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= 046626
(557 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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 63/246 (25%), Positives = 107/246 (43%), Gaps = 50/246 (20%)
Query: 14 RYLFVMDDVWNEDPKVWDELKSLLWGGAKGSKILVTTRSNKVA-SIMGT-----MRGTGG 67
R L ++DDVW+ W +L +IL+TTR V S+MG + + G
Sbjct: 237 RSLLILDDVWDS----W-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 287
Query: 68 YKLEGLPYESCLSLFMKCAFKEGQHKNPNLVKIGEEIVKKSGGIPLAVRTLGSLL--YGS 125
K +GL LSLF+ K +L + I+K+ G PL V +G+LL + +
Sbjct: 288 -KEKGL---EILSLFVNM-------KKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPN 336
Query: 126 TDEHYWEYVRDNEIWKLEQKEN----DILPALKLSYDQLPPHLKQCFAYCSIFPKDYDFD 181
E+Y + +++ + ++ + + + A+ +S + L +K + SI KD
Sbjct: 337 RWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVP 396
Query: 182 SVLLIRFWMAHGLLQSPNENEEPENIGMRYLNELLSRSFFQDFSNGMLPEGFEIFFFKMH 241
+ +L W E EE E+I L E +++S NG + F + +H
Sbjct: 397 TKVLCILW--------DMETEEVEDI----LQEFVNKSLLFCDRNG------KSFRYYLH 438
Query: 242 DLMHDL 247
DL D
Sbjct: 439 DLQVDF 444
>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 = 3e-04, Method: Compositional matrix adjust.
Identities = 63/246 (25%), Positives = 107/246 (43%), Gaps = 50/246 (20%)
Query: 14 RYLFVMDDVWNEDPKVWDELKSLLWGGAKGSKILVTTRSNKVA-SIMGT-----MRGTGG 67
R L ++DDVW+ W +L +IL+TTR V S+MG + + G
Sbjct: 243 RSLLILDDVWDS----W-----VLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLG 293
Query: 68 YKLEGLPYESCLSLFMKCAFKEGQHKNPNLVKIGEEIVKKSGGIPLAVRTLGSLL--YGS 125
K +GL LSLF+ K +L + I+K+ G PL V +G+LL + +
Sbjct: 294 -KEKGLEI---LSLFVNM-------KKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPN 342
Query: 126 TDEHYWEYVRDNEIWKLEQKEN----DILPALKLSYDQLPPHLKQCFAYCSIFPKDYDFD 181
E+Y + +++ + ++ + + + A+ +S + L +K + SI KD
Sbjct: 343 RWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVP 402
Query: 182 SVLLIRFWMAHGLLQSPNENEEPENIGMRYLNELLSRSFFQDFSNGMLPEGFEIFFFKMH 241
+ +L W E EE E+I L E +++S NG + F + +H
Sbjct: 403 TKVLCILW--------DMETEEVEDI----LQEFVNKSLLFCDRNG------KSFRYYLH 444
Query: 242 DLMHDL 247
DL D
Sbjct: 445 DLQVDF 450
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 64/245 (26%), Positives = 105/245 (42%), Gaps = 48/245 (19%)
Query: 14 RYLFVMDDVWNEDPKVWDELKSLLWGGAKGSKILVTTRSNKVA-SIMGTMR----GTGGY 68
R L ++DDVW DP V LK+ +IL+TTR V S+MG +G
Sbjct: 237 RSLLILDDVW--DPWV---LKAF----DNQCQILLTTRDKSVTDSVMGPKHVVPVESGLG 287
Query: 69 KLEGLPYESCLSLFMKCAFKEGQHKNPNLVKIGEEIVKKSGGIPLAVRTLGSLL--YGST 126
+ +GL LSLF+ K +L I+K+ G PL V +G+LL + +
Sbjct: 288 REKGLEI---LSLFVNM-------KKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNR 337
Query: 127 DEHYWEYVRDNEIWKLEQKEN----DILPALKLSYDQLPPHLKQCFAYCSIFPKDYDFDS 182
+Y +++ + ++ + + + A+ +S + L +K + SI KD +
Sbjct: 338 WAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPT 397
Query: 183 VLLIRFWMAHGLLQSPNENEEPENIGMRYLNELLSRSFFQDFSNGMLPEGFEIFFFKMHD 242
+L W E EE E+I L E +++S NG + F + +HD
Sbjct: 398 KVLCVLW--------DLETEEVEDI----LQEFVNKSLLFCNRNG------KSFCYYLHD 439
Query: 243 LMHDL 247
L D
Sbjct: 440 LQVDF 444
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 63/245 (25%), Positives = 104/245 (42%), Gaps = 48/245 (19%)
Query: 14 RYLFVMDDVWNEDPKVWDELKSLLWGGAKGSKILVTTRSNKVA-SIMGTMR----GTGGY 68
R L ++DDVW DP V LK+ +IL+TT V S+MG +G
Sbjct: 244 RSLLILDDVW--DPWV---LKAF----DNQCQILLTTSDKSVTDSVMGPKHVVPVESGLG 294
Query: 69 KLEGLPYESCLSLFMKCAFKEGQHKNPNLVKIGEEIVKKSGGIPLAVRTLGSLL--YGST 126
+ +GL LSLF+ K +L I+K+ G PL V +G+LL + +
Sbjct: 295 REKGLEI---LSLFVNM-------KKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNR 344
Query: 127 DEHYWEYVRDNEIWKLEQKEN----DILPALKLSYDQLPPHLKQCFAYCSIFPKDYDFDS 182
+Y +++ + ++ + + + A+ +S + L +K + SI KD +
Sbjct: 345 WAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPT 404
Query: 183 VLLIRFWMAHGLLQSPNENEEPENIGMRYLNELLSRSFFQDFSNGMLPEGFEIFFFKMHD 242
+L W E EE E+I L E +++S NG + F + +HD
Sbjct: 405 KVLCVLW--------DLETEEVEDI----LQEFVNKSLLFCNRNG------KSFCYYLHD 446
Query: 243 LMHDL 247
L D
Sbjct: 447 LQVDF 451
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 50/187 (26%), Positives = 75/187 (40%), Gaps = 26/187 (13%)
Query: 345 LRYLDLSDNDKIKKLPNSICELHSLQTLSLGGCRELEELPKDIRYLVSLRMFMVSTKQKS 404
L L L+ N ++ LP SI L+ L+ LS+ C EL ELP+ + ++ S
Sbjct: 129 LETLTLARN-PLRALPASIASLNRLRELSIRACPELTELPEPL-----------ASTDAS 176
Query: 405 LLESGIGCLSSLRFLMISDCENLEYFSLETLMLKDCESLNL-NLNIEMEGEESHCDRNKT 463
G+ L SLR + + L++ +SL + N + G H
Sbjct: 177 GEHQGLVNLQSLRL----EWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIH------ 226
Query: 464 RLHLRKLF-VXXXXXXXXXXXXXXXXSTKTLKNLIIRNCPNFMALPESLRNLEALETLAI 522
HL KL + LK LI+++C N + LP + L LE L +
Sbjct: 227 --HLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDL 284
Query: 523 GGCPALS 529
GC LS
Sbjct: 285 RGCVNLS 291
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 34/82 (41%)
Query: 312 LTSCISKSQFLRVIDLSETAIEVLSREIGNLKHLRYLDLSDNDKIKKLPNSICELHSLQT 371
L + I+ Q L+ + + + + L I +L L LDL ++ P L+
Sbjct: 198 LPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKR 257
Query: 372 LSLGGCRELEELPKDIRYLVSL 393
L L C L LP DI L L
Sbjct: 258 LILKDCSNLLTLPLDIHRLTQL 279
>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 = 0.45, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 31/47 (65%), Gaps = 3/47 (6%)
Query: 313 TSCISKSQFLRVIDLSETAIEV---LSREIGNLKHLRYLDLSDNDKI 356
T C+ K + L+ +DLS + IE + ++ NL+HL+YL+LS N+ +
Sbjct: 342 TRCLEKLENLQKLDLSHSDIEASDCCNLQLKNLRHLQYLNLSYNEPL 388
>pdb|4ECN|A Chain A, Crystal Structure Of A Leucine-Rich Repeat Protein
(Bt_0210) From Bacteroides Thetaiotaomicron Vpi-5482 At
2.80 A Resolution
Length = 876
Score = 32.0 bits (71), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 491 KTLKNLIIRNCPNFMALPESLRNLEALETLAIGGCPALSERCKPQTGEDWPKIA 544
K L ++ + NCPN LP+ L +L L++L I +S Q DW ++A
Sbjct: 491 KDLTDVELYNCPNXTQLPDFLYDLPELQSLNIACNRGIS---AAQLKADWTRLA 541
>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 = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 322 LRVIDLSETAIEVLSREIGNLKHLRYLDLSDNDKIKKLPNSICELHSLQTLSLGG 376
LRV+DLS + L E+G+ L+Y DN + LP L +LQ L + G
Sbjct: 272 LRVLDLSHNRLTSLPAELGSCFQLKYFYFFDN-MVTTLPWEFGNLCNLQFLGVEG 325
>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 = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 34/106 (32%), Positives = 51/106 (48%), Gaps = 10/106 (9%)
Query: 334 VLSREIGNLKHLRYLDLSDNDKIKKLPN-SICELHSLQTLSLGGCRELEELPKDIRYLVS 392
++ +E+ N KHL +DLS N++I L N S + L TL L R P+ L S
Sbjct: 45 LVPKELSNYKHLTLIDLS-NNRISTLSNQSFSNMTQLLTLILSYNRLRCIPPRTFDGLKS 103
Query: 393 LRMFMVSTKQKSLL-ESGIGCLSSLRFLMIS------DCENLEYFS 431
LR+ + S++ E LS+L L I DC N+++ S
Sbjct: 104 LRLLSLHGNDISVVPEGAFNDLSALSHLAIGANPLYCDC-NMQWLS 148
>pdb|1G9U|A Chain A, Crystal Structure Of Yopm-leucine Rich Effector Protein
From Yersinia Pestis
pdb|1JL5|A Chain A, Novel Molecular Architecture Of Yopm-A Leucine-Rich
Effector Protein From Yersinia Pestis
Length = 454
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 32/126 (25%), Positives = 55/126 (43%), Gaps = 26/126 (20%)
Query: 316 ISKSQFLRVIDLSETAIEVLS----------------REIGNLKHLRYLD--LSDNDKIK 357
+ S FL++ID+ +++ L E+ L++L +L +DN+ +K
Sbjct: 149 LQNSSFLKIIDVDNNSLKKLPDLPPSLEFIAAGNNQLEELPELQNLPFLTAIYADNNSLK 208
Query: 358 KLPNSICELHSLQTLSLGGCRELEELPKDIRYLVSLRMFMVSTKQKSLLESGIGCLSSLR 417
KLP+ L S+ + G LEELP+ L +L +LL++ SL
Sbjct: 209 KLPDLPLSLESI----VAGNNILEELPE----LQNLPFLTTIYADNNLLKTLPDLPPSLE 260
Query: 418 FLMISD 423
L + D
Sbjct: 261 ALNVRD 266
>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 = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%)
Query: 335 LSREIGNLKHLRYLDLSDNDKIKKLPNSICELHSLQTLSLGGCRELEELPKDIRYLVSLR 394
+ +EIG++ +L L+L ND +P+ + +L L L L + +P+ + L L
Sbjct: 648 IPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTMLT 707
Query: 395 MFMVSTKQKS 404
+S S
Sbjct: 708 EIDLSNNNLS 717
>pdb|3B2D|A Chain A, Crystal Structure Of Human Rp105MD-1 Complex
pdb|3B2D|B Chain B, Crystal Structure Of Human Rp105MD-1 Complex
Length = 603
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 315 CISKSQFLRVIDLSETAIEV---LSREIGNLKHLRYLDLSDNDKIKKLPNSICELHSLQT 371
C+ K L+ +DLS IE S ++ NL HL+ L+LS N+ + + E L+
Sbjct: 342 CLEKLGNLQTLDLSHNDIEASDCCSLQLKNLSHLQTLNLSHNEPLGLQSQAFKECPQLEL 401
Query: 372 LSLGGCR 378
L L R
Sbjct: 402 LDLAFTR 408
>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 = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%)
Query: 335 LSREIGNLKHLRYLDLSDNDKIKKLPNSICELHSLQTLSLGGCRELEELPKDIRYLVSL 393
+ +EIG++ +L L+L ND +P+ + +L L L L + +P+ + L L
Sbjct: 645 IPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTML 703
>pdb|2V9S|A Chain A, Second Lrr Domain Of Human Slit2
pdb|2V9S|B Chain B, Second Lrr Domain Of Human Slit2
pdb|2V9S|C Chain C, Second Lrr Domain Of Human Slit2
pdb|2V9S|D Chain D, Second Lrr Domain Of Human Slit2
Length = 220
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 325 IDLSETAIEVLSR-EIGNLKHLRYLDLSDNDKIKKLPNSICELHSLQTLSLGGCRELEEL 383
I L + I+V+ K LR +DLS+N + P++ L SL +L L G ++ EL
Sbjct: 37 IRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYG-NKITEL 95
Query: 384 PKDI 387
PK +
Sbjct: 96 PKSL 99
>pdb|2V9T|B Chain B, Complex Between The Second Lrr Domain Of Slit2 And The
First Ig Domain From Robo1
Length = 220
Score = 29.3 bits (64), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 325 IDLSETAIEVLSR-EIGNLKHLRYLDLSDNDKIKKLPNSICELHSLQTLSLGGCRELEEL 383
I L + I+V+ K LR +DLS+N + P++ L SL +L L G ++ EL
Sbjct: 37 IRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYG-NKITEL 95
Query: 384 PKDI 387
PK +
Sbjct: 96 PKSL 99
>pdb|3T6Q|A Chain A, Crystal Structure Of Mouse Rp105MD-1 Complex
pdb|3T6Q|B Chain B, Crystal Structure Of Mouse Rp105MD-1 Complex
Length = 606
Score = 28.5 bits (62), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 313 TSCISKSQFLRVIDLSETAIEV---LSREIGNLKHLRYLDLSDNDKIKKLPNSICELHSL 369
T C+ + LR +DLS IE + ++ NL HL+ L+LS N+ + + E L
Sbjct: 343 TGCLENLENLRELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNEPLSLKTEAFKECPQL 402
Query: 370 QTLSLGGCR 378
+ L L R
Sbjct: 403 ELLDLAFTR 411
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
0.320 0.137 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,778,179
Number of Sequences: 62578
Number of extensions: 640893
Number of successful extensions: 1410
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 1387
Number of HSP's gapped (non-prelim): 46
length of query: 557
length of database: 14,973,337
effective HSP length: 104
effective length of query: 453
effective length of database: 8,465,225
effective search space: 3834746925
effective search space used: 3834746925
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: 54 (25.4 bits)