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= 042849
(1019 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 45.4 bits (106), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 77/315 (24%), Positives = 104/315 (33%), Gaps = 146/315 (46%)
Query: 690 PFTLVQGPPGTGKTHTVWGMLNVIHLVQYQHYYNSLLKKLAPESYKQPNESNSDNVSMGS 749
P +L+QGPPGTGK TV V HL +
Sbjct: 376 PLSLIQGPPGTGK--TVTSATIVYHLSKIH------------------------------ 403
Query: 750 IDEVLQNMDQNLLRTLPKLCPKPRMLVCAPSNAATDELLTRVLDRGFIDGEMKVYRPDVA 809
K R+LVCAPSN A D L ++ D G +KV R
Sbjct: 404 ---------------------KDRILVCAPSNVAVDHLAAKLRDLG-----LKVVR---- 433
Query: 810 RVGVDSQTRAAQAVSVERRTEQLLVKSREEVIG-----WMHNLKGREAVLSQQIANLQRE 864
L KSRE+V +HNL GR
Sbjct: 434 ----------------------LTAKSREDVESSVSNLALHNLVGR-------------- 457
Query: 865 LNAAAFAVRSQGSVGVDPDVLMARDQNRDTLLQNLAAAVENRDKVLVEMSRFHILEGRFR 924
G+ G ++L +D+ + L+A+ R LV + IL
Sbjct: 458 -----------GAKGELKNLLKLKDE-----VGELSASDTKRFVKLVRKTEAEIL----- 496
Query: 925 PGSNFNLEEARASLEASFANEAEIVFTTVSSSGRKLFSRLTHGFDMVVIDEAAQASEVGV 984
N+A++V T +G K RL F V+IDE+ QASE
Sbjct: 497 -------------------NKADVVCCTCVGAGDK---RLDTKFRTVLIDESTQASEPEC 534
Query: 985 LPPLSLGAARCVLGG 999
L P+ GA + +L G
Sbjct: 535 LIPIVKGAKQVILVG 549
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 37.0 bits (84), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 968 FDMVVIDEAAQASEVGVLPPLSLGAARCVLGGGSSAAP 1005
FD+VVIDE AQA E PL L A +C+L G P
Sbjct: 367 FDVVVIDECAQALEASCWIPL-LKARKCILAGDHKQLP 403
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 37.0 bits (84), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 968 FDMVVIDEAAQASEVGVLPPLSLGAARCVLGGGSSAAP 1005
FD+VVIDE AQA E PL L A +C+L G P
Sbjct: 367 FDVVVIDECAQALEASCWIPL-LKARKCILAGDHKQLP 403
>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 340
Score = 34.3 bits (77), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 38/99 (38%), Gaps = 23/99 (23%)
Query: 623 MQTAILKPSPEHFPKYEHQTP-TMPECFTQNFIDHLHRTFNGPQLXXXXXXXXXXXXGTS 681
M T+ K S E+ P E P T+ E + QN + R F
Sbjct: 1 MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKF-------------------- 40
Query: 682 SGMTKSPWPFTLVQGPPGTGKTHTVWGMLNVIHLVQYQH 720
+ + P L GPPGTGKT T+ + I+ Y +
Sbjct: 41 --VDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSN 77
>pdb|3JVV|A Chain A, Crystal Structure Of P. Aeruginosa Pilt With Bound Amp-Pcp
pdb|3JVV|B Chain B, Crystal Structure Of P. Aeruginosa Pilt With Bound Amp-Pcp
pdb|3JVV|C Chain C, Crystal Structure Of P. Aeruginosa Pilt With Bound Amp-Pcp
pdb|3JVU|A Chain A, Crystal Structure Of Unliganded P. Aeruginosa Pilt
pdb|3JVU|B Chain B, Crystal Structure Of Unliganded P. Aeruginosa Pilt
pdb|3JVU|C Chain C, Crystal Structure Of Unliganded P. Aeruginosa Pilt
Length = 356
Score = 33.1 bits (74), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 688 PWPFTLVQGPPGTGKTHTVWGMLNVIHLVQYQHYYN 723
P LV GP G+GK+ T+ ML+ ++ +Y H
Sbjct: 122 PRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILT 157
>pdb|2XHL|A Chain A, Structure Of A Functional Derivative Of Clostridium
Botulinum Neurotoxin Type B
Length = 453
Score = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 32/135 (23%), Positives = 61/135 (45%), Gaps = 14/135 (10%)
Query: 839 EVIGWMHNLKGREAVLSQQIANLQRELNAAAFAVRSQGSV---GVDPDVLM-ARDQN-RD 893
E+I +H L G + + N ++ + A++++ G DP ++ + D++ D
Sbjct: 231 ELIHVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYD 290
Query: 894 TLLQNLAAAVENRDKVLVEMSRFHILEGRFRPGSNFNLEEARASLEASFANEAEIVFTTV 953
+LQN V+ +KVLV +S P N N+ + + + F ++E ++
Sbjct: 291 KVLQNFRGIVDRLNKVLVCIS---------DPNININIYKNKFKDKYKFVEDSEGKYSID 341
Query: 954 SSSGRKLFSRLTHGF 968
S KL+ L GF
Sbjct: 342 VESFDKLYKSLMFGF 356
>pdb|2ETF|A Chain A, Crystal Structure Of Full Length Botulinum Neurotoxin
(Type B) Light Chain
pdb|2ETF|B Chain B, Crystal Structure Of Full Length Botulinum Neurotoxin
(Type B) Light Chain
Length = 441
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 32/135 (23%), Positives = 61/135 (45%), Gaps = 14/135 (10%)
Query: 839 EVIGWMHNLKGREAVLSQQIANLQRELNAAAFAVRSQGSV---GVDPDVLM-ARDQN-RD 893
E+I +H L G + + N ++ + A++++ G DP ++ + D++ D
Sbjct: 231 ELIHVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYD 290
Query: 894 TLLQNLAAAVENRDKVLVEMSRFHILEGRFRPGSNFNLEEARASLEASFANEAEIVFTTV 953
+LQN V+ +KVLV +S P N N+ + + + F ++E ++
Sbjct: 291 KVLQNFRGIVDRLNKVLVCIS---------DPNININIYKNKFKDKYKFVEDSEGKYSID 341
Query: 954 SSSGRKLFSRLTHGF 968
S KL+ L GF
Sbjct: 342 VESFDKLYKSLMFGF 356
>pdb|1F82|A Chain A, Botulinum Neurotoxin Type B Catalytic Domain
Length = 424
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 32/135 (23%), Positives = 61/135 (45%), Gaps = 14/135 (10%)
Query: 839 EVIGWMHNLKGREAVLSQQIANLQRELNAAAFAVRSQGSV---GVDPDVLM-ARDQN-RD 893
E+I +H L G + + N ++ + A++++ G DP ++ + D++ D
Sbjct: 230 ELIHVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYD 289
Query: 894 TLLQNLAAAVENRDKVLVEMSRFHILEGRFRPGSNFNLEEARASLEASFANEAEIVFTTV 953
+LQN V+ +KVLV +S P N N+ + + + F ++E ++
Sbjct: 290 KVLQNFRGIVDRLNKVLVCIS---------DPNININIYKNKFKDKYKFVEDSEGKYSID 340
Query: 954 SSSGRKLFSRLTHGF 968
S KL+ L GF
Sbjct: 341 VESFDKLYKSLMFGF 355
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 939 EASFANEAEIVFTTVSSSGRKLFSRLTHGFDMVVIDEAAQASEVGVLPPLSLGAARCVLG 998
E A+++ T +G +++ F ++IDE+ QA+E + P+ LGA + +L
Sbjct: 489 ERELLMNADVICCTCVGAGDPRLAKMQ--FRSILIDESTQATEPECMVPVVLGAKQLILV 546
Query: 999 G 999
G
Sbjct: 547 G 547
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 690 PFTLVQGPPGTGKTHT 705
P +L+QGPPGTGKT T
Sbjct: 372 PLSLIQGPPGTGKTVT 387
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 939 EASFANEAEIVFTTVSSSGRKLFSRLTHGFDMVVIDEAAQASEVGVLPPLSLGAARCVLG 998
E A+++ T +G +++ F ++IDE+ QA+E + P+ LGA + +L
Sbjct: 312 ERELLMNADVICCTCVGAGDPRLAKMQ--FRSILIDESTQATEPECMVPVVLGAKQLILV 369
Query: 999 G 999
G
Sbjct: 370 G 370
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 690 PFTLVQGPPGTGKTHT 705
P +L+QGPPGTGKT T
Sbjct: 195 PLSLIQGPPGTGKTVT 210
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 939 EASFANEAEIVFTTVSSSGRKLFSRLTHGFDMVVIDEAAQASEVGVLPPLSLGAARCVLG 998
E A+++ T +G +++ F ++IDE+ QA+E + P+ LGA + +L
Sbjct: 313 ERELLMNADVICCTCVGAGDPRLAKMQ--FRSILIDESTQATEPECMVPVVLGAKQLILV 370
Query: 999 G 999
G
Sbjct: 371 G 371
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 690 PFTLVQGPPGTGKTHT 705
P +L+QGPPGTGKT T
Sbjct: 196 PLSLIQGPPGTGKTVT 211
>pdb|1EPW|A Chain A, Crystal Structure Of Clostridium Neurotoxin Type B
pdb|1F31|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With A Trisaccharide
pdb|1I1E|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With Doxorubicin
pdb|1G9A|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 3)
pdb|1G9B|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 1)
pdb|1G9C|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 4)
pdb|1G9D|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 2)
pdb|1S0B|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 4.0
pdb|1S0C|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 5.0
pdb|1S0D|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 5.5
pdb|1S0E|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 6.0
pdb|1S0F|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 7.0
pdb|1S0G|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B Apo Form
pdb|2NP0|A Chain A, Crystal Structure Of The Botulinum Neurotoxin Type B
Complexed With Synaptotagamin-Ii Ectodomain
Length = 1290
Score = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 43/92 (46%), Gaps = 11/92 (11%)
Query: 879 GVDPDVLM-ARDQN-RDTLLQNLAAAVENRDKVLVEMSRFHILEGRFRPGSNFNLEEARA 936
G DP ++ + D++ D +LQN V+ +KVLV +S P N N+ + +
Sbjct: 273 GQDPSIITPSTDKSIYDKVLQNFRGIVDRLNKVLVCIS---------DPNININIYKNKF 323
Query: 937 SLEASFANEAEIVFTTVSSSGRKLFSRLTHGF 968
+ F ++E ++ S KL+ L GF
Sbjct: 324 KDKYKFVEDSEGKYSIDVESFDKLYKSLMFGF 355
>pdb|3ZUQ|A Chain A, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type B-Derivative, Lc-B-Gs-Hn-B
Length = 906
Score = 31.2 bits (69), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 43/92 (46%), Gaps = 11/92 (11%)
Query: 879 GVDPDVLM-ARDQN-RDTLLQNLAAAVENRDKVLVEMSRFHILEGRFRPGSNFNLEEARA 936
G DP ++ + D++ D +LQN V+ +KVLV +S P N N+ + +
Sbjct: 274 GQDPSIITPSTDKSIYDKVLQNFRGIVDRLNKVLVCIS---------DPNININIYKNKF 324
Query: 937 SLEASFANEAEIVFTTVSSSGRKLFSRLTHGF 968
+ F ++E ++ S KL+ L GF
Sbjct: 325 KDKYKFVEDSEGKYSIDVESFDKLYKSLMFGF 356
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
0.313 0.130 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,070,011
Number of Sequences: 62578
Number of extensions: 1177845
Number of successful extensions: 2084
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2060
Number of HSP's gapped (non-prelim): 28
length of query: 1019
length of database: 14,973,337
effective HSP length: 108
effective length of query: 911
effective length of database: 8,214,913
effective search space: 7483785743
effective search space used: 7483785743
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (26.2 bits)