 254
I GM G GK+ +A + V + S ++G F V WV V Q L+ T L +S
Sbjct: 158 IHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDES 217
Query: 255 VTSK-PADVDDDLNLLQVCLREKLAGKKFLLVLDDVWSRRNDDWDLICSPLKAGARGSKI 313
+ + P ++++ + L++ + K + LL+LDDVW D W LKA +I
Sbjct: 218 FSQRLPLNIEEAKDRLRILMLRK--HPRSLLILDDVW----DSW-----VLKAFDSQCQI 266
Query: 314 IITTRDSSIAAS-MGTVAAHHLEC-LAFE---DCSSIFMNQAFENRNTGISPDLETIGAE 368
++TTRD S+ S MG +E L E + S+F+N DL
Sbjct: 267 LLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMK--------KADLPEQAHS 318
Query: 369 IVNKCEGLLLAVKRMGIILRSREDKGEWY--DMLNRNIWDL----PHDESSILQTLGLSY 422
I+ +C+G L V +G +LR ++ E+Y + N+ + +D ++ + + +S
Sbjct: 319 IIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISV 378
Query: 423 HHLPPHLKQCFAYCSVFPAGYEFDKEKLVLLWMAEGFVQQSNAKKKLEEVGREYFHELVS 482
L +K + S+ + + L +LW E EEV + E V+
Sbjct: 379 EMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME-----------TEEV-EDILQEFVN 426
Query: 483 RS-FFRQSVHNSSLYVMHGLMKDLARFVSGEFCFRLED 519
+S F S Y +H L D F++ + C +L+D
Sbjct: 427 KSLLFCDRNGKSFRYYLHDLQVD---FLTEKNCSQLQD 461
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 47.4 bits (111), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 81/324 (25%), Positives = 140/324 (43%), Gaps = 54/324 (16%)
Query: 205 IVGMGGIGKTTVA-QLVYNDSRVDGRFDLKV-WVCVSDQFD---VLRVTTTILK-----S 254
I GM G GK+ +A + V + S ++G F V WV + Q ++++ ++ S
Sbjct: 152 IYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEES 211
Query: 255 VTSK-PADVDDDLNLLQVCLREKLAGKKFLLVLDDVWSRRNDDWDLICSPLKAGARGSKI 313
+ + P ++++ + L+V + K + LL+LDDVW D W LKA +I
Sbjct: 212 FSQRLPLNIEEAKDRLRVLMLRK--HPRSLLILDDVW----DPW-----VLKAFDNQCQI 260
Query: 314 IITTRDSSIAAS-MGTVAAHHLEC-LAFE---DCSSIFMNQAFENRNTGISPDLETIGAE 368
++TTRD S+ S MG +E L E + S+F+N E DL
Sbjct: 261 LLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE--------DLPAEAHS 312
Query: 369 IVNKCEGLLLAVKRMGIILRSREDKGEWY--DMLNRNIWDL----PHDESSILQTLGLSY 422
I+ +C+G L V +G +LR ++ +Y + N+ + +D ++ + + +S
Sbjct: 313 IIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISV 372
Query: 423 HHLPPHLKQCFAYCSVFPAGYEFDKEKLVLLWMAEGFVQQSNAKKKLEEVGREYFHELVS 482
L +K + S+ + + L +LW E EEV + E V+
Sbjct: 373 EMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE-----------TEEV-EDILQEFVN 420
Query: 483 RS-FFRQSVHNSSLYVMHGLMKDL 505
+S F S Y +H L D
Sbjct: 421 KSLLFCNRNGKSFCYYLHDLQVDF 444
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 44.3 bits (103), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 80/324 (24%), Positives = 139/324 (42%), Gaps = 54/324 (16%)
Query: 205 IVGMGGIGKTTVA-QLVYNDSRVDGRFDLKV-WVCVSDQFD---VLRVTTTILK-----S 254
I GM G GK+ +A + V + S ++G F V WV + Q ++++ ++ S
Sbjct: 159 IYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEES 218
Query: 255 VTSK-PADVDDDLNLLQVCLREKLAGKKFLLVLDDVWSRRNDDWDLICSPLKAGARGSKI 313
+ + P ++++ + L+V + K + LL+LDDVW D W LKA +I
Sbjct: 219 FSQRLPLNIEEAKDRLRVLMLRK--HPRSLLILDDVW----DPW-----VLKAFDNQCQI 267
Query: 314 IITTRDSSIAAS-MGTVAAHHLEC-LAFE---DCSSIFMNQAFENRNTGISPDLETIGAE 368
++TT D S+ S MG +E L E + S+F+N E DL
Sbjct: 268 LLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKE--------DLPAEAHS 319
Query: 369 IVNKCEGLLLAVKRMGIILRSREDKGEWY--DMLNRNIWDL----PHDESSILQTLGLSY 422
I+ +C+G L V +G +LR ++ +Y + N+ + +D ++ + + +S
Sbjct: 320 IIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISV 379
Query: 423 HHLPPHLKQCFAYCSVFPAGYEFDKEKLVLLWMAEGFVQQSNAKKKLEEVGREYFHELVS 482
L +K + S+ + + L +LW E EEV + E V+
Sbjct: 380 EMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE-----------TEEV-EDILQEFVN 427
Query: 483 RS-FFRQSVHNSSLYVMHGLMKDL 505
+S F S Y +H L D
Sbjct: 428 KSLLFCNRNGKSFCYYLHDLQVDF 451
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 28/54 (51%)
Query: 583 LPRLKCLRVLSFSACRITALPDSVGDLKHLRYLDLSRTAIKQLPDSTGNLCNLQ 636
+ L LRVL S R+T+LP +G L+Y + LP GNLCNLQ
Sbjct: 266 IKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQ 319
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 48/97 (49%), Gaps = 1/97 (1%)
Query: 589 LRVLSFSACRITALPDSVGDLKHLRYLDLSRTAIKQLPDSTGNLCNLQSIILLECYSLSK 648
L L + +T LP + +L +LR LDLS + LP G+ L+ + ++
Sbjct: 249 LTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNM-VTT 307
Query: 649 LPTDLGNLTGLRHLRMSGSRLREMPMKMYKLKNLQTL 685
LP + GNL L+ L + G+ L + +K+ K++ L
Sbjct: 308 LPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGL 344
Score = 31.2 bits (69), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 5/81 (6%)
Query: 598 RITALPDSVGDLKHLRYLDLSRTAIKQLPDSTGNL--CNLQSIILLECYSLSKLPTDLGN 655
R+ DS D + LDLS I + + N+ + + + L SL++LP ++ N
Sbjct: 212 RMVMPKDSKYDDQLWHALDLSNLQIFNI---SANIFKYDFLTRLYLNGNSLTELPAEIKN 268
Query: 656 LTGLRHLRMSGSRLREMPMKM 676
L+ LR L +S +RL +P ++
Sbjct: 269 LSNLRVLDLSHNRLTSLPAEL 289
>pdb|2WFH|A Chain A, The Human Slit 2 Dimerization Domain D4
pdb|2WFH|B Chain B, The Human Slit 2 Dimerization Domain D4
Length = 193
Score = 39.3 bits (90), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 35/129 (27%), Positives = 55/129 (42%), Gaps = 18/129 (13%)
Query: 570 GVSYLADRVPRDILPRLKCLRVLSFSACRITALPDSVGDLKHLRYLDLSRTAIKQLPD-S 628
G+ L +PRD+ L + T +P + + KHL +DLS I L + S
Sbjct: 21 GLKVLPKGIPRDVTE-------LYLDGNQFTLVPKELSNYKHLTLIDLSNNRISTLSNQS 73
Query: 629 TGNLCNLQSIIL----LECYSLSKLPTDLGNLTGLRHLRMSGSRLREMPMKMYKLKNLQT 684
N+ L ++IL L C P L LR L + G+ + +P + +L
Sbjct: 74 FSNMTQLLTLILSYNRLRCIP----PRTFDGLKSLRLLSLHGNDISVVPEGAF--NDLSA 127
Query: 685 LSHFVVGKD 693
LSH +G +
Sbjct: 128 LSHLAIGAN 136
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 35.8 bits (81), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 30/101 (29%), Positives = 51/101 (50%), Gaps = 5/101 (4%)
Query: 589 LRVLSFSACRITALPDSVGD-LKHLRYLDLSRTAIKQLPDST-GNLCNLQSIILLECYSL 646
L+ L + ++ ALP V D L L LDL + LP + L +L+ + + C L
Sbjct: 66 LKELYLGSNQLGALPVGVFDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLKELFMC-CNKL 124
Query: 647 SKLPTDLGNLTGLRHLRMSGSRLREMPMKMYKLKNLQTLSH 687
++LP + LT L HL + ++L+ +P + L +L+H
Sbjct: 125 TELPRGIERLTHLTHLALDQNQLKSIPHGAF--DRLSSLTH 163
>pdb|3G06|A Chain A, The Salmonella Virulence Effector Ssph2 Functions As A Novel
E3 Ligase
Length = 622
Score = 34.7 bits (78), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 46/160 (28%), Positives = 73/160 (45%), Gaps = 16/160 (10%)
Query: 981 LSILMCP--NLVELPTFLPSLKTLEIDGCQKLAALPKLPSILELELNNCDGKVLHSTGGH 1038
++ L+ P NL LP P L+TLE+ G Q L +LP LP L LEL+ + H
Sbjct: 63 ITTLVIPDNNLTSLPALPPELRTLEVSGNQ-LTSLPVLPPGL-LELSIFSNPLTHLPALP 120
Query: 1039 RSLTYMRIC--QISKLDCLVEGYFQHFTALEELQI-----SHLAELMTLSNKIGLRSLL- 1090
L + I Q++ L L G + + +L S L +L +N++ +L
Sbjct: 121 SGLCKLWIFGNQLTSLPVLPPGLQELSVSDNQLASLPALPSELCKLWAYNNQLTSLPMLP 180
Query: 1091 -SLQRLEIS--ECPYFKELPEKFYELSTLKVLRISNCPSL 1127
LQ L +S + LP + Y+L R+++ P+L
Sbjct: 181 SGLQELSVSDNQLASLPTLPSELYKLWAYNN-RLTSLPAL 219
>pdb|2O6S|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
pdb|2O6S|B Chain B, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
Length = 208
Score = 34.3 bits (77), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 29/109 (26%), Positives = 52/109 (47%), Gaps = 3/109 (2%)
Query: 578 VPRDILPRLKCLRVLSFSACRITALPDSV-GDLKHLRYLDLSRTAIKQLPDSTGNLCNLQ 636
+P + L L L ++ +LP+ V L L YL+LS ++ LP+ +
Sbjct: 43 LPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQL 102
Query: 637 SIILLECYSLSKLPTDL-GNLTGLRHLRMSGSRLREMPMKMY-KLKNLQ 683
+ L L LP + LT L+ LR+ ++L+ +P ++ +L +LQ
Sbjct: 103 KELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQ 151
Score = 30.4 bits (67), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 4/89 (4%)
Query: 600 TALPDSVGDLKHLRYLDLSRTAIKQLPDSTGNLCNLQSIILLECYSLSKLPTDLGN-LTG 658
T++P G YLDL ++K LP+ + + + L L LP + N LT
Sbjct: 20 TSVP--TGIPAQTTYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTS 77
Query: 659 LRHLRMSGSRLREMPMKMY-KLKNLQTLS 686
L +L +S ++L+ +P ++ KL L+ L+
Sbjct: 78 LTYLNLSTNQLQSLPNGVFDKLTQLKELA 106
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 33.9 bits (76), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 58/131 (44%), Gaps = 27/131 (20%)
Query: 559 TFLPLDPTGEIGVSYLADRVPRD-ILPRLKCLRVLSFSACRI--TALPDSVGDLKHLRYL 615
FL L + +S+ RV + I L L VL + LPD +L++L +L
Sbjct: 416 VFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFL 475
Query: 616 DLSRTAIKQLPDSTGNLCNLQSIILLECYSLSKLPTDLGNLTGLRHLRMSGSRLREMPMK 675
DLS+ ++QL PT +L+ L+ L M+ ++L+ +P
Sbjct: 476 DLSQCQLEQLS-----------------------PTAFNSLSSLQVLNMASNQLKSVPDG 512
Query: 676 MY-KLKNLQTL 685
++ +L +LQ +
Sbjct: 513 IFDRLTSLQKI 523
>pdb|3RG1|A Chain A, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|E Chain E, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|I Chain I, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|M Chain M, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|B Chain B, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|F Chain F, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|J Chain J, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|N Chain N, Crystal Structure Of The Rp105MD-1 Complex
Length = 612
Score = 33.1 bits (74), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 49/107 (45%), Gaps = 5/107 (4%)
Query: 568 EIGVSYLADRVPRDILPRLKCLRVLSFSACRI-TALPDSVGDLKHLRYLDLSRTAIKQLP 626
++ ++L + P L LRVL+ S C + T+ + L+ LR+L+L + +
Sbjct: 405 DVAFTHLHVKAPHSPFQNLHLLRVLNLSHCLLDTSNQHLLAGLQDLRHLNLQGNSFQDGS 464
Query: 627 DSTGNLC----NLQSIILLECYSLSKLPTDLGNLTGLRHLRMSGSRL 669
S NL +L+ +IL C LS L + HL +S + L
Sbjct: 465 ISKTNLLQMVGSLEILILSSCNLLSIDQQAFHGLRNVNHLDLSHNSL 511
>pdb|1P8T|A Chain A, Crystal Structure Of Nogo-66 Receptor
Length = 285
Score = 32.7 bits (73), Expect = 1.6, Method: Composition-based stats.
Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 26/107 (24%)
Query: 589 LRVLSFSACRITAL-PDSVGDLKHLRYLDLSRTAIKQLPDSTGNLCNLQSIILLECYSLS 647
L L C + L P L L+YL L A++ LPD T
Sbjct: 106 LHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFR---------------- 149
Query: 648 KLPTDLGNLTGLRHLRMSGSRLREMPMKMYKLKNLQTLSHFVVGKDR 694
DLGNLT HL + G+R+ +P + + + L +L ++ ++R
Sbjct: 150 ----DLGNLT---HLFLHGNRISSVPERAF--RGLHSLDRLLLHQNR 187
>pdb|1OZN|A Chain A, 1.5a Crystal Structure Of The Nogo Receptor Ligand Binding
Domain Reveals A Convergent Recognition Scaffold
Mediating Inhibition Of Myelination
Length = 285
Score = 32.7 bits (73), Expect = 1.7, Method: Composition-based stats.
Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 26/107 (24%)
Query: 589 LRVLSFSACRITAL-PDSVGDLKHLRYLDLSRTAIKQLPDSTGNLCNLQSIILLECYSLS 647
L L C + L P L L+YL L A++ LPD T
Sbjct: 107 LHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFR---------------- 150
Query: 648 KLPTDLGNLTGLRHLRMSGSRLREMPMKMYKLKNLQTLSHFVVGKDR 694
DLGNLT HL + G+R+ +P + + + L +L ++ ++R
Sbjct: 151 ----DLGNLT---HLFLHGNRISSVPERAF--RGLHSLDRLLLHQNR 188
>pdb|2ZXQ|A Chain A, Crystal Structure Of Endo-Alpha-N-Acetylgalactosaminidase
From Bifidobacterium Longum (Engbf)
Length = 1376
Score = 32.3 bits (72), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 42/100 (42%), Gaps = 6/100 (6%)
Query: 236 VCVSDQFDVLRVTTTILKSVTSKPAD----VDDDLNLLQVCLREKLAGKKFLLVLDDVWS 291
V V + + T + S T KP D V +D N+ L +WS
Sbjct: 153 VSVRSSQENAQFTGARMSSNTQKPGDTNFAVTEDTNVTDSDYTYGFISGAGLSA--GLWS 210
Query: 292 RRNDDWDLICSPLKAGARGSKIIITTRDSSIAASMGTVAA 331
D + +P++ G++ +++ TT+ + A S+G +A
Sbjct: 211 NSEHDGTYVAAPVRGGSQNTRVYATTQQTGDATSLGLASA 250
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 32.3 bits (72), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 45/168 (26%), Positives = 72/168 (42%), Gaps = 23/168 (13%)
Query: 578 VPRDILPRLKCLRVLSFSACRITALPDSVGDLKHLRYLDLSRTAIKQLPDSTGNLCNLQS 637
VP+ I + L ++ + I A D+ L HL L L R +I+Q+ G L S
Sbjct: 69 VPQGIPSNTRYLNLMENNIQMIQA--DTFRHLHHLEVLQLGRNSIRQI--EVGAFNGLAS 124
Query: 638 IILLECYS--LSKLPTD-LGNLTGLRHLRMSGSRLREMPMKMYKLKNLQTLSHFVVGKDR 694
+ LE + L+ +P+ L+ LR L + + + +P Y + +L
Sbjct: 125 LNTLELFDNWLTVIPSGAFEYLSKLRELWLRNNPIESIP--SYAFNRVPSLMRL------ 176
Query: 695 GSGIKDLKEMQQLQ--GELVISGLQNVICFTDAMEANLKDKKELTQLV 740
DL E+++L+ E GL N+ M N+KD LT LV
Sbjct: 177 -----DLGELKKLEYISEGAFEGLFNLKYLNLGM-CNIKDMPNLTPLV 218
>pdb|2O6R|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B61
Length = 177
Score = 32.3 bits (72), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 49/97 (50%), Gaps = 3/97 (3%)
Query: 592 LSFSACRITALPDSVGD-LKHLRYLDLSRTAIKQLPDSTGNLCNLQSIILLECYSLSKLP 650
L + ++ +LP V D L L L LS+ I+ LPD + +I+ L L LP
Sbjct: 33 LELESNKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHENKLQSLP 92
Query: 651 TDL-GNLTGLRHLRMSGSRLREMPMKMY-KLKNLQTL 685
+ LT L+ L + ++L+ +P ++ +L +LQ +
Sbjct: 93 NGVFDKLTQLKELALDTNQLKSVPDGIFDRLTSLQKI 129
>pdb|4G8A|A Chain A, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
pdb|4G8A|B Chain B, Crystal Structure Of Human Tlr4 Polymorphic Variant D299g
And T399i In Complex With Md-2 And Lps
Length = 635
Score = 32.0 bits (71), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 48/193 (24%), Positives = 78/193 (40%), Gaps = 40/193 (20%)
Query: 559 TFLPLDPTGEIGVSYLADRVPRD-ILPRLKCLRVLSFSACRI--TALPDSVGDLKHLRYL 615
FL L + +S+ RV + I L L VL + LPD +L++L +L
Sbjct: 440 VFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFL 499
Query: 616 DLSRTAIKQLPDSTGNLCNLQSIILLECYSLSKLPTDLGNLTGLRHLRMSGSRLREMPMK 675
DLS+ ++QL PT +L+ L+ L MS + +
Sbjct: 500 DLSQCQLEQLS-----------------------PTAFNSLSSLQVLNMSHNNFFSLDTF 536
Query: 676 MYK-LKNLQ----TLSHFVVGKDRGSGIKDLKEMQQLQGELVISGL-QNVICFTDAMEAN 729
YK L +LQ +L+H + K +E+Q L L QN T ++
Sbjct: 537 PYKCLNSLQVLDYSLNHIMTSKK--------QELQHFPSSLAFLNLTQNDFACTCEHQSF 588
Query: 730 LKDKKELTQLVLQ 742
L+ K+ QL+++
Sbjct: 589 LQWIKDQRQLLVE 601
>pdb|3FXI|A Chain A, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
pdb|3FXI|B Chain B, Crystal Structure Of The Human Tlr4-Human Md-2-E.Coli Lps
Ra Complex
Length = 605
Score = 31.6 bits (70), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 48/193 (24%), Positives = 78/193 (40%), Gaps = 40/193 (20%)
Query: 559 TFLPLDPTGEIGVSYLADRVPRD-ILPRLKCLRVLSFSACRI--TALPDSVGDLKHLRYL 615
FL L + +S+ RV + I L L VL + LPD +L++L +L
Sbjct: 416 VFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFL 475
Query: 616 DLSRTAIKQLPDSTGNLCNLQSIILLECYSLSKLPTDLGNLTGLRHLRMSGSRLREMPMK 675
DLS+ ++QL PT +L+ L+ L MS + +
Sbjct: 476 DLSQCQLEQLS-----------------------PTAFNSLSSLQVLNMSHNNFFSLDTF 512
Query: 676 MYK-LKNLQ----TLSHFVVGKDRGSGIKDLKEMQQLQGELVISGL-QNVICFTDAMEAN 729
YK L +LQ +L+H + K +E+Q L L QN T ++
Sbjct: 513 PYKCLNSLQVLDYSLNHIMTSKK--------QELQHFPSSLAFLNLTQNDFACTCEHQSF 564
Query: 730 LKDKKELTQLVLQ 742
L+ K+ QL+++
Sbjct: 565 LQWIKDQRQLLVE 577
>pdb|1YLN|A Chain A, The Crystal Structure Of The Protein Of Unknown Function
Vca0042 From Vibrio Cholerae O1
Length = 252
Score = 31.6 bits (70), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 589 LRVLSFSACRITALP----DSVGDLKHLR-YLDLSRTAIKQLPDSTGNLCNLQSIILLEC 643
LR LS S CR P VGDL L + DL T K P TG +CNLQ +
Sbjct: 160 LRDLSRSGCRFITPPLGKTYQVGDLVALEIFSDLRGT--KTFPPLTGKICNLQRSLHHAR 217
Query: 644 YSLSKLPTDLGNLTG-LRHLRMSGSRL 669
Y L N L L+ +G++L
Sbjct: 218 YGLEFNEEGRNNAKNLLAQLKFNGTKL 244
>pdb|2RDE|A Chain A, Crystal Structure Of Vca0042 Complexed With C-Di-Gmp
pdb|2RDE|B Chain B, Crystal Structure Of Vca0042 Complexed With C-Di-Gmp
Length = 251
Score = 31.2 bits (69), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 589 LRVLSFSACRITALP----DSVGDLKHLR-YLDLSRTAIKQLPDSTGNLCNLQSIILLEC 643
LR LS S CR P VGDL L + DL T K P TG +CNLQ +
Sbjct: 159 LRDLSRSGCRFITPPLGKTYQVGDLVALEIFSDLRGT--KTFPPLTGKICNLQRSLHHAR 216
Query: 644 YSL 646
Y L
Sbjct: 217 YGL 219
>pdb|3KYG|A Chain A, Crystal Structure Of Vca0042 (L135r) Complexed With
C-Di-Gmp
pdb|3KYG|B Chain B, Crystal Structure Of Vca0042 (L135r) Complexed With
C-Di-Gmp
Length = 227
Score = 31.2 bits (69), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 589 LRVLSFSACRITALP----DSVGDLKHLR-YLDLSRTAIKQLPDSTGNLCNLQSIILLEC 643
LR LS S CR P VGDL L + DL T K P TG +CNLQ +
Sbjct: 140 LRDLSRSGCRFITPPLGKTYQVGDLVALEIFSDLRGT--KTFPPLTGKICNLQRSLHHAR 197
Query: 644 YSL 646
Y L
Sbjct: 198 YGL 200
>pdb|2Z66|A Chain A, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|B Chain B, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|C Chain C, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
pdb|2Z66|D Chain D, Crystal Structure Of The Vt3 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 306
Score = 31.2 bits (69), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 48/192 (25%), Positives = 78/192 (40%), Gaps = 40/192 (20%)
Query: 560 FLPLDPTGEIGVSYLADRVPRD-ILPRLKCLRVLSFSACRITA--LPDSVGDLKHLRYLD 616
FL L + +S+ RV + I L L VL + LPD +L++L +LD
Sbjct: 122 FLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLD 181
Query: 617 LSRTAIKQLPDSTGNLCNLQSIILLECYSLSKLPTDLGNLTGLRHLRMSGSRLREMPMKM 676
LS+ ++QL PT +L+ L+ L MS + +
Sbjct: 182 LSQCQLEQLS-----------------------PTAFNSLSSLQVLNMSHNNFFSLDTFP 218
Query: 677 YK-LKNLQ----TLSHFVVGKDRGSGIKDLKEMQQLQGELVISGL-QNVICFTDAMEANL 730
YK L +LQ +L+H + K +E+Q L L QN T ++ L
Sbjct: 219 YKCLNSLQVLDYSLNHIMTSKK--------QELQHFPSSLAFLNLTQNDFACTCEHQSFL 270
Query: 731 KDKKELTQLVLQ 742
+ K+ QL+++
Sbjct: 271 QWIKDQRQLLVE 282
>pdb|3CVR|A Chain A, Crystal Structure Of The Full Length Ipah3
Length = 571
Score = 30.8 bits (68), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 974 EFPCLLELSILMCPN-LVELPTFLPSLKTLEIDGCQKLAALPKLPSILE 1021
E P LE + C N L LP SLK L++D Q L LP+LP++LE
Sbjct: 97 ELPASLEY-LDACDNRLSTLPELPASLKHLDVDNNQ-LTXLPELPALLE 143
>pdb|3UL8|A Chain A, Crystal Structure Of The Tv3 Mutant V134l
Length = 279
Score = 30.4 bits (67), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 30/111 (27%), Positives = 45/111 (40%), Gaps = 27/111 (24%)
Query: 589 LRVLSFSACRITALPD-SVGDLKHLRYLDLSRTAIKQLP-DSTGNLCNLQSIILLECYSL 646
L+VL S C I + D + L HL L L+ I+ L + L +LQ ++ LE
Sbjct: 56 LQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVALETNLA 115
Query: 647 S-------------------------KLPTDLGNLTGLRHLRMSGSRLREM 672
S KLP NLT L HL +S ++++ +
Sbjct: 116 SLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSI 166
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.138 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 41,033,035
Number of Sequences: 62578
Number of extensions: 1734936
Number of successful extensions: 3688
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 35
Number of HSP's that attempted gapping in prelim test: 3621
Number of HSP's gapped (non-prelim): 84
length of query: 1399
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1288
effective length of database: 8,027,179
effective search space: 10339006552
effective search space used: 10339006552
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 bits)