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= 038509
(806 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 183 bits (465), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 147/458 (32%), Positives = 216/458 (47%), Gaps = 66/458 (14%)
Query: 377 NLLFPSQSTKRRSIKAAPFVPFNSLNEEQTRSVEIILGCKGAPPYVIYGPPGTGKTMTLV 436
+++ Q KR + + P LN Q +V+ +L P +I GPPGTGKT+T
Sbjct: 161 DVIIKCQLPKRFTAQGLP-----DLNHSQVYAVKTVLQ---RPLSLIQGPPGTGKTVTSA 212
Query: 437 EAILQVYSTREHSRILVCAASNSAADHMLERLISNEVAGIKENEILRLNATSRPYEDVPT 496
+ + + + + +LVCA SN A D + E++ G+K ++RL A SR D P
Sbjct: 213 TIVYHL-ARQGNGPVLVCAPSNIAVDQLTEKI---HQTGLK---VVRLCAKSREAIDSPV 265
Query: 497 DFIRFCFFEESIFKCPPREAL---------------GRYRIIISTYMSSSLLNTNGI--- 538
F+ ++ P + L RYR + T L+N + I
Sbjct: 266 SFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCT 325
Query: 539 ---------KRGNFSHIFLDEAGQASEPESMIPIANLCTKQTVVVLAGDPKQLGPVIYSK 589
+ F I +DE+ QA+EPE M+P+ L KQ ++L GD QLGPV+ K
Sbjct: 326 CVGAGDPRLAKMQFRSILIDESTQATEPECMVPVV-LGAKQ--LILVGDHCQLGPVVMCK 382
Query: 590 DAETFGLGKSYLERLFECEFYRNGDEGYVTKLVRNYRCHPAILDLPSKLFYGGELLACKD 649
A GL +S ERL +L YR HPA+ PS +FY G L
Sbjct: 383 KAAKAGLSQSLFERLVVLGIRP-------IRLQVQYRMHPALSAFPSNIFYEGSLQNGVT 435
Query: 650 DATSLSSAKVDIFPNKDFPVLFFGIQGCDEREGNNPSWFNRFEVSKVVDIINKLRENTEL 709
A + +P D P+ F+ QG +E + S+ NR E + V I KL +
Sbjct: 436 AADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLK-AGA 494
Query: 710 NETDIGVITPYRQQ------VLKIKKVLETWDMPDVKVGTVEQFQGQEREVIIVSTVRST 763
IG+ITPY Q ++ L T +V++ +V+ FQG+E++ II+S VR+
Sbjct: 495 KPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRA- 553
Query: 764 VKHNEFDRTYCLGFLSNPRRFNVAITRARSLLIIVGNP 801
NE +GFL++PRR NVA+TRAR +IIVGNP
Sbjct: 554 ---NEHQ---GIGFLNDPRRLNVALTRARYGVIIVGNP 585
>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 = 183 bits (464), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 145/458 (31%), Positives = 214/458 (46%), Gaps = 66/458 (14%)
Query: 377 NLLFPSQSTKRRSIKAAPFVPFNSLNEEQTRSVEIILGCKGAPPYVIYGPPGTGKTMTLV 436
+++ Q KR + + P LN Q +V+ +L P +I GPPGTGKT+T
Sbjct: 338 DVIIKCQLPKRFTAQGLP-----DLNHSQVYAVKTVLQ---RPLSLIQGPPGTGKTVTSA 389
Query: 437 EAILQVYSTREHSRILVCAASNSAADHMLERLISNEVAGIKENEILRLNATSRPYEDVPT 496
+ + + + + +LVCA SN A D + E++ G+K ++RL A SR D P
Sbjct: 390 TIVYHL-ARQGNGPVLVCAPSNIAVDQLTEKI---HQTGLK---VVRLCAKSREAIDSPV 442
Query: 497 DFIRFCFFEESIFKCPPREAL---------------GRYRIIISTYMSSSLLNTNGI--- 538
F+ ++ P + L RYR + T L+N + I
Sbjct: 443 SFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCT 502
Query: 539 ---------KRGNFSHIFLDEAGQASEPESMIPIANLCTKQTVVVLAGDPKQLGPVIYSK 589
+ F I +DE+ QA+EPE M+P+ L KQ ++L GD QLGPV+ K
Sbjct: 503 CVGAGDPRLAKMQFRSILIDESTQATEPECMVPVV-LGAKQ--LILVGDHCQLGPVVMCK 559
Query: 590 DAETFGLGKSYLERLFECEFYRNGDEGYVTKLVRNYRCHPAILDLPSKLFYGGELLACKD 649
A GL +S ERL +L YR HPA+ PS +FY G L
Sbjct: 560 KAAKAGLSQSLFERLVVLGIRP-------IRLQVQYRMHPALSAFPSNIFYEGSLQNGVT 612
Query: 650 DATSLSSAKVDIFPNKDFPVLFFGIQGCDEREGNNPSWFNRFEVSKVVDIINKLRENTEL 709
A + +P D P+ F+ QG +E + S+ NR E + V I KL +
Sbjct: 613 AADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLK-AGA 671
Query: 710 NETDIGVITPYRQQ------VLKIKKVLETWDMPDVKVGTVEQFQGQEREVIIVSTVRST 763
IG+ITPY Q ++ L T +V++ +V+ FQG+E++ II+S VR+
Sbjct: 672 KPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRAN 731
Query: 764 VKHNEFDRTYCLGFLSNPRRFNVAITRARSLLIIVGNP 801
+GFL++PRR NVA+TRAR +IIVGNP
Sbjct: 732 EHQG-------IGFLNDPRRLNVALTRARYGVIIVGNP 762
>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 = 183 bits (464), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 147/458 (32%), Positives = 216/458 (47%), Gaps = 66/458 (14%)
Query: 377 NLLFPSQSTKRRSIKAAPFVPFNSLNEEQTRSVEIILGCKGAPPYVIYGPPGTGKTMTLV 436
+++ Q KR + + P LN Q +V+ +L P +I GPPGTGKT+T
Sbjct: 162 DVIIKCQLPKRFTAQGLP-----DLNHSQVYAVKTVLQ---RPLSLIQGPPGTGKTVTSA 213
Query: 437 EAILQVYSTREHSRILVCAASNSAADHMLERLISNEVAGIKENEILRLNATSRPYEDVPT 496
+ + + + + +LVCA SN A D + E++ G+K ++RL A SR D P
Sbjct: 214 TIVYHL-ARQGNGPVLVCAPSNIAVDQLTEKI---HQTGLK---VVRLCAKSREAIDSPV 266
Query: 497 DFIRFCFFEESIFKCPPREAL---------------GRYRIIISTYMSSSLLNTNGI--- 538
F+ ++ P + L RYR + T L+N + I
Sbjct: 267 SFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCT 326
Query: 539 ---------KRGNFSHIFLDEAGQASEPESMIPIANLCTKQTVVVLAGDPKQLGPVIYSK 589
+ F I +DE+ QA+EPE M+P+ L KQ ++L GD QLGPV+ K
Sbjct: 327 CVGAGDPRLAKMQFRSILIDESTQATEPECMVPVV-LGAKQ--LILVGDHCQLGPVVMCK 383
Query: 590 DAETFGLGKSYLERLFECEFYRNGDEGYVTKLVRNYRCHPAILDLPSKLFYGGELLACKD 649
A GL +S ERL +L YR HPA+ PS +FY G L
Sbjct: 384 KAAKAGLSQSLFERLVVLGIRP-------IRLQVQYRMHPALSAFPSNIFYEGSLQNGVT 436
Query: 650 DATSLSSAKVDIFPNKDFPVLFFGIQGCDEREGNNPSWFNRFEVSKVVDIINKLRENTEL 709
A + +P D P+ F+ QG +E + S+ NR E + V I KL +
Sbjct: 437 AADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLK-AGA 495
Query: 710 NETDIGVITPYRQQ------VLKIKKVLETWDMPDVKVGTVEQFQGQEREVIIVSTVRST 763
IG+ITPY Q ++ L T +V++ +V+ FQG+E++ II+S VR+
Sbjct: 496 KPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRA- 554
Query: 764 VKHNEFDRTYCLGFLSNPRRFNVAITRARSLLIIVGNP 801
NE +GFL++PRR NVA+TRAR +IIVGNP
Sbjct: 555 ---NEHQ---GIGFLNDPRRLNVALTRARYGVIIVGNP 586
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 168 bits (425), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 142/444 (31%), Positives = 208/444 (46%), Gaps = 77/444 (17%)
Query: 398 FNSLNEEQTRSVEIILGCKGAPPYVIYGPPGTGKTMTLVEAILQVYSTREHSRILVCAAS 457
F LN Q+ +V +L P +I GPPGTGKT+T + + S RILVCA S
Sbjct: 358 FAQLNSSQSNAVSHVLQ---RPLSLIQGPPGTGKTVTSATIVYHL-SKIHKDRILVCAPS 413
Query: 458 NSAADHMLERLISNEVAGIKENEILRLNATSRPYEDVPTDFIRFCFFEESIFKCPPREAL 517
N A DH+ +L G+K ++RL A SR EDV + ++ R A
Sbjct: 414 NVAVDHLAAKL---RDLGLK---VVRLTAKSR--EDVESSVSNL-----ALHNLVGRGAK 460
Query: 518 GRYRIIISTYMSSSLLNTNGIKR--------------------------------GNFSH 545
G + ++ L+ + KR F
Sbjct: 461 GELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLDTKFRT 520
Query: 546 IFLDEAGQASEPESMIPIANLCTKQTVVVLAGDPKQLGPVIYSKDAETFGLGKSYLERLF 605
+ +DE+ QASEPE +IPI KQ V+L GD +QLGPVI + A GL +S ERL
Sbjct: 521 VLIDESTQASEPECLIPIVK-GAKQ--VILVGDHQQLGPVILERKAADAGLKQSLFERLI 577
Query: 606 ECEFYRNGDEGYV-TKLVRNYRCHPAILDLPSKLFYGGELL-ACKDDATSLSSAKVDIFP 663
G+V +L YR +P + + PS +FY G L + ++ ++K +P
Sbjct: 578 SL--------GHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFP-WP 628
Query: 664 NKDFPVLFFGIQGCDEREGNNPSWFNRFEVSKVVDIINKLRENTELNETDIGVITPYRQQ 723
+ P++F+ G +E N S+ NR E II KL + + IGVITPY Q
Sbjct: 629 IRGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRDG-VKPEQIGVITPYEGQ 687
Query: 724 VLKIKKVLETWDMPD------VKVGTVEQFQGQEREVIIVSTVRSTVKHNEFDRTYCLGF 777
I + ++ D V+V +V+ FQG+E++ II+S VR+ + +GF
Sbjct: 688 RAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRA-------NEQQAIGF 740
Query: 778 LSNPRRFNVAITRARSLLIIVGNP 801
L +PRR NV +TRA+ L+I+GNP
Sbjct: 741 LRDPRRLNVGLTRAKYGLVILGNP 764
>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 = 135 bits (341), Expect = 6e-32, Method: Compositional matrix adjust.
Identities = 158/570 (27%), Positives = 238/570 (41%), Gaps = 100/570 (17%)
Query: 301 SLVHGDFVFVKLAA-ANADAKKGSIYRVEADEVILKF--AKEFHTQHRNGSLYNVSFTYN 357
S GD V + AA + G + RV V + F + +F + Y + N
Sbjct: 80 SFTSGDIVGLYDAANEGSQLATGILTRVTQKSVTVAFDESHDFQQSLDRENSYRLLKLAN 139
Query: 358 RINMRRMYQAVQAAENLEPN-------LLFPSQSTKRRSIKAAPFVPFNS-LNEEQTRSV 409
+ RR+ +A+ A + +LF +S + + P FN+ L+ Q +V
Sbjct: 140 DVTYRRLKKALIALKKYHSGPASSLIEVLF-GRSAPSPASEIHPLTFFNTCLDTSQKEAV 198
Query: 410 EIILGCKGAPPYVIYGPPGTGKTMTLVEAILQVYSTREHSRILVCAASNSAADHMLERLI 469
L K +I+GPPGTGKT T+VE ILQ + ++ ++L CA SN A D+++ERL
Sbjct: 199 LFALSQKELA--IIHGPPGTGKTTTVVEIILQ--AVKQGLKVLCCAPSNIAVDNLVERL- 253
Query: 470 SNEVAGIKENEILRLNATSRPYE-------------------------DVPTDFIRFCFF 504
+ + ILRL +R E D+ F++
Sbjct: 254 -----ALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRKDIDQVFVKNKKT 308
Query: 505 EESIFKCPPREALGRYRIIIS----TYMSSSLLNTNGIKRGN----------------FS 544
++ K R + R + M SL + N + N F
Sbjct: 309 QDKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADGPLKLLPESYFD 368
Query: 545 HIFLDEAGQASEPESMIPIANLCTKQTVVVLAGDPKQLGPVIYSKDAETFGLGKSYLERL 604
+ +DE QA E IP+ K +LAGD KQL P S A GL S +ERL
Sbjct: 369 VVVIDECAQALEASCWIPL----LKARKCILAGDHKQLPPTTVSHKAALAGLSLSLMERL 424
Query: 605 FECEFYRNGDEGYVTKLVRNYRCHPAILDLPSKLFYGGELLACKDDATSLSSAKVDIFPN 664
E R V L YR H AI+ S Y G+L A A L +
Sbjct: 425 AEEYGAR-----VVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAAT 479
Query: 665 KD--FPVLFFGIQGC--------DEREGNNPSWFNRFEVSKVVDIINKLRENTELNETDI 714
++ P+L GC DE+ NP EV V I L + + DI
Sbjct: 480 EETGVPLLLVDTAGCGLFELEEEDEQSKGNPG-----EVRLVSLHIQAL-VDAGVPARDI 533
Query: 715 GVITPYRQQVLKIKKVLETWDMPDVKVGTVEQFQGQEREVIIVSTVRSTVKHNEFDRTYC 774
V++PY QV +++ L P++++ +V+ FQG+E+E +I+S VRS +R
Sbjct: 534 AVVSPYNLQVDLLRQSL-VHRHPELEIKSVDGFQGREKEAVILSFVRS-------NRKGE 585
Query: 775 LGFLSNPRRFNVAITRARSLLIIVGNPHIV 804
+GFL+ RR NVA+TRAR + ++ + V
Sbjct: 586 VGFLAEDRRINVAVTRARRHVAVICDSRTV 615
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 135 bits (341), Expect = 6e-32, Method: Compositional matrix adjust.
Identities = 158/570 (27%), Positives = 238/570 (41%), Gaps = 100/570 (17%)
Query: 301 SLVHGDFVFVKLAA-ANADAKKGSIYRVEADEVILKF--AKEFHTQHRNGSLYNVSFTYN 357
S GD V + AA + G + RV V + F + +F + Y + N
Sbjct: 80 SFTSGDIVGLYDAANEGSQLATGILTRVTQKSVTVAFDESHDFQLSLDRENSYRLLKLAN 139
Query: 358 RINMRRMYQAVQAAENLEPN-------LLFPSQSTKRRSIKAAPFVPFNS-LNEEQTRSV 409
+ RR+ +A+ A + +LF +S + + P FN+ L+ Q +V
Sbjct: 140 DVTYRRLKKALIALKKYHSGPASSLIEVLF-GRSAPSPASEIHPLTFFNTCLDTSQKEAV 198
Query: 410 EIILGCKGAPPYVIYGPPGTGKTMTLVEAILQVYSTREHSRILVCAASNSAADHMLERLI 469
L K +I+GPPGTGKT T+VE ILQ + ++ ++L CA SN A D+++ERL
Sbjct: 199 LFALSQKELA--IIHGPPGTGKTTTVVEIILQ--AVKQGLKVLCCAPSNIAVDNLVERL- 253
Query: 470 SNEVAGIKENEILRLNATSRPYE-------------------------DVPTDFIRFCFF 504
+ + ILRL +R E D+ F++
Sbjct: 254 -----ALCKQRILRLGHPARLLESIQQHSLDAVLARSDSAQIVADIRKDIDQVFVKNKKT 308
Query: 505 EESIFKCPPREALGRYRIIIS----TYMSSSLLNTNGIKRGN----------------FS 544
++ K R + R + M SL + N + N F
Sbjct: 309 QDKREKSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADGPLKLLPESYFD 368
Query: 545 HIFLDEAGQASEPESMIPIANLCTKQTVVVLAGDPKQLGPVIYSKDAETFGLGKSYLERL 604
+ +DE QA E IP+ K +LAGD KQL P S A GL S +ERL
Sbjct: 369 VVVIDECAQALEASCWIPL----LKARKCILAGDHKQLPPTTVSHKAALAGLSLSLMERL 424
Query: 605 FECEFYRNGDEGYVTKLVRNYRCHPAILDLPSKLFYGGELLACKDDATSLSSAKVDIFPN 664
E R V L YR H AI+ S Y G+L A A L +
Sbjct: 425 AEEYGAR-----VVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAAT 479
Query: 665 KD--FPVLFFGIQGC--------DEREGNNPSWFNRFEVSKVVDIINKLRENTELNETDI 714
++ P+L GC DE+ NP EV V I L + + DI
Sbjct: 480 EETGVPLLLVDTAGCGLFELEEEDEQSKGNPG-----EVRLVSLHIQAL-VDAGVPARDI 533
Query: 715 GVITPYRQQVLKIKKVLETWDMPDVKVGTVEQFQGQEREVIIVSTVRSTVKHNEFDRTYC 774
V++PY QV +++ L P++++ +V+ FQG+E+E +I+S VRS +R
Sbjct: 534 AVVSPYNLQVDLLRQSL-VHRHPELEIKSVDGFQGREKEAVILSFVRS-------NRKGE 585
Query: 775 LGFLSNPRRFNVAITRARSLLIIVGNPHIV 804
+GFL+ RR NVA+TRAR + ++ + V
Sbjct: 586 VGFLAEDRRINVAVTRARRHVAVICDSRTV 615
>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 = 37.4 bits (85), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 382 SQSTKRRSIKAAPFVPF---NSLNE-----EQTRSVEIILGCKGAPPYVIYGPPGTGKTM 433
S ST++RS + P+V +L+E E +V + P + YGPPGTGKT
Sbjct: 2 STSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTS 61
Query: 434 TLVEAILQVYSTREHSRILVCAASN 458
T+V ++Y + +L AS+
Sbjct: 62 TIVALAREIYGKNYSNMVLELNASD 86
>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 353
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 413 LGCKGAPPYVIYGPPGTGKTMTLVEAILQVYS-TREHSRILVCAASNSAADHMLERLISN 471
L P + YGPPGTGKT T++ ++Y SRIL AS+ ++ + N
Sbjct: 53 LKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKN 112
>pdb|2EGU|A Chain A, Crystal Structure Of O-Acetylserine Sulfhydrase From
Geobacillus Kaustophilus Hta426
Length = 308
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 85 IRIYCSEPANSLTLSLMEPPSGKPDPQKDQGFLEGF 120
I+IY EPA+S LS GKP P K QG GF
Sbjct: 197 IKIYAVEPADSPVLS-----GGKPGPHKIQGIGAGF 227
>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|B Chain B, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|C Chain C, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|D Chain D, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
Length = 447
Score = 33.9 bits (76), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 422 VIYGPPGTGKTMTLVEAILQVYSTREHSRILVCAASNSAADHMLERLISNEVAGIKE--- 478
+++GPPGTGKT TL E I + Y+ + RI + +ER N AG +
Sbjct: 54 ILWGPPGTGKT-TLAEVIAR-YANADVERISAVTSGVKEIREAIERARQNRNAGRRTILF 111
Query: 479 -NEILRLNATSR 489
+E+ R N + +
Sbjct: 112 VDEVHRFNKSQQ 123
>pdb|3UPU|A Chain A, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
pdb|3UPU|B Chain B, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
pdb|3UPU|C Chain C, Crystal Structure Of The T4 Phage Sf1b Helicase Dda
Length = 459
Score = 33.1 bits (74), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 33/91 (36%), Positives = 47/91 (51%), Gaps = 8/91 (8%)
Query: 398 FNSLNEEQTRSVEIIL-GCKGAPPYV-IYGPPGTGKTMTLVEAILQ-VYSTREHSRILVC 454
F+ L E Q + I+ K +V I GP GTG T TL + I++ + ST E IL
Sbjct: 23 FDDLTEGQKNAFNIVXKAIKEKKHHVTINGPAGTGAT-TLTKFIIEALISTGETGIIL-- 79
Query: 455 AASNSAADHMLERLISNEVAGIKENEILRLN 485
AA AA +L +L E + I + IL++N
Sbjct: 80 AAPTHAAKKILSKLSGKEASTI--HSILKIN 108
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
Length = 3245
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 404 EQTRSVEIILGCKGAP-PYVIYGPPGTGKTMTLVEAI 439
+ TR V+++ P ++ GPPG+GKTMTL +
Sbjct: 1289 DTTRHVDVLHAWLSEHRPLILCGPPGSGKTMTLTSTL 1325
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 404 EQTRSVEIILGCKGAP-PYVIYGPPGTGKTMTLVEAI 439
+ TR V+++ P ++ GPPG+GKTMTL +
Sbjct: 1289 DTTRHVDVLHAWLSEHRPLILCGPPGSGKTMTLTSTL 1325
>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 428
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/23 (65%), Positives = 19/23 (82%), Gaps = 3/23 (13%)
Query: 419 PP--YVIYGPPGTGKTMTLVEAI 439
PP ++YGPPGTGKTM LV+A+
Sbjct: 205 PPRGVLLYGPPGTGKTM-LVKAV 226
>pdb|3MGG|A Chain A, Crystal Structure Of Methyl Transferase From
Methanosarcina Mazei
pdb|3MGG|B Chain B, Crystal Structure Of Methyl Transferase From
Methanosarcina Mazei
Length = 276
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 470 SNEVAGIKENEILRLNATSRPYEDVPTDFIRFCFFEESIFKCPPREALGRYRIII 524
+ E GIK + L+ N S P+ED D I CF E + P EAL + ++
Sbjct: 80 NTEKNGIKNVKFLQANIFSLPFEDSSFDHIFVCFVLEHL--QSPEEALKSLKKVL 132
>pdb|2VHF|A Chain A, Structure Of The Cyld Usp Domain
pdb|2VHF|B Chain B, Structure Of The Cyld Usp Domain
Length = 374
Score = 29.6 bits (65), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 695 KVVDIINKLRENTELNETDIGVITPYRQQV---LKIKKVLETWDMPDVKVGTVEQF 747
K + K+ + ELN TD+ TP + ++ L + + E +D PD+ G ++QF
Sbjct: 179 KDFKLFKKIFPSLELNITDLLEDTPRQCRICGGLAMYECRECYDDPDISAGKIKQF 234
>pdb|3BAN|A Chain A, The Crystal Structure Of Mannonate Dehydratase From
Streptococcus Suis Serotype2
pdb|3BAN|B Chain B, The Crystal Structure Of Mannonate Dehydratase From
Streptococcus Suis Serotype2
pdb|3BDK|A Chain A, Crystal Structure Of Streptococcus Suis Mannonate
Dehydratase Complexed With Substrate Analogue
pdb|3BDK|B Chain B, Crystal Structure Of Streptococcus Suis Mannonate
Dehydratase Complexed With Substrate Analogue
pdb|3DBN|A Chain A, Crystal Structure Of The Streptoccocus Suis Serotype2 D-
Mannonate Dehydratase In Complex With Its Substrate
pdb|3DBN|B Chain B, Crystal Structure Of The Streptoccocus Suis Serotype2 D-
Mannonate Dehydratase In Complex With Its Substrate
pdb|3FVM|A Chain A, Crystal Structure Of Steptococcus Suis Mannonate
Dehydratase With Metal Mn++
pdb|3FVM|B Chain B, Crystal Structure Of Steptococcus Suis Mannonate
Dehydratase With Metal Mn++
Length = 386
Score = 29.3 bits (64), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 419 PPYVIYGPPGTGKTMTLVEAILQVYSTREHSRILVCAASNSAADHMLERLISNEVAGIKE 478
PPY I+G P VE L +Y + EH+ I +C S A+D + L E A +K
Sbjct: 223 PPYGIFGLPRIITGQEAVERFLNLYDS-EHNGITMCVGS-YASDPKNDVLAMTEYA-LKR 279
Query: 479 NEI 481
N I
Sbjct: 280 NRI 282
>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In
Complex With Adp
pdb|3D8B|B Chain B, Crystal Structure Of Human Fidgetin-Like Protein 1 In
Complex With Adp
Length = 357
Score = 29.3 bits (64), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 410 EIILGCKGAPPYVI-YGPPGTGKTM 433
+I G +G P ++ +GPPGTGKT+
Sbjct: 108 DIFTGLRGPPKGILLFGPPGTGKTL 132
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 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,229,371
Number of Sequences: 62578
Number of extensions: 960893
Number of successful extensions: 2124
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2079
Number of HSP's gapped (non-prelim): 26
length of query: 806
length of database: 14,973,337
effective HSP length: 107
effective length of query: 699
effective length of database: 8,277,491
effective search space: 5785966209
effective search space used: 5785966209
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: 55 (25.8 bits)