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= 043039
(949 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 52/186 (27%), Positives = 84/186 (45%), Gaps = 30/186 (16%)
Query: 281 KVLLVLDDVWTEDGNKWESFQRCLINAHRGSKILVTTRKETVA-RMIGSTCVISIEE-LS 338
+ LL+LDDVW + W L +IL+TTR ++V ++G V+ +E L
Sbjct: 237 RSLLILDDVW----DSW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 287
Query: 339 EPECWSLFKRFAFLNRSRSDCKQLEEIGRKITWKCKGLPLAVKTIGSLLRFKKAREEW-- 396
+ + + F+N ++D L E I +CKG PL V IG+LLR R E+
Sbjct: 288 KEKGLEILS--LFVNMKKAD---LPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYL 342
Query: 397 --------QSILDSEIWQVEEFEKNLLPALLLSYNDLPNEIKRCFSYCAVLPKECYVDRD 448
+ I S + E ++ A+ +S L +IK ++ ++L K+ V
Sbjct: 343 KQLQNKQFKRIRKSSSYDYEALDE----AMSISVEMLREDIKDYYTDLSILQKDVKVPTK 398
Query: 449 ELIKLW 454
L LW
Sbjct: 399 VLCILW 404
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 43.9 bits (102), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 32/101 (31%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 580 PSFFDQLTCLRALRIGKYGDDAIERIPNGI-EKLIHLRYLKLFFVGIEELPET-FCELFN 637
P FD L L+ L +G + + +P G+ + L L L L + LP F L +
Sbjct: 57 PGVFDSLINLKELYLGS---NQLGALPVGVFDSLTQLTVLDLGTNQLTVLPSAVFDRLVH 113
Query: 638 LQNLDLRRCSKFKRLPQNIGKLVNLRHLIFDEDDLDYMPKG 678
L+ L C+K LP+ I +L +L HL D++ L +P G
Sbjct: 114 LKEL-FMCCNKLTELPRGIERLTHLTHLALDQNQLKSIPHG 153
>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 = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 52/186 (27%), Positives = 84/186 (45%), Gaps = 30/186 (16%)
Query: 281 KVLLVLDDVWTEDGNKWESFQRCLINAHRGSKILVTTRKETVA-RMIGSTCVISIEE-LS 338
+ LL+LDDVW + W L +IL+TTR ++V ++G V+ +E L
Sbjct: 243 RSLLILDDVW----DSW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 293
Query: 339 EPECWSLFKRFAFLNRSRSDCKQLEEIGRKITWKCKGLPLAVKTIGSLLRFKKAREEW-- 396
+ + + F+N ++D L E I +CKG PL V IG+LLR R E+
Sbjct: 294 KEKGLEILS--LFVNMKKAD---LPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYL 348
Query: 397 --------QSILDSEIWQVEEFEKNLLPALLLSYNDLPNEIKRCFSYCAVLPKECYVDRD 448
+ I S + E ++ A+ +S L +IK ++ ++L K+ V
Sbjct: 349 KQLQNKQFKRIRKSSSYDYEALDE----AMSISVEMLREDIKDYYTDLSILQKDVKVPTK 404
Query: 449 ELIKLW 454
L LW
Sbjct: 405 VLCILW 410
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 50/186 (26%), Positives = 82/186 (44%), Gaps = 30/186 (16%)
Query: 281 KVLLVLDDVWTEDGNKWESFQRCLINAHRGSKILVTTRKETVA-RMIGSTCVISIEE-LS 338
+ LL+LDDVW + W L +IL+TTR ++V ++G V+ +E L
Sbjct: 237 RSLLILDDVW----DPW-----VLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLG 287
Query: 339 EPECWSLFKRFAFLNRSRSDCKQLEEIGRKITWKCKGLPLAVKTIGSLLRFKKAR----- 393
+ + F+N + D L I +CKG PL V IG+LLR R
Sbjct: 288 REKGLEILS--LFVNMKKED---LPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYL 342
Query: 394 -----EEWQSILDSEIWQVEEFEKNLLPALLLSYNDLPNEIKRCFSYCAVLPKECYVDRD 448
++++ I S + E ++ A+ +S L +IK ++ ++L K+ V
Sbjct: 343 RQLQNKQFKRIRKSSSYDYEALDE----AMSISVEMLREDIKDYYTDLSILQKDVKVPTK 398
Query: 449 ELIKLW 454
L LW
Sbjct: 399 VLCVLW 404
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 36/154 (23%), Positives = 63/154 (40%), Gaps = 12/154 (7%)
Query: 579 MPSFFDQLTCLRALRIGKYGDDAIERIPNGIEKLIHLRYLKLFFVGIEELPETFCELFNL 638
+P F DQ L L+ + +P+ ++ L L L + LP + L L
Sbjct: 93 LPQFPDQAFRLSHLQHXTIDAAGLXELPDTXQQFAGLETLTLARNPLRALPASIASLNRL 152
Query: 639 QNLDLRRCSKFKRLPQNIGK---------LVNLRHLIFDEDDLDYMPKGMGSLTGLRTLS 689
+ L +R C + LP+ + LVNL+ L + + +P + +L L++L
Sbjct: 153 RELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNLKSLK 212
Query: 690 EFVAVSGGGKYGSKACNLDGLRHMNHLRGSLKIR 723
+ S G +L L ++ LRG +R
Sbjct: 213 --IRNSPLSALGPAIHHLPKLEELD-LRGCTALR 243
Score = 39.3 bits (90), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 41/145 (28%), Positives = 61/145 (42%), Gaps = 14/145 (9%)
Query: 555 SFPVSIFNAKKLRSLLIQG-YSLQHMPSFFDQ---------LTCLRALRIGKYGDDAIER 604
+ P SI + +LR L I+ L +P L L++LR+ G I
Sbjct: 141 ALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTG---IRS 197
Query: 605 IPNGIEKLIHLRYLKLFFVGIEELPETFCELFNLQNLDLRRCSKFKRLPQNIGKLVNLRH 664
+P I L +L+ LK+ + L L L+ LDLR C+ + P G L+
Sbjct: 198 LPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKR 257
Query: 665 LIF-DEDDLDYMPKGMGSLTGLRTL 688
LI D +L +P + LT L L
Sbjct: 258 LILKDCSNLLTLPLDIHRLTQLEKL 282
Score = 38.5 bits (88), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 52/203 (25%), Positives = 82/203 (40%), Gaps = 43/203 (21%)
Query: 778 LESLQISFYEVKARFPNWILSLNKLRMLCLSFCKKCEIMP-PLGK------------LQS 824
LE+L ++ ++A P I SLN+LR L + C + +P PL LQS
Sbjct: 129 LETLTLARNPLRA-LPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQS 187
Query: 825 LEVLDIWEMHGIKRVGDEV------------------LGIEIIAFPRLKKFTLWSLDGWE 866
L + E GI+ + + LG I P+L++ L
Sbjct: 188 LRL----EWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALR 243
Query: 867 EWEFIEENITIMPQLNSLAIRDCSKLKMLPDQVLRSTTLKKLEINDCPILEKSFKEAAGD 926
+ I L L ++DCS L LP + R T L+KL++ C L + A
Sbjct: 244 NYPPI---FGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIA-- 298
Query: 927 ERSKISCIPIVIIDSRYVQIDRH 949
+ +CI I++ Q+D+H
Sbjct: 299 -QLPANCI-ILVPPHLQAQLDQH 319
Score = 32.7 bits (73), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 33/106 (31%), Positives = 43/106 (40%), Gaps = 3/106 (2%)
Query: 555 SFPVSIFNAKKLRSLLIQGYSLQHMPSFFDQLTCLRALRIGKYGDDAIERIPNGIEKLIH 614
S P SI N + L+SL I+ L + L L L + G A+ P
Sbjct: 197 SLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDL--RGCTALRNYPPIFGGRAP 254
Query: 615 LRYLKLF-FVGIEELPETFCELFNLQNLDLRRCSKFKRLPQNIGKL 659
L+ L L + LP L L+ LDLR C RLP I +L
Sbjct: 255 LKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQL 300
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 38.1 bits (87), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 82/188 (43%), Gaps = 34/188 (18%)
Query: 281 KVLLVLDDVWTEDGNKW--ESF-QRCLINAHRGSKILVTTRKETVARMIGSTCVISIEE- 336
+ LL+LDDVW + W ++F +C I +L T+ K ++G V+ +E
Sbjct: 244 RSLLILDDVW----DPWVLKAFDNQCQI-------LLTTSDKSVTDSVMGPKHVVPVESG 292
Query: 337 LSEPECWSLFKRFAFLNRSRSDCKQLEEIGRKITWKCKGLPLAVKTIGSLLRFKKAR--- 393
L + + F+N + D L I +CKG PL V IG+LLR R
Sbjct: 293 LGREKGLEILS--LFVNMKKED---LPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAY 347
Query: 394 -------EEWQSILDSEIWQVEEFEKNLLPALLLSYNDLPNEIKRCFSYCAVLPKECYVD 446
++++ I S + E ++ A+ +S L +IK ++ ++L K+ V
Sbjct: 348 YLRQLQNKQFKRIRKSSSYDYEALDE----AMSISVEMLREDIKDYYTDLSILQKDVKVP 403
Query: 447 RDELIKLW 454
L LW
Sbjct: 404 TKVLCVLW 411
>pdb|1OGQ|A Chain A, The Crystal Structure Of Pgip (Polygalacturonase
Inhibiting Protein), A Leucine Rich Repeat Protein
Involved In Plant Defense
Length = 313
Score = 37.4 bits (85), Expect = 0.042, Method: Composition-based stats.
Identities = 32/111 (28%), Positives = 49/111 (44%), Gaps = 3/111 (2%)
Query: 579 MPSFFDQLTCLRALRIGKYGDDAIERIPNGIEKLIHLRYLKLFFVGIE-ELPETFCELFN 637
+PS L L L IG ++ + IP I KL L YL + + +P+ ++
Sbjct: 68 IPSSLANLPYLNFLYIGGI-NNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKT 126
Query: 638 LQNLDLRRCSKFKRLPQNIGKLVNLRHLIFDEDDLD-YMPKGMGSLTGLRT 687
L LD + LP +I L NL + FD + + +P GS + L T
Sbjct: 127 LVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFT 177
>pdb|3QFL|A Chain A, Coiled-Coil Domain-Dependent Homodimerization Of
Intracellular Mla Immune Receptors Defines A Minimal
Functional Module For Triggering Cell Death
Length = 115
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 47/80 (58%), Gaps = 9/80 (11%)
Query: 23 EQVRLVTGVEKEVKRLQDNLEAIQAVL---ADAERRQVKEEHVRLWLDKLKQASYDIDDV 79
E+ +L GV+K ++ L LE+ A L + R Q+ + +LW D++++ SY I+DV
Sbjct: 16 EEFKLHKGVKKNIEDLGKELESXNAALIKIGEVPREQLDSQD-KLWADEVRELSYVIEDV 74
Query: 80 LDEWNTARGKLQNEGVDADN 99
+D++ +Q +G+ +D+
Sbjct: 75 VDKF-----LVQVDGIKSDD 89
>pdb|3ZYO|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
And Immunoglobulin Domain Of Netrin-G Ligand-3
Length = 411
Score = 34.3 bits (77), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 48/93 (51%), Gaps = 6/93 (6%)
Query: 554 ASFPVSIFNA-KKLRSLLIQGYSLQHMPSF-FDQLTCLRALRIGKYGDDAIERIPNG-IE 610
+ P F KLR L ++ ++ +PS+ F+++ LR L +G+ +E I E
Sbjct: 96 TTVPTQAFEYLSKLRELWLRNNPIESIPSYAFNRVPSLRRLDLGEL--KRLEYISEAAFE 153
Query: 611 KLIHLRYLKLFFVGIEELPETFCELFNLQNLDL 643
L++LRYL L ++++P L L+ L+L
Sbjct: 154 GLVNLRYLNLGMCNLKDIPN-LTALVRLEELEL 185
>pdb|3ZYN|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
pdb|3ZYN|B Chain B, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
Length = 321
Score = 33.9 bits (76), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 36/139 (25%), Positives = 58/139 (41%), Gaps = 31/139 (22%)
Query: 554 ASFPVSIFNA-KKLRSLLIQGYSLQHMPSF-FDQLTCLRALRIGKYGDDAIERIPNG-IE 610
+ P F KLR L ++ ++ +PS+ F+++ LR L +G+ +E I E
Sbjct: 96 TTVPTQAFEYLSKLRELWLRNNPIESIPSYAFNRVPSLRRLDLGEL--KRLEYISEAAFE 153
Query: 611 KLIHLRYLKLFFVGIEELPETFCELFNLQNLDLRRCSKFKRLPQNIGKLVNLRHLIFDED 670
L++LRYL L ++++P N+ LV L L +
Sbjct: 154 GLVNLRYLNLGMCNLKDIP-------------------------NLTALVRLEELELSGN 188
Query: 671 DLDYM-PKGMGSLTGLRTL 688
LD + P LT LR L
Sbjct: 189 RLDLIRPGSFQGLTSLRKL 207
>pdb|3NF5|A Chain A, Crystal Structure Of The C-Terminal Domain Of Nuclear Pore
Complex Component Nup116 From Candida Glabrata
pdb|3NF5|B Chain B, Crystal Structure Of The C-Terminal Domain Of Nuclear Pore
Complex Component Nup116 From Candida Glabrata
Length = 164
Score = 33.9 bits (76), Expect = 0.48, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 31/52 (59%)
Query: 861 SLDGWEEWEFIEENITIMPQLNSLAIRDCSKLKMLPDQVLRSTTLKKLEIND 912
SLDG ++ EF++EN I P L++LA +++ + + V+ + K+E D
Sbjct: 2 SLDGIDDLEFVDENYYISPSLDTLATLSKYEIQKVENLVVGNKQYGKIEFLD 53
>pdb|3ZYJ|A Chain A, Netring1 In Complex With Ngl1
pdb|3ZYJ|C Chain C, Netring1 In Complex With Ngl1
Length = 440
Score = 33.5 bits (75), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 5/82 (6%)
Query: 564 KKLRSLLIQGYSLQHMPSF-FDQLTCLRALRIGKYGDDAIERIPNG-IEKLIHLRYLKLF 621
KL+ L ++ ++ +PS+ F+++ LR L +G+ + I G E L +LRYL L
Sbjct: 136 SKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGEL--KRLSYISEGAFEGLSNLRYLNLA 193
Query: 622 FVGIEELPETFCELFNLQNLDL 643
+ E+P L L LDL
Sbjct: 194 MCNLREIPN-LTPLIKLDELDL 214
>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 = 33.5 bits (75), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 3/84 (3%)
Query: 558 VSIFNAKKLRSLLIQGYSLQHMPSFFDQLTCLRALRIGKYGDDAIERIPNGIEKLIHLRY 617
+IF L L + G SL +P+ L+ LR L + + + +P + L+Y
Sbjct: 241 ANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSH---NRLTSLPAELGSCFQLKY 297
Query: 618 LKLFFVGIEELPETFCELFNLQNL 641
F + LP F L NLQ L
Sbjct: 298 FYFFDNMVTTLPWEFGNLCNLQFL 321
>pdb|3RIZ|A Chain A, Crystal Structure Of The Plant Steroid Receptor Bri1
Ectodomain
pdb|3RJ0|A Chain A, Plant Steroid Receptor Bri1 Ectodomain In Complex With
Brassinolide
Length = 772
Score = 32.7 bits (73), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 357 SDCKQLEEIGRKITWKCKGLPLAVKTIGSLLRFKKAREEWQSILDSEIWQVEEFEKNLLP 416
S+C +L + + +P ++GSL + + + W ++L+ EI Q + K L
Sbjct: 412 SNCSELVSLHLSFNYLSGTIP---SSLGSLSKLRDLKL-WLNMLEGEIPQELMYVKTL-E 466
Query: 417 ALLLSYNDLPNEIKRCFSYCAVL 439
L+L +NDL EI S C L
Sbjct: 467 TLILDFNDLTGEIPSGLSNCTNL 489
>pdb|3RGX|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
pdb|3RGZ|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
Length = 768
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 5/83 (6%)
Query: 357 SDCKQLEEIGRKITWKCKGLPLAVKTIGSLLRFKKAREEWQSILDSEIWQVEEFEKNLLP 416
S+C +L + + +P ++GSL + + + W ++L+ EI Q + K L
Sbjct: 415 SNCSELVSLHLSFNYLSGTIP---SSLGSLSKLRDLKL-WLNMLEGEIPQELMYVKTL-E 469
Query: 417 ALLLSYNDLPNEIKRCFSYCAVL 439
L+L +NDL EI S C L
Sbjct: 470 TLILDFNDLTGEIPSGLSNCTNL 492
>pdb|1DG3|A Chain A, Structure Of Human Guanylate Binding Protein-1 In
Nucleotide Free Form
pdb|1F5N|A Chain A, Human Guanylate Binding Protein-1 In Complex With The Gtp
Analogue, Gmppnp
Length = 592
Score = 32.3 bits (72), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 81 DEWNTARGKLQNEGVDADNALSFLQKLC-SSFFPAASCFGFEQLFLRRDIAKKIKEMNET 139
DE+ T KL+ D + L +LC FFP CF F++ RR +A+ K +E
Sbjct: 199 DEYLTYSLKLKKGTSQKDETFN-LPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEE 257
Query: 140 LD 141
LD
Sbjct: 258 LD 259
>pdb|2B8W|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GmpALF4
pdb|2B8W|B Chain B, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GmpALF4
pdb|2B92|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GdpALF3
pdb|2B92|B Chain B, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With GdpALF3
pdb|2BC9|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With Non-Hydrolysable Gtp Analogue Gppnhp
pdb|2D4H|A Chain A, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With Gmp
pdb|2D4H|B Chain B, Crystal-Structure Of The N-Terminal Large Gtpase Domain Of
Human Guanylate Binding Protein 1 (Hgbp1) In Complex
With Gmp
Length = 328
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 81 DEWNTARGKLQNEGVDADNALSFLQKLC-SSFFPAASCFGFEQLFLRRDIAKKIKEMNET 139
DE+ T KL+ D + L +LC FFP CF F++ RR +A+ K +E
Sbjct: 210 DEYLTYSLKLKKGTSQKDETFN-LPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEE 268
Query: 140 LD 141
LD
Sbjct: 269 LD 270
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 31.6 bits (70), Expect = 2.5, Method: Composition-based stats.
Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 608 GIEKLIHLRYLKLFFVGIEELPETFCELFNLQNLDLRRCSKFKRLPQNI-GKLVNLRHLI 666
GI+ L ++RYL L + ++ EL NL L L ++ + LP + KL NL+ L+
Sbjct: 58 GIQYLPNVRYLALGGNKLHDI-SALKELTNLTYLILTG-NQLQSLPNGVFDKLTNLKELV 115
Query: 667 FDEDDLDYMPKGM-GSLTGLRTLS 689
E+ L +P G+ LT L L+
Sbjct: 116 LVENQLQSLPDGVFDKLTNLTYLN 139
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 31.2 bits (69), Expect = 3.0, Method: Composition-based stats.
Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 4/83 (4%)
Query: 608 GIEKLIHLRYLKLFFVGIEELPETFCELFNLQNLDLRRCSKFKRLPQNI-GKLVNLRHLI 666
GI+ L ++RYL L + ++ EL NL L L ++ + LP + KL NL+ L+
Sbjct: 58 GIQYLPNVRYLALGGNKLHDI-SALKELTNLTYLILTG-NQLQSLPNGVFDKLTNLKELV 115
Query: 667 FDEDDLDYMPKGM-GSLTGLRTL 688
E+ L +P G+ LT L L
Sbjct: 116 LVENQLQSLPDGVFDKLTNLTYL 138
>pdb|3ZYI|A Chain A, Netring2 In Complex With Ngl2
Length = 452
Score = 31.2 bits (69), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 5/82 (6%)
Query: 564 KKLRSLLIQGYSLQHMPSF-FDQLTCLRALRIGKYGDDAIERIPNG-IEKLIHLRYLKLF 621
KLR L ++ ++ +PS+ F+++ L L +G+ +E I G E L +L+YL L
Sbjct: 147 SKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGEL--KKLEYISEGAFEGLFNLKYLNLG 204
Query: 622 FVGIEELPETFCELFNLQNLDL 643
I+++P L L+ L++
Sbjct: 205 MCNIKDMPN-LTPLVGLEELEM 225
>pdb|2Z63|A Chain A, Crystal Structure Of The Tv8 Hybrid Of Human Tlr4 And
Hagfish Vlrb.61
Length = 570
Score = 31.2 bits (69), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 37/121 (30%), Positives = 53/121 (43%), Gaps = 8/121 (6%)
Query: 564 KKLRSLLIQGYSLQHMPSF--FDQLTCLRALRIGK-YGDDAIERIPNGIEKLIHLRYLKL 620
++L L Q +L+ M F F L L L I + A I NG+ L LK+
Sbjct: 396 EQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSL---EVLKM 452
Query: 621 FFVGIEE--LPETFCELFNLQNLDLRRCSKFKRLPQNIGKLVNLRHLIFDEDDLDYMPKG 678
+E LP+ F EL NL LDL +C + P L +L+ L + L +P G
Sbjct: 453 AGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMASNQLKSVPDG 512
Query: 679 M 679
+
Sbjct: 513 I 513
>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 = 30.8 bits (68), Expect = 3.5, Method: Composition-based stats.
Identities = 28/100 (28%), Positives = 46/100 (46%), Gaps = 3/100 (3%)
Query: 569 LLIQGYSLQHMP-SFFDQLTCLRALRIGKYGDDAIERIPNGIEKLIHLRYLKLFFVGIEE 627
L ++ LQ +P FD+LT L L + G L+YL L F G+
Sbjct: 33 LELESNKLQSLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSDFGTTSLKYLDLSFNGVIT 92
Query: 628 LPETFCELFNLQNLDLRRCSKFKRLPQNIGKLVNLRHLIF 667
+ F L L++LD + S K++ + ++LR+LI+
Sbjct: 93 MSSNFLGLEQLEHLDFQH-SNLKQMSE-FSVFLSLRNLIY 130
>pdb|3A4L|A Chain A, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3A4L|B Chain B, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3A4M|A Chain A, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3A4M|B Chain B, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3A4N|A Chain A, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3A4N|B Chain B, Crystal Structure Of Archaeal O-Phosphoseryl-Trna(Sec)
Kinase
pdb|3AM1|A Chain A, Crystal Structure Of O-Phosphoseryl-Trna Kinase Complexed
With Anticodon-StemLOOP TRUNCATED TRNA(SEC)
Length = 260
Score = 30.8 bits (68), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 52/110 (47%), Gaps = 19/110 (17%)
Query: 201 IQVISLVGMGGIGKTTLAQLAYNDADVSNNFNVMIWVCVSDPF-DVFRVWKAIIENLDGY 259
I +I L G+ G+GK+T ++ N A + + N+ + V SD + F VWK E
Sbjct: 4 IMLIILTGLPGVGKSTFSK---NLAKILSKNNIDVIVLGSDLIRESFPVWKEKYEEFIK- 59
Query: 260 TPDLGELNTLHQLINNRIGGKKVLLVLDDVWTEDGNKWESFQRCLINAHR 309
+ ++LI++ + V++ +D N + S +R LIN +
Sbjct: 60 -------KSTYRLIDSALKNYWVIV-------DDTNYYNSMRRDLINIAK 95
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 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,613,470
Number of Sequences: 62578
Number of extensions: 1080386
Number of successful extensions: 2918
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 2865
Number of HSP's gapped (non-prelim): 67
length of query: 949
length of database: 14,973,337
effective HSP length: 108
effective length of query: 841
effective length of database: 8,214,913
effective search space: 6908741833
effective search space used: 6908741833
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)