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= 041971
(1044 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 159 bits (403), Expect = 7e-39, Method: Compositional matrix adjust.
Identities = 100/264 (37%), Positives = 146/264 (55%), Gaps = 11/264 (4%)
Query: 368 LVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLPAMVESKVSNEACFGRSLFERLSYL 427
++IDE+ Q E E +P+ L G K +L GD CQL +V K + +A +SLFERL L
Sbjct: 519 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 577
Query: 428 GYSKHLLSIQYRMHPSISCFPNSYFYENKIRDSSTVRKRSYEKRFLHGPMYGPYSFINVF 487
G L +QYRMHP++S FP++ FYE +++ T R + P F V
Sbjct: 578 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 637
Query: 488 GGREEFIEH--SCRNMVEVSVVMKILLNLYKAWIDSKEKLSIGIVSPYSAQ---VVAIQE 542
G+EE S N E + V KI L KA + IGI++PY Q +V +
Sbjct: 638 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 694
Query: 543 KLGSKYVNSAGFAVKVMSIDGFQGGEEDLIIISTVRSNNGGSIGFLSNSKRVNVALTRAR 602
GS + V++ S+D FQG E+D II+S VR+N IGFL++ +R+NVALTRAR
Sbjct: 695 FSGSLHTKLYQ-EVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRAR 753
Query: 603 HCLWILGNARTLTRKKSVWEALVH 626
+ + I+GN + L+ K+ +W L++
Sbjct: 754 YGVIIVGNPKALS-KQPLWNHLLN 776
Score = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 8/71 (11%)
Query: 28 LNDSQAQAVLSCLRQMRCDHKATIQLIWGPPGTGKTKTVSMLLVILL-QMKFRTLVCTPT 86
LN SQ AV + L++ + LI GPPGTGKT T + ++ L Q LVC P+
Sbjct: 357 LNHSQVYAVKTVLQR-------PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS 409
Query: 87 NVAIKELAARV 97
N+A+ +L ++
Sbjct: 410 NIAVDQLTEKI 420
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 159 bits (402), Expect = 7e-39, Method: Compositional matrix adjust.
Identities = 100/264 (37%), Positives = 146/264 (55%), Gaps = 11/264 (4%)
Query: 368 LVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLPAMVESKVSNEACFGRSLFERLSYL 427
++IDE+ Q E E +P+ L G K +L GD CQL +V K + +A +SLFERL L
Sbjct: 342 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 400
Query: 428 GYSKHLLSIQYRMHPSISCFPNSYFYENKIRDSSTVRKRSYEKRFLHGPMYGPYSFINVF 487
G L +QYRMHP++S FP++ FYE +++ T R + P F V
Sbjct: 401 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 460
Query: 488 GGREEFIEH--SCRNMVEVSVVMKILLNLYKAWIDSKEKLSIGIVSPYSAQ---VVAIQE 542
G+EE S N E + V KI L KA + IGI++PY Q +V +
Sbjct: 461 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 517
Query: 543 KLGSKYVNSAGFAVKVMSIDGFQGGEEDLIIISTVRSNNGGSIGFLSNSKRVNVALTRAR 602
GS + V++ S+D FQG E+D II+S VR+N IGFL++ +R+NVALTRAR
Sbjct: 518 FSGSLHTKLYQ-EVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRAR 576
Query: 603 HCLWILGNARTLTRKKSVWEALVH 626
+ + I+GN + L+ K+ +W L++
Sbjct: 577 YGVIIVGNPKALS-KQPLWNHLLN 599
Score = 46.2 bits (108), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 8/71 (11%)
Query: 28 LNDSQAQAVLSCLRQMRCDHKATIQLIWGPPGTGKTKTVSMLLVILL-QMKFRTLVCTPT 86
LN SQ AV + L++ + LI GPPGTGKT T + ++ L Q LVC P+
Sbjct: 180 LNHSQVYAVKTVLQR-------PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS 232
Query: 87 NVAIKELAARV 97
N+A+ +L ++
Sbjct: 233 NIAVDQLTEKI 243
>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 = 159 bits (402), Expect = 7e-39, Method: Compositional matrix adjust.
Identities = 100/264 (37%), Positives = 146/264 (55%), Gaps = 11/264 (4%)
Query: 368 LVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLPAMVESKVSNEACFGRSLFERLSYL 427
++IDE+ Q E E +P+ L G K +L GD CQL +V K + +A +SLFERL L
Sbjct: 343 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 401
Query: 428 GYSKHLLSIQYRMHPSISCFPNSYFYENKIRDSSTVRKRSYEKRFLHGPMYGPYSFINVF 487
G L +QYRMHP++S FP++ FYE +++ T R + P F V
Sbjct: 402 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 461
Query: 488 GGREEFIEH--SCRNMVEVSVVMKILLNLYKAWIDSKEKLSIGIVSPYSAQ---VVAIQE 542
G+EE S N E + V KI L KA + IGI++PY Q +V +
Sbjct: 462 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 518
Query: 543 KLGSKYVNSAGFAVKVMSIDGFQGGEEDLIIISTVRSNNGGSIGFLSNSKRVNVALTRAR 602
GS + V++ S+D FQG E+D II+S VR+N IGFL++ +R+NVALTRAR
Sbjct: 519 FSGSLHTKLYQ-EVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRAR 577
Query: 603 HCLWILGNARTLTRKKSVWEALVH 626
+ + I+GN + L+ K+ +W L++
Sbjct: 578 YGVIIVGNPKALS-KQPLWNHLLN 600
Score = 46.2 bits (108), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 8/71 (11%)
Query: 28 LNDSQAQAVLSCLRQMRCDHKATIQLIWGPPGTGKTKTVSMLLVILL-QMKFRTLVCTPT 86
LN SQ AV + L++ + LI GPPGTGKT T + ++ L Q LVC P+
Sbjct: 181 LNHSQVYAVKTVLQR-------PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS 233
Query: 87 NVAIKELAARV 97
N+A+ +L ++
Sbjct: 234 NIAVDQLTEKI 244
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 154 bits (389), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 96/278 (34%), Positives = 151/278 (54%), Gaps = 11/278 (3%)
Query: 368 LVIDEAAQLKESESTIPLQLSGIKHAVLFGDECQLPAMVESKVSNEACFGRSLFERLSYL 427
++IDE+ Q E E IP+ + G K +L GD QL ++ + + +A +SLFERL L
Sbjct: 521 VLIDESTQASEPECLIPI-VKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISL 579
Query: 428 GYSKHLLSIQYRMHPSISCFPNSYFYENKIRDSSTVRKRSYEKRFLHGPMYG-PYSFINV 486
G+ L +QYRM+P +S FP++ FYE +++ T+ +R+ P+ G P F
Sbjct: 580 GHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWAN 639
Query: 487 FGGREEFIEH--SCRNMVEVSVVMKILLNLYKAWIDSKEKLSIGIVSPYSAQVVAIQE-- 542
+G REE + S N +E +I+ L++ D + IG+++PY Q I +
Sbjct: 640 YG-REEISANGTSFLNRIEAMNCERIITKLFR---DGVKPEQIGVITPYEGQRAYILQYM 695
Query: 543 KLGSKYVNSAGFAVKVMSIDGFQGGEEDLIIISTVRSNNGGSIGFLSNSKRVNVALTRAR 602
++ V+V S+D FQG E+D II+S VR+N +IGFL + +R+NV LTRA+
Sbjct: 696 QMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAK 755
Query: 603 HCLWILGNARTLTRKKSVWEALVHDANARQCFFNADDD 640
+ L ILGN R+L R ++W L+ + C D
Sbjct: 756 YGLVILGNPRSLAR-NTLWNHLLIHFREKGCLVEGTLD 792
Score = 53.1 bits (126), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 51/89 (57%), Gaps = 15/89 (16%)
Query: 26 STLNDSQAQAVLSCLRQMRCDHKATIQLIWGPPGTGKTKTVSMLLVILLQM-KFRTLVCT 84
+ LN SQ+ AV L++ + LI GPPGTGKT T + ++ L ++ K R LVC
Sbjct: 359 AQLNSSQSNAVSHVLQR-------PLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCA 411
Query: 85 PTNVAIKELAA-------RVVKLVKESVE 106
P+NVA+ LAA +VV+L +S E
Sbjct: 412 PSNVAVDHLAAKLRDLGLKVVRLTAKSRE 440
>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 = 114 bits (285), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 95/316 (30%), Positives = 156/316 (49%), Gaps = 29/316 (9%)
Query: 341 LKRASLFLSTASSSYMLHSVAMEP---LNFLVIDEAAQLKESESTIPLQLSGIKHAVLFG 397
L A++ L+T + + + + P + +VIDE AQ E+ IPL + + +L G
Sbjct: 340 LTSANVVLATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKA--RKCILAG 397
Query: 398 DECQLPAMVESKVSNEACFGRSLFERLS--YLGYSKHLLSIQYRMHPSISCFPNSYFYEN 455
D QLP S + A SL ERL+ Y L++QYRMH +I + + Y
Sbjct: 398 DHKQLPPTTVSHKAALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLG 457
Query: 456 KIRDSSTVRKRSYEKRFLHGPMYG-----PYSFINVFG----GREEFIEHSCRNMVEVSV 506
++ S+V + + R L G P ++ G EE E S N EV +
Sbjct: 458 QLTAHSSVAR--HLLRDLPGVAATEETGVPLLLVDTAGCGLFELEEEDEQSKGNPGEVRL 515
Query: 507 VMKILLNLYKAWIDSKEKLSIGIVSPYSAQVVAIQEKLGSKYVNSAGFAVKVMSIDGFQG 566
V + L A + +++ I +VSPY+ QV +++ L ++ +++ S+DGFQG
Sbjct: 516 VSLHIQALVDAGVPARD---IAVVSPYNLQVDLLRQSLVHRHPE-----LEIKSVDGFQG 567
Query: 567 GEEDLIIISTVRSNNGGSIGFLSNSKRVNVALTRARHCLWILGNARTLTRK---KSVWEA 623
E++ +I+S VRSN G +GFL+ +R+NVA+TRAR + ++ ++RT+ K++ E
Sbjct: 568 REKEAVILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSRTVNNHAFLKTLVEY 627
Query: 624 LVHDANARQCFFNADD 639
R F DD
Sbjct: 628 FTQHGEVRTAFEYLDD 643
Score = 52.0 bits (123), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 47/83 (56%), Gaps = 7/83 (8%)
Query: 25 SSTLNDSQAQAVLSCLRQMRCDHKATIQLIWGPPGTGKTKTVSMLLVILLQMKFRTLVCT 84
++ L+ SQ +AVL L Q + +I GPPGTGKT TV +++ ++ + L C
Sbjct: 187 NTCLDTSQKEAVLFALSQKE------LAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCA 240
Query: 85 PTNVAIKELAARVVKLVKESVER 107
P+N+A+ L R+ L K+ + R
Sbjct: 241 PSNIAVDNLVERLA-LCKQRILR 262
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 114 bits (284), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 95/316 (30%), Positives = 156/316 (49%), Gaps = 29/316 (9%)
Query: 341 LKRASLFLSTASSSYMLHSVAMEP---LNFLVIDEAAQLKESESTIPLQLSGIKHAVLFG 397
L A++ L+T + + + + P + +VIDE AQ E+ IPL + + +L G
Sbjct: 340 LTSANVVLATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKA--RKCILAG 397
Query: 398 DECQLPAMVESKVSNEACFGRSLFERLS--YLGYSKHLLSIQYRMHPSISCFPNSYFYEN 455
D QLP S + A SL ERL+ Y L++QYRMH +I + + Y
Sbjct: 398 DHKQLPPTTVSHKAALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLG 457
Query: 456 KIRDSSTVRKRSYEKRFLHGPMYG-----PYSFINVFG----GREEFIEHSCRNMVEVSV 506
++ S+V + + R L G P ++ G EE E S N EV +
Sbjct: 458 QLTAHSSVAR--HLLRDLPGVAATEETGVPLLLVDTAGCGLFELEEEDEQSKGNPGEVRL 515
Query: 507 VMKILLNLYKAWIDSKEKLSIGIVSPYSAQVVAIQEKLGSKYVNSAGFAVKVMSIDGFQG 566
V + L A + +++ I +VSPY+ QV +++ L ++ +++ S+DGFQG
Sbjct: 516 VSLHIQALVDAGVPARD---IAVVSPYNLQVDLLRQSLVHRHPE-----LEIKSVDGFQG 567
Query: 567 GEEDLIIISTVRSNNGGSIGFLSNSKRVNVALTRARHCLWILGNARTLTRK---KSVWEA 623
E++ +I+S VRSN G +GFL+ +R+NVA+TRAR + ++ ++RT+ K++ E
Sbjct: 568 REKEAVILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSRTVNNHAFLKTLVEY 627
Query: 624 LVHDANARQCFFNADD 639
R F DD
Sbjct: 628 FTQHGEVRTAFEYLDD 643
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 47/83 (56%), Gaps = 7/83 (8%)
Query: 25 SSTLNDSQAQAVLSCLRQMRCDHKATIQLIWGPPGTGKTKTVSMLLVILLQMKFRTLVCT 84
++ L+ SQ +AVL L Q + +I GPPGTGKT TV +++ ++ + L C
Sbjct: 187 NTCLDTSQKEAVLFALSQKE------LAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCA 240
Query: 85 PTNVAIKELAARVVKLVKESVER 107
P+N+A+ L R+ L K+ + R
Sbjct: 241 PSNIAVDNLVERLA-LCKQRILR 262
>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 = 35.4 bits (80), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 16 WNETFGPSLSSTLNDSQAQ-AVLSCLRQMRCDHKATIQLIWGPPGTGKTKTVSML 69
W E + P TL++ Q V++ +R+ + K L +GPPGTGKT T+ L
Sbjct: 15 WVEKYRPE---TLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVAL 66
>pdb|1BGP|A Chain A, Crystal Structure Of Barley Grain Peroxidase 1
Length = 309
Score = 31.6 bits (70), Expect = 2.3, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 85 PTNVAIKELAARVVKLVKESVERDCRDALFFPLGDILLLGNNERLKVDSGVEEIYLDYRV 144
P N+ ++ A + V +++ +ER+CR A+ DIL L + + V G DYRV
Sbjct: 75 PPNLTLRPSAFKAVNDIRDRLERECRGAV-VSCSDILALAARDSVVVSGGP-----DYRV 128
>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 = 31.6 bits (70), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 58 PGTGKT-KTVSMLLVILLQMKFRTLVCTPTNVAIKELA 94
PG+GKT K + ++ +Q + RT V PT V E+A
Sbjct: 30 PGSGKTRKILPQIIKDAIQQRLRTAVLAPTRVVAAEMA 67
>pdb|3EVG|A Chain A, Crystal Structure Of Dengue-2 Virus Methyltransferase
Complexed With S-Adenosyl-L-Homocysteine
Length = 275
Score = 31.2 bits (69), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 495 EHSCRNMVEVSVVMKILLNLYKAWIDSKEKLSIGIVSPYSAQVVAIQEKLGSKY 548
E S VE +++L NL + W+++ + I +++PY V+ E L KY
Sbjct: 149 ESSPNPTVEAGRTLRVL-NLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKY 201
>pdb|2WV9|A Chain A, Crystal Structure Of The Ns3 Protease-Helicase From Murray
Valley Encephalitis Virus
Length = 673
Score = 31.2 bits (69), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 58 PGTGKTKTV-SMLLVILLQMKFRTLVCTPTNVAIKELAARV----VKLVKESVERD 108
PG GKT+ + ++ +Q + RT V PT V E+A + V+ + +V+R+
Sbjct: 250 PGAGKTRRILPQIIKDAIQKRLRTAVLAPTRVVAAEMAEALRGLPVRYLTPAVQRE 305
>pdb|2V8O|A Chain A, Structure Of The Murray Valley Encephalitis Virus Rna
Helicase To 1.9a Resolution
Length = 444
Score = 31.2 bits (69), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 58 PGTGKTKTV-SMLLVILLQMKFRTLVCTPTNVAIKELAARV----VKLVKESVERD 108
PG GKT+ + ++ +Q + RT V PT V E+A + V+ + +V+R+
Sbjct: 21 PGAGKTRRILPQIIKDAIQKRLRTAVLAPTRVVAAEMAEALRGLPVRYLTPAVQRE 76
>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 = 3.7, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 15/57 (26%)
Query: 53 LIWGPPGTGKTKTVSMLLVILLQMKFRTLVCTPTNVAIKELAARV--VKLVKESVER 107
++WGPPGTGKT ++ N ++ ++A VK ++E++ER
Sbjct: 54 ILWGPPGTGKTTLAE-------------VIARYANADVERISAVTSGVKEIREAIER 97
>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 = 30.8 bits (68), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 41/100 (41%), Gaps = 16/100 (16%)
Query: 16 WNETFGP-SLSSTLNDSQAQAVLS-CLRQMRCDHKATIQLIWGPPGTGKTKTVSMLLVIL 73
W E + P +L A VL L+ H L +GPPGTGKT T+ L L
Sbjct: 27 WVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH----MLFYGPPGTGKTSTILALTKEL 82
Query: 74 LQ---MKFRTLVCTPTNVAIKELAARVVKLVKESVERDCR 110
MK R L ++ R + +V+E V+ R
Sbjct: 83 YGPDLMKSRILELNASD-------ERGISIVREKVKNFAR 115
>pdb|2R7K|A Chain A, Crystal Structure Of Faicar Synthetase (Purp) From M.
Jannaschii Complexed With Amppcp And Aicar
pdb|2R7L|A Chain A, Crystal Structure Of Faicar Synthetase (Purp) From M.
Jannaschii Complexed With Atp And Aicar
pdb|2R7M|A Chain A, Crystal Structure Of Faicar Synthetase (Purp) From M.
Jannaschii Complexed With Amp
pdb|2R7N|A Chain A, Crystal Structure Of Faicar Synthetase (Purp) From M.
Jannaschii Complexed With Adp And Faicar
Length = 361
Score = 30.4 bits (67), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 721 SSLHIIKQFKVEGFYIICTIDIVKESQY--------FQVLKVWDILPLEDVPKVVARLDN 772
+SLHI+K K+EGF +C ++ Y F + + + E++ + + L++
Sbjct: 28 TSLHILKGAKLEGFSTVCITMKGRDVPYKRFKVADKFIYVDNFSDIKNEEIQEKLRELNS 87
Query: 773 IYVKYTAEFINHCKEKSIEGNLEVP 797
I V + + FI +C ++E + VP
Sbjct: 88 IVVPHGS-FIAYCGLDNVENSFLVP 111
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 30.0 bits (66), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 1/76 (1%)
Query: 13 EGVWNETFGPSLSSTLNDSQAQAVLSCLRQMRCDHKATIQLIWGPPGTGKTKTVSMLLVI 72
EG E F SL L ++Q +A M K +L+ G G+GKT + ++
Sbjct: 354 EGKLAEEFIKSLPFKLTNAQKRAHQEIRNDM-ISEKPMNRLLQGDVGSGKTVVAQLAILD 412
Query: 73 LLQMKFRTLVCTPTNV 88
+ F+T PT++
Sbjct: 413 NYEAGFQTAFMVPTSI 428
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 0.136 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,762,350
Number of Sequences: 62578
Number of extensions: 1068608
Number of successful extensions: 2665
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2626
Number of HSP's gapped (non-prelim): 28
length of query: 1044
length of database: 14,973,337
effective HSP length: 109
effective length of query: 935
effective length of database: 8,152,335
effective search space: 7622433225
effective search space used: 7622433225
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: 57 (26.6 bits)