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= 038763
(690 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 305 bits (780), Expect = 8e-83, Method: Compositional matrix adjust.
Identities = 247/698 (35%), Positives = 349/698 (50%), Gaps = 104/698 (14%)
Query: 13 LDEFTQRMSELLRIERDAELEFTQEELNAVPTPDENSDSSKPIEFLVSHGRAPQELCDTI 72
++ F + +LL +ERDAE+E + + EN ++ L S G +C +
Sbjct: 4 VESFVTKQLDLLELERDAEVEERR-------SWQENIS----LKELQSRG-----VC--L 45
Query: 73 CNLFVVSTSTGLGGMHLVLF---RVEGNHRLPPTTLSPGDMVCVRVCDSRGACATSCIQG 129
L V S TGL G LV F R LP + + GD+V + + G+ + I
Sbjct: 46 LKLQVSSQRTGLYGRLLVTFEPRRYGSAAALPSNSFTSGDIVGLYDAANEGSQLATGILT 105
Query: 130 FVHNLGEDGCTISVALESRHGDPTFSKLFGKSVRID---RIQGLADTLTYERNCEALMLL 186
V +++VA + H F +S+ + R+ LA+ +TY R +AL+ L
Sbjct: 106 RVTQ-----KSVTVAFDESHD-------FQQSLDRENSYRLLKLANDVTYRRLKKALIAL 153
Query: 187 QKNGLHKRNPSIAAVVTLFGDKEDVTWLEENDLADWSEVKLDGIMGKTFDDSQKKAIALG 246
+K + P+ + + LFG + + SE+ D SQK+A+
Sbjct: 154 KK---YHSGPASSLIEVLFG---------RSAPSPASEIHPLTFFNTCLDTSQKEAVLFA 201
Query: 247 LNKKRPLLIIQGPPGTGKTGLLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNI 306
L++K L II GPPGTGKT + EII +AV+QG +VL AP+N AVDN+VE+L+ I
Sbjct: 202 LSQKE-LAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALCKQRI 260
Query: 307 VRVGNPARISPAVASKSLGEIV-KSKLASFVAEFERKKSDLRKDLRQCL------KDDSL 359
+R+G+PAR+ ++ SL ++ +S A VA D+RKD+ Q +D
Sbjct: 261 LRLGHPARLLESIQQHSLDAVLARSDSAQIVA-------DIRKDIDQVFVKNKKTQDKRE 313
Query: 360 AAGIRXXXXXXXXXXXXXXXXXXXXXXSSAQVVLATNTGA-ADPLIRRL--DTFDLV--- 413
+ R +SA VVLATNTGA AD ++ L FD+V
Sbjct: 314 KSNFRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADGPLKLLPESYFDVVVID 373
Query: 414 ----------------GKRCILAGDQCQLAPVILSRKALEGGIGVSLLERAATLHEGVLA 457
++CILAGD QL P +S KA G+ +SL+ER A + +
Sbjct: 374 ECAQALEASCWIPLLKARKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAEEYGARVV 433
Query: 458 TKLTTQYRMNDAIASWASKEMYGGSLISSSTVASHLLVDTPFVKPTWITQCPLLLLDTRL 517
LT QYRM+ AI WAS MY G L + S+VA HLL D P V T T PLLL+DT
Sbjct: 434 RTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEETGVPLLLVDT-- 491
Query: 518 PYGSLSLGCE----EHLDLAGTGSFYNEGEAEIVVHHVFSLICAGVSPSAIAVQSPYVAQ 573
GC E D G N GE +V H+ +L+ AGV IAV SPY Q
Sbjct: 492 ------AGCGLFELEEEDEQSKG---NPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQ 542
Query: 574 VQHLRERL-DDLPEAAGVEVATIDSFQGREADAVIISMVRSNTLGAVGFLGDSRRMNVAI 632
V LR+ L PE +E+ ++D FQGRE +AVI+S VRSN G VGFL + RR+NVA+
Sbjct: 543 VDLLRQSLVHRHPE---LEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRINVAV 599
Query: 633 TRACKHVAVVCDSSTICHNTFLARLLRHIRYFGRVKHA 670
TRA +HVAV+CDS T+ ++ FL L+ + G V+ A
Sbjct: 600 TRARRHVAVICDSRTVNNHAFLKTLVEYFTQHGEVRTA 637
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 304 bits (778), Expect = 1e-82, Method: Compositional matrix adjust.
Identities = 248/695 (35%), Positives = 348/695 (50%), Gaps = 98/695 (14%)
Query: 13 LDEFTQRMSELLRIERDAELEFTQEELNAVPTPDENSDSSKPIEFLVSHGRAPQELCDTI 72
++ F + +LL +ERDAE+E + + EN ++ L S G +C +
Sbjct: 4 VESFVTKQLDLLELERDAEVEERR-------SWQENIS----LKELQSRG-----VC--L 45
Query: 73 CNLFVVSTSTGLGGMHLVLF---RVEGNHRLPPTTLSPGDMVCVRVCDSRGACATSCIQG 129
L V S TGL G LV F R LP + + GD+V + + G+ + I
Sbjct: 46 LKLQVSSQRTGLYGRLLVTFEPRRYGSAAALPSNSFTSGDIVGLYDAANEGSQLATGILT 105
Query: 130 FVHNLGEDGCTISVALESRHGDPTFSKLFGKSVRIDRIQGLADTLTYERNCEALMLLQKN 189
V +++VA + H D S S R+ + LA+ +TY R +AL+ L+K
Sbjct: 106 RVTQ-----KSVTVAFDESH-DFQLSLDRENSYRLLK---LANDVTYRRLKKALIALKK- 155
Query: 190 GLHKRNPSIAAVVTLFGDKEDVTWLEENDLADWSEVKLDGIMGKTFDDSQKKAIALGLNK 249
+ P+ + + LFG + + SE+ D SQK+A+ L++
Sbjct: 156 --YHSGPASSLIEVLFG---------RSAPSPASEIHPLTFFNTCLDTSQKEAVLFALSQ 204
Query: 250 KRPLLIIQGPPGTGKTGLLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIVRV 309
K L II GPPGTGKT + EII +AV+QG +VL AP+N AVDN+VE+L+ I+R+
Sbjct: 205 KE-LAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALCKQRILRL 263
Query: 310 GNPARISPAVASKSLGEIV-KSKLASFVAEFERKKSDLRKDLRQCL------KDDSLAAG 362
G+PAR+ ++ SL ++ +S A VA D+RKD+ Q +D +
Sbjct: 264 GHPARLLESIQQHSLDAVLARSDSAQIVA-------DIRKDIDQVFVKNKKTQDKREKSN 316
Query: 363 IRXXXXXXXXXXXXXXXXXXXXXXSSAQVVLATNTGA-ADPLIRRL--DTFDLV------ 413
R +SA VVLATNTGA AD ++ L FD+V
Sbjct: 317 FRNEIKLLRKELKEREEAAMLESLTSANVVLATNTGASADGPLKLLPESYFDVVVIDECA 376
Query: 414 -------------GKRCILAGDQCQLAPVILSRKALEGGIGVSLLERAATLHEGVLATKL 460
++CILAGD QL P +S KA G+ +SL+ER A + + L
Sbjct: 377 QALEASCWIPLLKARKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLAEEYGARVVRTL 436
Query: 461 TTQYRMNDAIASWASKEMYGGSLISSSTVASHLLVDTPFVKPTWITQCPLLLLDTRLPYG 520
T QYRM+ AI WAS MY G L + S+VA HLL D P V T T PLLL+DT
Sbjct: 437 TVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEETGVPLLLVDT----- 491
Query: 521 SLSLGCE----EHLDLAGTGSFYNEGEAEIVVHHVFSLICAGVSPSAIAVQSPYVAQVQH 576
GC E D G N GE +V H+ +L+ AGV IAV SPY QV
Sbjct: 492 ---AGCGLFELEEEDEQSKG---NPGEVRLVSLHIQALVDAGVPARDIAVVSPYNLQVDL 545
Query: 577 LRERL-DDLPEAAGVEVATIDSFQGREADAVIISMVRSNTLGAVGFLGDSRRMNVAITRA 635
LR+ L PE +E+ ++D FQGRE +AVI+S VRSN G VGFL + RR+NVA+TRA
Sbjct: 546 LRQSLVHRHPE---LEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRINVAVTRA 602
Query: 636 CKHVAVVCDSSTICHNTFLARLLRHIRYFGRVKHA 670
+HVAV+CDS T+ ++ FL L+ + G V+ A
Sbjct: 603 RRHVAVICDSRTVNNHAFLKTLVEYFTQHGEVRTA 637
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 180 bits (456), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 149/460 (32%), Positives = 216/460 (46%), Gaps = 65/460 (14%)
Query: 235 FDDSQKKAIALGLNKKRPLLIIQGPPGTGKTGLLKEIIARAVQ-QGERVLVTAPTNAAVD 293
+ SQ A++ L +RPL +IQGPPGTGKT I+ + +R+LV AP+N AVD
Sbjct: 361 LNSSQSNAVSHVL--QRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVD 418
Query: 294 NMVEKLSDVGLNIVRVGNPAR--ISPAVASKSLGEIVKSKLASFVAEFERKKSDLRKDLR 351
++ KL D+GL +VR+ +R + +V++ +L +V K +L+ L+
Sbjct: 419 HLAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLVGRG----------AKGELKNLLK 468
Query: 352 QCLKDDSLAAGIRXXXXXXXXXXXXXXXXXXXXXXSSAQVVLATNTGAADPLIRRLDT-F 410
LKD+ + + A VV T GA D +RLDT F
Sbjct: 469 --LKDE-----VGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGD---KRLDTKF 518
Query: 411 DLV--------------------GKRCILAGDQCQLAPVILSRKALEGGIGVSLLERAAT 450
V K+ IL GD QL PVIL RKA + G+ SL ER +
Sbjct: 519 RTVLIDESTQASEPECLIPIVKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLIS 578
Query: 451 LHEGVLATKLTTQYRMNDAIASWASKEMYGGSLISSSTVASHLLVDTPFVKPTWITQCPL 510
L G + +L QYRMN ++ + S Y GSL + T+ + ++ F P I P+
Sbjct: 579 L--GHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWP--IRGIPM 634
Query: 511 LLLDTRLPYGSLSLGCEEHLDLAGTGSFYNEGEAEIVVHHVFSLICAGVSPSAIAVQSPY 570
+ YG E + GT SF N EA + L GV P I V +PY
Sbjct: 635 MFWAN---YG------REEISANGT-SFLNRIEAMNCERIITKLFRDGVKPEQIGVITPY 684
Query: 571 VAQVQHLRERLD-----DLPEAAGVEVATIDSFQGREADAVIISMVRSNTLGAVGFLGDS 625
Q ++ + + D VEVA++D+FQGRE D +I+S VR+N A+GFL D
Sbjct: 685 EGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDP 744
Query: 626 RRMNVAITRACKHVAVVCDSSTICHNTFLARLLRHIRYFG 665
RR+NV +TRA + ++ + ++ NT LL H R G
Sbjct: 745 RRLNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFREKG 784
>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 = 171 bits (432), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 133/441 (30%), Positives = 200/441 (45%), Gaps = 59/441 (13%)
Query: 250 KRPLLIIQGPPGTGKTGLLKEIIARAVQQGE-RVLVTAPTNAAVDNMVEKLSDVGLNIVR 308
+RPL +IQGPPGTGKT I+ +QG VLV AP+N AVD + EK+ GL +VR
Sbjct: 194 QRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVR 253
Query: 309 VGNPARISPAVASKSLGEIVKSKLASFVAEFERKKSDLRKDLR--QCLKDDSLAAGIRXX 366
+ +R E + S ++ + + D +L+ Q LKD++
Sbjct: 254 LCAKSR-----------EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDET-----GEL 297
Query: 367 XXXXXXXXXXXXXXXXXXXXSSAQVVLATNTGAADPLIRRLDTFDLV------------- 413
+A V+ T GA DP + ++ ++
Sbjct: 298 SSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECM 357
Query: 414 ------GKRCILAGDQCQLAPVILSRKALEGGIGVSLLERAATLHEGVLATKLTTQYRMN 467
K+ IL GD CQL PV++ +KA + G+ SL ER L G+ +L QYRM+
Sbjct: 358 VPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL--GIRPIRLQVQYRMH 415
Query: 468 DAIASWASKEMYGGSLISSSTVASHLLVDTPFVKPTWITQCPLLLLDTRLPYGSLSLGCE 527
A++++ S Y GSL + T A + F P P+ T+ G E
Sbjct: 416 PALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQ--PDKPMFFYVTQ--------GQE 465
Query: 528 EHLDLAGTG-SFYNEGEAEIVVHHVFSLICAGVSPSAIAVQSPYVAQVQHLRERLD---- 582
E +A +G S+ N EA V L+ AG P I + +PY Q +L + +
Sbjct: 466 E---IASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGS 522
Query: 583 -DLPEAAGVEVATIDSFQGREADAVIISMVRSNTLGAVGFLGDSRRMNVAITRACKHVAV 641
VE+A++D+FQGRE D +I+S VR+N +GFL D RR+NVA+TRA V +
Sbjct: 523 LHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVII 582
Query: 642 VCDSSTICHNTFLARLLRHIR 662
V + + LL + +
Sbjct: 583 VGNPKALSKQPLWNHLLNYYK 603
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 171 bits (432), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 133/441 (30%), Positives = 200/441 (45%), Gaps = 59/441 (13%)
Query: 250 KRPLLIIQGPPGTGKTGLLKEIIARAVQQGE-RVLVTAPTNAAVDNMVEKLSDVGLNIVR 308
+RPL +IQGPPGTGKT I+ +QG VLV AP+N AVD + EK+ GL +VR
Sbjct: 193 QRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVR 252
Query: 309 VGNPARISPAVASKSLGEIVKSKLASFVAEFERKKSDLRKDLR--QCLKDDSLAAGIRXX 366
+ +R E + S ++ + + D +L+ Q LKD++
Sbjct: 253 LCAKSR-----------EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDET-----GEL 296
Query: 367 XXXXXXXXXXXXXXXXXXXXSSAQVVLATNTGAADPLIRRLDTFDLV------------- 413
+A V+ T GA DP + ++ ++
Sbjct: 297 SSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECM 356
Query: 414 ------GKRCILAGDQCQLAPVILSRKALEGGIGVSLLERAATLHEGVLATKLTTQYRMN 467
K+ IL GD CQL PV++ +KA + G+ SL ER L G+ +L QYRM+
Sbjct: 357 VPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL--GIRPIRLQVQYRMH 414
Query: 468 DAIASWASKEMYGGSLISSSTVASHLLVDTPFVKPTWITQCPLLLLDTRLPYGSLSLGCE 527
A++++ S Y GSL + T A + F P P+ T+ G E
Sbjct: 415 PALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQ--PDKPMFFYVTQ--------GQE 464
Query: 528 EHLDLAGTG-SFYNEGEAEIVVHHVFSLICAGVSPSAIAVQSPYVAQVQHLRERLD---- 582
E +A +G S+ N EA V L+ AG P I + +PY Q +L + +
Sbjct: 465 E---IASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGS 521
Query: 583 -DLPEAAGVEVATIDSFQGREADAVIISMVRSNTLGAVGFLGDSRRMNVAITRACKHVAV 641
VE+A++D+FQGRE D +I+S VR+N +GFL D RR+NVA+TRA V +
Sbjct: 522 LHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVII 581
Query: 642 VCDSSTICHNTFLARLLRHIR 662
V + + LL + +
Sbjct: 582 VGNPKALSKQPLWNHLLNYYK 602
>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 = 170 bits (431), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 133/441 (30%), Positives = 200/441 (45%), Gaps = 59/441 (13%)
Query: 250 KRPLLIIQGPPGTGKTGLLKEIIARAVQQGE-RVLVTAPTNAAVDNMVEKLSDVGLNIVR 308
+RPL +IQGPPGTGKT I+ +QG VLV AP+N AVD + EK+ GL +VR
Sbjct: 370 QRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVR 429
Query: 309 VGNPARISPAVASKSLGEIVKSKLASFVAEFERKKSDLRKDLR--QCLKDDSLAAGIRXX 366
+ +R E + S ++ + + D +L+ Q LKD++
Sbjct: 430 LCAKSR-----------EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDET-----GEL 473
Query: 367 XXXXXXXXXXXXXXXXXXXXSSAQVVLATNTGAADPLIRRLDTFDLV------------- 413
+A V+ T GA DP + ++ ++
Sbjct: 474 SSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECM 533
Query: 414 ------GKRCILAGDQCQLAPVILSRKALEGGIGVSLLERAATLHEGVLATKLTTQYRMN 467
K+ IL GD CQL PV++ +KA + G+ SL ER L G+ +L QYRM+
Sbjct: 534 VPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL--GIRPIRLQVQYRMH 591
Query: 468 DAIASWASKEMYGGSLISSSTVASHLLVDTPFVKPTWITQCPLLLLDTRLPYGSLSLGCE 527
A++++ S Y GSL + T A + F P P+ T+ G E
Sbjct: 592 PALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQ--PDKPMFFYVTQ--------GQE 641
Query: 528 EHLDLAGTG-SFYNEGEAEIVVHHVFSLICAGVSPSAIAVQSPYVAQVQHLRERLD---- 582
E +A +G S+ N EA V L+ AG P I + +PY Q +L + +
Sbjct: 642 E---IASSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGS 698
Query: 583 -DLPEAAGVEVATIDSFQGREADAVIISMVRSNTLGAVGFLGDSRRMNVAITRACKHVAV 641
VE+A++D+FQGRE D +I+S VR+N +GFL D RR+NVA+TRA V +
Sbjct: 699 LHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVII 758
Query: 642 VCDSSTICHNTFLARLLRHIR 662
V + + LL + +
Sbjct: 759 VGNPKALSKQPLWNHLLNYYK 779
>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 = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 8/74 (10%)
Query: 234 TFDD---SQKKAIAL---GLNKKRPLLIIQGPPGTGKTGLLKEIIARAVQQGER-VLVTA 286
TFDD QK A + + +K+ + I GP GTG T L K II + GE +++ A
Sbjct: 22 TFDDLTEGQKNAFNIVXKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAA 81
Query: 287 PTNAAVDNMVEKLS 300
PT+AA ++ KLS
Sbjct: 82 PTHAA-KKILSKLS 94
>pdb|2WV9|A Chain A, Crystal Structure Of The Ns3 Protease-Helicase From Murray
Valley Encephalitis Virus
Length = 673
Score = 37.7 bits (86), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 34/102 (33%), Positives = 49/102 (48%), Gaps = 12/102 (11%)
Query: 230 IMGKTFDDSQKKAIALGLNKKRPLLIIQGPPGTGKTG-LLKEIIARAVQQGERVLVTAPT 288
+ G+ ++ +A + KKR L ++ PG GKT +L +II A+Q+ R V APT
Sbjct: 220 VQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPT 279
Query: 289 NAAVDNMVEKLSDVGLNIVRVGNPAR-ISPAVASKSLG-EIV 328
M E L G P R ++PAV + G EIV
Sbjct: 280 RVVAAEMAEALR---------GLPVRYLTPAVQREHSGNEIV 312
>pdb|2V8O|A Chain A, Structure Of The Murray Valley Encephalitis Virus Rna
Helicase To 1.9a Resolution
Length = 444
Score = 37.7 bits (86), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 32/83 (38%), Positives = 41/83 (49%), Gaps = 12/83 (14%)
Query: 249 KKRPLLIIQGPPGTGKTG-LLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIV 307
KKR L ++ PG GKT +L +II A+Q+ R V APT M E L
Sbjct: 10 KKRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPTRVVAAEMAEALR------- 62
Query: 308 RVGNPAR-ISPAVASKSLG-EIV 328
G P R ++PAV + G EIV
Sbjct: 63 --GLPVRYLTPAVQREHSGNEIV 83
>pdb|2Z83|A Chain A, Crystal Structure Of Catalytic Domain Of Japanese
Encephalitis Virus Ns3 HelicaseNUCLEOSIDE TRIPHOSPHATASE
At A Resolution 1.8
Length = 459
Score = 37.0 bits (84), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 249 KKRPLLIIQGPPGTGKT-GLLKEIIARAVQQGERVLVTAPTNAAVDNMVEKL 299
+KR + ++ PG+GKT +L +II A+QQ R V APT M E L
Sbjct: 19 RKRQMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLAPTRVVAAEMAEAL 70
>pdb|2BHR|A Chain A, Dengue Virus Rna Helicase
pdb|2BHR|B Chain B, Dengue Virus Rna Helicase
pdb|2BMF|A Chain A, Dengue Virus Rna Helicase At 2.4a
pdb|2BMF|B Chain B, Dengue Virus Rna Helicase At 2.4a
Length = 451
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 249 KKRPLLIIQGPPGTGKTG-LLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIV 307
+K+ L I+ PG GKT L I+ A+++G R L+ APT M E L GL I
Sbjct: 17 RKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALR--GLPI- 73
Query: 308 RVGNPA 313
R PA
Sbjct: 74 RYQTPA 79
>pdb|2GBW|A Chain A, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1
pdb|2GBW|C Chain C, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1
pdb|2GBW|E Chain E, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1
pdb|2GBX|A Chain A, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1 Bound To Biphenyl
pdb|2GBX|C Chain C, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1 Bound To Biphenyl
pdb|2GBX|E Chain E, Crystal Structure Of Biphenyl 2,3-Dioxygenase From
Sphingomonas Yanoikuyae B1 Bound To Biphenyl
Length = 454
Score = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 108 GDMVCVRVCDSRGACATSC-IQGFVHNLGEDGCTISVALESR--HGDPTFSKLFGKSVRI 164
G+ +C DS A A C G+V G+DG + V LESR H KL KSVR+
Sbjct: 84 GNQICH--ADSGNAKAFVCNYHGWV--FGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRV 139
Query: 165 DRIQGL 170
+ +G
Sbjct: 140 ETYKGF 145
>pdb|2JLS|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Adp
Length = 451
Score = 33.1 bits (74), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 40/83 (48%), Gaps = 12/83 (14%)
Query: 249 KKRPLLIIQGPPGTGKTG-LLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIV 307
+K+ L I+ PG GKT +L I+ A+++ R L+ APT M E L
Sbjct: 17 RKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALR------- 69
Query: 308 RVGNPARI-SPAVASKSLG-EIV 328
G P R +PAV S G EIV
Sbjct: 70 --GLPIRYQTPAVKSDHTGREIV 90
>pdb|2JLR|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Amppnp
Length = 451
Score = 33.1 bits (74), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 40/83 (48%), Gaps = 12/83 (14%)
Query: 249 KKRPLLIIQGPPGTGKTG-LLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIV 307
+K+ L I+ PG GKT +L I+ A+++ R L+ APT M E L
Sbjct: 17 RKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALR------- 69
Query: 308 RVGNPARI-SPAVASKSLG-EIV 328
G P R +PAV S G EIV
Sbjct: 70 --GLPIRYQTPAVKSDHTGREIV 90
>pdb|2JLU|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna
pdb|2JLU|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna
pdb|2JLV|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And
Amppnp
pdb|2JLV|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And
Amppnp
pdb|2JLW|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna2
pdb|2JLW|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna2
pdb|2JLX|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And Adp-
Vanadate
pdb|2JLX|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And Adp-
Vanadate
pdb|2JLZ|A Chain A, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And Adp
pdb|2JLZ|B Chain B, Dengue Virus 4 Ns3 Helicase In Complex With Ssrna And Adp
Length = 451
Score = 33.1 bits (74), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 40/83 (48%), Gaps = 12/83 (14%)
Query: 249 KKRPLLIIQGPPGTGKTG-LLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIV 307
+K+ L I+ PG GKT +L I+ A+++ R L+ APT M E L
Sbjct: 17 RKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALR------- 69
Query: 308 RVGNPARI-SPAVASKSLG-EIV 328
G P R +PAV S G EIV
Sbjct: 70 --GLPIRYQTPAVKSDHTGREIV 90
>pdb|2VBC|A Chain A, Crystal Structure Of The Ns3 Protease-Helicase From Dengue
Virus
Length = 618
Score = 32.7 bits (73), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 40/83 (48%), Gaps = 12/83 (14%)
Query: 249 KKRPLLIIQGPPGTGKTG-LLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIV 307
+K+ L I+ PG GKT +L I+ A+++ R L+ APT M E L
Sbjct: 184 RKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALR------- 236
Query: 308 RVGNPARI-SPAVASKSLG-EIV 328
G P R +PAV S G EIV
Sbjct: 237 --GLPIRYQTPAVKSDHTGREIV 257
>pdb|2WZQ|A Chain A, Insertion Mutant E173gp174 Of The Ns3 Protease-Helicase
From Dengue Virus
Length = 619
Score = 32.7 bits (73), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 40/83 (48%), Gaps = 12/83 (14%)
Query: 249 KKRPLLIIQGPPGTGKTG-LLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIV 307
+K+ L I+ PG GKT +L I+ A+++ R L+ APT M E L
Sbjct: 185 RKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALR------- 237
Query: 308 RVGNPARI-SPAVASKSLG-EIV 328
G P R +PAV S G EIV
Sbjct: 238 --GLPIRYQTPAVKSDHTGREIV 258
>pdb|2WHX|A Chain A, A Second Conformation Of The Ns3 Protease-Helicase From
Dengue Virus
Length = 618
Score = 32.7 bits (73), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 40/83 (48%), Gaps = 12/83 (14%)
Query: 249 KKRPLLIIQGPPGTGKTG-LLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIV 307
+K+ L I+ PG GKT +L I+ A+++ R L+ APT M E L
Sbjct: 184 RKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALR------- 236
Query: 308 RVGNPARI-SPAVASKSLG-EIV 328
G P R +PAV S G EIV
Sbjct: 237 --GLPIRYQTPAVKSDHTGREIV 257
>pdb|2CKF|A Chain A, Crystal Structure Of The Terminal Component Of The Pah-
Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1
pdb|2CKF|C Chain C, Crystal Structure Of The Terminal Component Of The Pah-
Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1
pdb|2CKF|E Chain E, Crystal Structure Of The Terminal Component Of The Pah-
Hydroxylating Dioxygenase From Sphingomonas Sp Chy-1
Length = 454
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 108 GDMVCVRVCDSRGACATSC-IQGFVHNLGEDGCTISVALESR--HGDPTFSKLFGKSVRI 164
G+ +C DS A A C G+V+ G+DG + V LESR H +L KSVR+
Sbjct: 84 GNQICH--ADSGNAKAFVCNYHGWVY--GQDGSLVDVPLESRCYHNKLDKQELAAKSVRV 139
Query: 165 DRIQGL 170
+ +G
Sbjct: 140 ETYKGF 145
>pdb|4AG5|A Chain A, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
pdb|4AG5|B Chain B, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
pdb|4AG5|C Chain C, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
pdb|4AG5|D Chain D, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
Length = 392
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 256 IQGPPGTGKTGLLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIVRVGNPARI 315
I PG GK+ K ++ R QG RV++ P M KL V +N G +I
Sbjct: 40 ILAKPGAGKSFTAKMLLLREYMQGSRVIIIDPER-EYKEMCRKLGGVWINC--TGGEGKI 96
Query: 316 SP 317
+P
Sbjct: 97 NP 98
>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 = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/21 (66%), Positives = 17/21 (80%), Gaps = 1/21 (4%)
Query: 254 LIIQGPPGTGKTGLLKEIIAR 274
+I+ GPPGTGKT L E+IAR
Sbjct: 53 MILWGPPGTGKT-TLAEVIAR 72
>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 = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 13/72 (18%)
Query: 208 KEDVTWLEENDLADWSEVKLDGIMGKT-FDDSQKKAIALGLNKKRPLLIIQGPPGTGKT- 265
KE++ W+E+ + LD + G+ + +K + G K P L+ GPPGTGKT
Sbjct: 10 KENLPWVEK-----YRPETLDEVYGQNEVITTVRKFVDEG---KLPHLLFYGPPGTGKTS 61
Query: 266 ---GLLKEIIAR 274
L +EI +
Sbjct: 62 TIVALAREIYGK 73
>pdb|4HSE|A Chain A, Crystal Structure Of Clpb Nbd1 In Complex With Guanidinium
Chloride And Adp
Length = 397
Score = 30.4 bits (67), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 223 SEVKLDGIMGKTFDDSQKKAIALGLNKKRPLLIIQGPPGTGKTGLLKEIIARAVQ 277
+E KLD ++G+ + + I L K P+LI G PG GKT +++ + R V+
Sbjct: 28 AEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLI--GEPGVGKTAIVEGLAQRIVK 80
>pdb|1QVR|A Chain A, Crystal Structure Analysis Of Clpb
pdb|1QVR|B Chain B, Crystal Structure Analysis Of Clpb
pdb|1QVR|C Chain C, Crystal Structure Analysis Of Clpb
Length = 854
Score = 30.4 bits (67), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 223 SEVKLDGIMGKTFDDSQKKAIALGLNKKRPLLIIQGPPGTGKTGLLKEIIARAVQ 277
+E KLD ++G+ + + I L K P+LI G PG GKT +++ + R V+
Sbjct: 165 AEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLI--GEPGVGKTAIVEGLAQRIVK 217
>pdb|2NN6|G Chain G, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 289
Score = 30.4 bits (67), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 633 TRACKHVAVVCDSS-TICHNTFLARLLRHIRYFGRVKHAEPGSFGGSGL 680
RAC V VVC C + L + GR++H EPGS G G+
Sbjct: 71 ARACSRVRVVCGPGLRRCGDRLL------VTKCGRLRHKEPGSGSGGGV 113
>pdb|1E9R|A Chain A, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Trigonal Form In Complex With Sulphate.
pdb|1E9R|B Chain B, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Trigonal Form In Complex With Sulphate.
pdb|1E9R|D Chain D, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Trigonal Form In Complex With Sulphate.
pdb|1E9R|E Chain E, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Trigonal Form In Complex With Sulphate.
pdb|1E9R|F Chain F, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Trigonal Form In Complex With Sulphate.
pdb|1E9R|G Chain G, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Trigonal Form In Complex With Sulphate.
pdb|1E9S|A Chain A, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|B Chain B, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|D Chain D, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|E Chain E, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|F Chain F, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|G Chain G, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|H Chain H, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|I Chain I, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|J Chain J, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|K Chain K, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|L Chain L, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1E9S|M Chain M, Bacterial Conjugative Coupling Protein Trwbdeltan70.
Unbound Monoclinic Form.
pdb|1GKI|A Chain A, Plasmid Coupling Protein Trwb In Complex With Adp And
Mg2+.
pdb|1GKI|B Chain B, Plasmid Coupling Protein Trwb In Complex With Adp And
Mg2+.
pdb|1GKI|D Chain D, Plasmid Coupling Protein Trwb In Complex With Adp And
Mg2+.
pdb|1GKI|E Chain E, Plasmid Coupling Protein Trwb In Complex With Adp And
Mg2+.
pdb|1GKI|F Chain F, Plasmid Coupling Protein Trwb In Complex With Adp And
Mg2+.
pdb|1GKI|G Chain G, Plasmid Coupling Protein Trwb In Complex With Adp And
Mg2+.
pdb|1GL7|A Chain A, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolisable Atp-Analogue Adpnp.
pdb|1GL7|B Chain B, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolisable Atp-Analogue Adpnp.
pdb|1GL7|D Chain D, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolisable Atp-Analogue Adpnp.
pdb|1GL7|E Chain E, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolisable Atp-Analogue Adpnp.
pdb|1GL7|F Chain F, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolisable Atp-Analogue Adpnp.
pdb|1GL7|G Chain G, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolisable Atp-Analogue Adpnp
Length = 437
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 254 LIIQGPPGTGKTGLLKEIIARAVQQGERVLVTAPT 288
L++ G GTGK+ LL+E+ + +G+R+++ P
Sbjct: 56 LLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPN 90
>pdb|1GL6|A Chain A, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolysable Gtp Analogue Gdpnp
pdb|1GL6|B Chain B, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolysable Gtp Analogue Gdpnp
pdb|1GL6|D Chain D, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolysable Gtp Analogue Gdpnp
pdb|1GL6|E Chain E, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolysable Gtp Analogue Gdpnp
pdb|1GL6|F Chain F, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolysable Gtp Analogue Gdpnp
pdb|1GL6|G Chain G, Plasmid Coupling Protein Trwb In Complex With The Non-
Hydrolysable Gtp Analogue Gdpnp
Length = 436
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 254 LIIQGPPGTGKTGLLKEIIARAVQQGERVLVTAPT 288
L++ G GTGK+ LL+E+ + +G+R+++ P
Sbjct: 55 LLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPN 89
>pdb|3M6A|A Chain A, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|B Chain B, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|C Chain C, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|D Chain D, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|E Chain E, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
pdb|3M6A|F Chain F, Crystal Structure Of Bacillus Subtilis Lon C-Terminal
Domain
Length = 543
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 250 KRPLLIIQGPPGTGKTGLLKEI 271
K P+L + GPPG GKT L K I
Sbjct: 107 KGPILCLAGPPGVGKTSLAKSI 128
>pdb|1YE8|A Chain A, Crystal Structure Of Thep1 From The Hyperthermophile
Aquifex Aeolicus
Length = 178
Score = 29.6 bits (65), Expect = 5.8, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 254 LIIQGPPGTGKTGLLKEIIAR 274
+II G PG GKT L+K+I+ R
Sbjct: 3 IIITGEPGVGKTTLVKKIVER 23
>pdb|4DWJ|A Chain A, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|B Chain B, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|C Chain C, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|D Chain D, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|E Chain E, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|F Chain F, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|G Chain G, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4DWJ|H Chain H, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With Thymidine
Monophosphate
pdb|4EAQ|A Chain A, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With
3'-Azido-3'-Deoxythymidine-5'-Monophosphate
pdb|4EAQ|B Chain B, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Complex With
3'-Azido-3'-Deoxythymidine-5'-Monophosphate
pdb|4F4I|A Chain A, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Apo-Form
pdb|4F4I|B Chain B, Crystal Structure Of Thymidylate Kinase From
Staphylococcus Aureus In Apo-Form
Length = 229
Score = 29.6 bits (65), Expect = 5.9, Method: Composition-based stats.
Identities = 12/52 (23%), Positives = 24/52 (46%)
Query: 248 NKKRPLLIIQGPPGTGKTGLLKEIIARAVQQGERVLVTAPTNAAVDNMVEKL 299
N + +GP G+GKT ++ E+ R V+ + ++ P + K+
Sbjct: 23 NAMSAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKI 74
>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C-
Terminal Aaa-Atpase Domain
Length = 274
Score = 29.3 bits (64), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 210 DVTWLEENDLADWSEVKLDGIMGKTFDDSQKKAIALGLNKKRPLLIIQGPPGTGKTGLLK 269
+VTW + L D E I+ + Q KA+ L +++ GPPG GKT L K
Sbjct: 6 NVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAG---VLLAGPPGCGKTLLAK 62
Query: 270 EI 271
+
Sbjct: 63 AV 64
>pdb|2FYF|A Chain A, Structure Of A Putative Phosphoserine Aminotransferase
From Mycobacterium Tuberculosis
pdb|2FYF|B Chain B, Structure Of A Putative Phosphoserine Aminotransferase
From Mycobacterium Tuberculosis
pdb|3VOM|A Chain A, Structure Of A Putative Phosphoserine Aminotransferase
From Mycobacterium Tuberculosis
pdb|3VOM|B Chain B, Structure Of A Putative Phosphoserine Aminotransferase
From Mycobacterium Tuberculosis
Length = 398
Score = 29.3 bits (64), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 43/208 (20%), Positives = 78/208 (37%), Gaps = 27/208 (12%)
Query: 33 EFTQEELNAVPTPDENSDSSKPIEFLVSHGRAPQELCDTICNLFVVSTSTGLGGMHLVLF 92
EF+ + +AV +N +PI G AP+ D ++ + + G+ + +
Sbjct: 129 EFSAKFASAV---SKNPFVGEPIIITSDPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVR 185
Query: 93 RVEGNHRLPPTTLSPGDMVCVRVCDSRGACATSCIQGFVHNLGEDGCTISVALESRHGDP 152
R EG+ + V D ATS G ++ E ++ D
Sbjct: 186 RPEGSDD------------ALVVID-----ATSGAGGLPVDIAETDAYYFAPQKNFASDG 228
Query: 153 TFSKLFGKSVRIDRIQGLADTLTYERNCEALMLLQKNGLHKRNPSIAAVVTLFGDKEDVT 212
+ RI+ +A T + + +L + +N L + + A+ TL E +
Sbjct: 229 GLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKNQTYNTPAIATLALLAEQID 288
Query: 213 WLEENDLADWSEVKLDGIMGKTFDDSQK 240
WL N DW+ + +T D SQ+
Sbjct: 289 WLVGNGGLDWA-------VKRTADSSQR 309
>pdb|4AG6|A Chain A, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
pdb|4AG6|B Chain B, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
pdb|4AG6|C Chain C, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
pdb|4AG6|D Chain D, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
Length = 392
Score = 28.9 bits (63), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 256 IQGPPGTGKTGLLKEIIARAVQQGERVLVTAPTNAAVDNMVEKLSDVGLNIVRVGNPARI 315
I PG GK+ K ++ R QG RV++ P KL V +N G +I
Sbjct: 40 ILAKPGAGKSFTAKXLLLREYXQGSRVIIIDPER-EYKEXCRKLGGVWINC--TGGEGKI 96
Query: 316 SP 317
+P
Sbjct: 97 NP 98
>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
pdb|3CF1|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
pdb|3CF1|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
pdb|3CF2|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF2|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF2|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF2|D Chain D, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF3|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADP
pdb|3CF3|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADP
pdb|3CF3|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADP
Length = 806
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 22/33 (66%), Gaps = 6/33 (18%)
Query: 244 ALGLNKKRPLLIIQGPPGTGKTGLLKEIIARAV 276
A+G+ R +L+ GPPGTGKT +IARAV
Sbjct: 232 AIGVKPPRGILLY-GPPGTGKT-----LIARAV 258
>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A
Length = 816
Score = 28.9 bits (63), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 22/33 (66%), Gaps = 6/33 (18%)
Query: 244 ALGLNKKRPLLIIQGPPGTGKTGLLKEIIARAV 276
A+G+ R +L+ GPPGTGKT +IARAV
Sbjct: 232 AIGVKPPRGILLY-GPPGTGKT-----LIARAV 258
>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs
pdb|3HU3|B Chain B, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs
Length = 489
Score = 28.9 bits (63), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 22/33 (66%), Gaps = 6/33 (18%)
Query: 244 ALGLNKKRPLLIIQGPPGTGKTGLLKEIIARAV 276
A+G+ R +L+ GPPGTGKT +IARAV
Sbjct: 232 AIGVKPPRGILLY-GPPGTGKT-----LIARAV 258
>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
pdb|3HU2|B Chain B, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
pdb|3HU2|C Chain C, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
pdb|3HU2|D Chain D, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
pdb|3HU2|E Chain E, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
pdb|3HU2|F Chain F, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs
Length = 489
Score = 28.9 bits (63), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 22/33 (66%), Gaps = 6/33 (18%)
Query: 244 ALGLNKKRPLLIIQGPPGTGKTGLLKEIIARAV 276
A+G+ R +L+ GPPGTGKT +IARAV
Sbjct: 232 AIGVKPPRGILLY-GPPGTGKT-----LIARAV 258
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
0.319 0.135 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,289,583
Number of Sequences: 62578
Number of extensions: 773292
Number of successful extensions: 2513
Number of sequences better than 100.0: 54
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 37
Number of HSP's that attempted gapping in prelim test: 2447
Number of HSP's gapped (non-prelim): 72
length of query: 690
length of database: 14,973,337
effective HSP length: 106
effective length of query: 584
effective length of database: 8,340,069
effective search space: 4870600296
effective search space used: 4870600296
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)