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= 003873
(790 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1SXJ|A Chain A, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 516
Score = 191 bits (484), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 139/425 (32%), Positives = 205/425 (48%), Gaps = 38/425 (8%)
Query: 346 WTEKYRPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQ---NDASAEKAAIL 402
WT KY P ++ GN+ V +L WLA+W +K+N K + + +AA+L
Sbjct: 29 WTVKYAPTNLQQVCGNKGSVMKLKNWLANWEN------SKKNSFKHAGKDGSGVFRAAML 82
Query: 403 SGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKA--DAKISKGIGGSNANSIKELVSNE 460
G PG+GKTTAA LV Q LG+ +E NASD R K +A + + N + + NE
Sbjct: 83 YGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNAL--DNMSVVGYFKHNE 140
Query: 461 ALSANMDRSKHPKTVLIMDEVDGMSAGDRGGIADLXXXXXXXXXXXXXXXNDRYSQKLKS 520
+ N++ KH V+IMDEVDGMS GDRGG+ L N+R K++
Sbjct: 141 E-AQNLN-GKH--FVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRP 196
Query: 521 LVNYCSDLRFRKPRKQEIAKRLMQIANAEGLEVNEIALEELADRVNGDIRMAINQLQYMS 580
C D++FR+P I RLM IA E +++ ++ L GDIR IN L +S
Sbjct: 197 FDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTIS 256
Query: 581 LSLSVIKYDDIRQRLLSSAKDEDISPFTAVDKLF------GFNGGKLRMDERIDLSMSDP 634
+ I +++I + + K+ + PF K+ ++++I L D
Sbjct: 257 TTTKTINHENINEISKAWEKNIALKPFDIAHKMLDGQIYSDIGSRNFTLNDKIALYFDDF 316
Query: 635 DLVPLLIQENYINYRPSSAGRDEVKRLSLIARAAESISDGDIFNVQIRRNXXXXXXXXXX 694
D PL+IQENY++ RPS + L +A AA IS GDI +IR +
Sbjct: 317 DFTPLMIQENYLSTRPSVLKPGQ-SHLEAVAEAANCISLGDIVEKKIRSSEQLWSLLPLH 375
Query: 695 XA-SCIIPAALMHGQRETLEQGERNFNRFGGWLGKNSTMGKNLRLLEDLHFHHLASRKSK 753
S + PA+ + G G NF WLG+NS K RLL+++H+H ++
Sbjct: 376 AVLSSVYPASKVAGHMA----GRINFT---AWLGQNSKSAKYYRLLQEIHYH------TR 422
Query: 754 LGRDT 758
LG T
Sbjct: 423 LGTST 427
>pdb|2K7F|A Chain A, Haddock Calculated Model Of The Complex Between The Brct
Region Of Rfc P140 And Dsdna
pdb|2K6G|A Chain A, Solution Structure Of The Dna Binding Brct Domain From The
Large Subunit Of Human Replication Factor C
Length = 109
Score = 111 bits (278), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 52/99 (52%), Positives = 73/99 (73%)
Query: 180 FMNFGERKDPPHKGEKEVPEGAPDCLGGLTFVISGTLDSLEREEAEDLIKRHGGRVTGSV 239
+ ++ R+ P G KE+P+GA +CL GL FVI+G L+S+ER+EA+ LI+R+GG+VTG+V
Sbjct: 8 YRSYLNREGPKALGSKEIPKGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNV 67
Query: 240 SKKTNYLLCDEDIAGAKSTKAKELGTPFLTEDGLFDMIR 278
SKKTNYL+ D +KS KA LGT + EDGL ++IR
Sbjct: 68 SKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 106
>pdb|2EBU|A Chain A, Solution Structure Of The Brct Domain From Human
Replication Factor C Large Subunit 1
Length = 112
Score = 106 bits (265), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 50/86 (58%), Positives = 67/86 (77%)
Query: 193 GEKEVPEGAPDCLGGLTFVISGTLDSLEREEAEDLIKRHGGRVTGSVSKKTNYLLCDEDI 252
G KE+P+GA +CL GL FVI+G L+S+ER+EA+ LI+R+GG+VTG+VSKKTNYL+ D
Sbjct: 11 GSKEIPKGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDS 70
Query: 253 AGAKSTKAKELGTPFLTEDGLFDMIR 278
+KS KA LGT + EDGL ++IR
Sbjct: 71 GQSKSDKAAALGTKIIDEDGLLNLIR 96
>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHQ|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHQ|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|A Chain A, Replication Factor C Adpnp Complex
pdb|2CHV|B Chain B, Replication Factor C Adpnp Complex
pdb|2CHV|C Chain C, Replication Factor C Adpnp Complex
pdb|2CHV|D Chain D, Replication Factor C Adpnp Complex
pdb|2CHV|E Chain E, Replication Factor C Adpnp Complex
pdb|2CHV|F Chain F, Replication Factor C Adpnp Complex
Length = 319
Score = 83.6 bits (205), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 77/305 (25%), Positives = 130/305 (42%), Gaps = 45/305 (14%)
Query: 345 TWTEKYRPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSG 404
W EKYRP+T +E+VG +++++L ++ N L + SG
Sbjct: 6 IWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHL--------------------LFSG 45
Query: 405 SPGMGKT-TAAKLVCQMLGFQ----AIEVNASDSRGKADAKISKGIGGSNANSIKELVSN 459
PG GKT TA L + G IE+NASD RG + + IKE
Sbjct: 46 PPGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVR----------HKIKEFART 95
Query: 460 EALSANMDRSKHPKTVLIMDEVDGMSAGDRGGIADLXXXXXXXXXXXXXXXNDRYSQKLK 519
+ P ++ +DE D ++A + + + S+ ++
Sbjct: 96 APIGG------APFKIIFLDEADALTADAQAALR--RTMEMYSKSCRFILSCNYVSRIIE 147
Query: 520 SLVNYCSDLRFRKPRKQEIAKRLMQIANAEGLEVNEIALEELADRVNGDIRMAINQLQYM 579
+ + C+ RF+ K+ + KRL++I EG+++ E LE L GD R AIN LQ
Sbjct: 148 PIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGA 207
Query: 580 SLSLSVIKYDDIRQRLLSSAKDEDISPFTAVDKLFGFNGGKLRMDE-RIDLSMSDPDLVP 638
+ V+ D I Q + ++A+ E+++ F + +D ++ MS D+V
Sbjct: 208 AAIGEVVDADTIYQ-ITATARPEEMTELIQTALKGNFMEARELLDRLMVEYGMSGEDIVA 266
Query: 639 LLIQE 643
L +E
Sbjct: 267 QLFRE 271
>pdb|1IQP|A Chain A, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|B Chain B, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|C Chain C, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|D Chain D, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|E Chain E, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
pdb|1IQP|F Chain F, Crystal Structure Of The Clamp Loader Small Subunit From
Pyrococcus Furiosus
Length = 327
Score = 82.0 bits (201), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 70/238 (29%), Positives = 110/238 (46%), Gaps = 45/238 (18%)
Query: 346 WTEKYRPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGS 405
W EKYRP+ ++IVG + +VK+L + ++ TG+ + + +G
Sbjct: 15 WVEKYRPQRLDDIVGQEHIVKRL--------KHYVKTGSMPH------------LLFAGP 54
Query: 406 PGMGKTTAA-KLVCQMLG----FQAIEVNASDSRGKADAKISKGIGGSNANSIKELVSNE 460
PG+GKTTAA L ++ G +E+NASD RG N I+E V
Sbjct: 55 PGVGKTTAALALARELFGENWRHNFLELNASDERG--------------INVIREKVKEF 100
Query: 461 ALSANMDRSKHPKTVLIMDEVDGMSAGDRGGIADLXXXXXXXXXXXXXXXNDRYSQKL-K 519
A + + + ++ +DE D ++ + L + YS K+ +
Sbjct: 101 ARTKPIGGASF--KIIFLDEADALTQDAQQA---LRRTMEMFSSNVRFILSCNYSSKIIE 155
Query: 520 SLVNYCSDLRFRKPRKQEIAKRLMQIANAEGLEVNEIALEELADRVNGDIRMAINQLQ 577
+ + C+ RFR R ++IAKRL IA EGLE+ E L+ + GD+R AIN LQ
Sbjct: 156 PIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQ 213
>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2
pdb|2CHG|B Chain B, Replication Factor C Domains 1 And 2
pdb|2CHG|C Chain C, Replication Factor C Domains 1 And 2
pdb|2CHG|D Chain D, Replication Factor C Domains 1 And 2
Length = 226
Score = 80.1 bits (196), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 70/254 (27%), Positives = 109/254 (42%), Gaps = 45/254 (17%)
Query: 346 WTEKYRPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGS 405
W EKYRP+T +E+VG +++++L ++ N L + SG
Sbjct: 7 WVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHL--------------------LFSGP 46
Query: 406 PGMGKT-TAAKLVCQMLGFQ----AIEVNASDSRGKADAKISKGIGGSNANSIKELVSNE 460
PG GKT TA L + G IE+NASD RG + + IKE
Sbjct: 47 PGTGKTATAIALARDLFGENWRDNFIEMNASDERGIDVVR----------HKIKEFARTA 96
Query: 461 ALSANMDRSKHPKTVLIMDEVDGMSAGDRGGIADLXXXXXXXXXXXXXXXNDRY-SQKLK 519
+ P ++ +DE D ++A + A L + Y S+ ++
Sbjct: 97 PIGG------APFKIIFLDEADALTADAQ---AALRRTMEMYSKSCRFILSCNYVSRIIE 147
Query: 520 SLVNYCSDLRFRKPRKQEIAKRLMQIANAEGLEVNEIALEELADRVNGDIRMAINQLQYM 579
+ + C+ RF+ K+ + KRL++I EG+++ E LE L GD R AIN LQ
Sbjct: 148 PIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGGDFRKAINALQGA 207
Query: 580 SLSLSVIKYDDIRQ 593
+ V+ D I Q
Sbjct: 208 AAIGEVVDADTIYQ 221
>pdb|1SXJ|B Chain B, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 323
Score = 77.0 bits (188), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 65/239 (27%), Positives = 107/239 (44%), Gaps = 42/239 (17%)
Query: 344 LTWTEKYRPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILS 403
L W EKYRP+ ++IVGN++ + +L N + I+S
Sbjct: 9 LPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHM--------------------IIS 48
Query: 404 GSPGMGKTTAAK-LVCQMLGFQ----AIEVNASDSRGKADAKISKGIGGSNANSIKELVS 458
G PG+GKTT+ L ++LG +E+NASD RG + N IK
Sbjct: 49 GMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVR----------NQIKHFAQ 98
Query: 459 NEALSANMDRSKHPKTVLIMDEVDGMSAGDRGGIADLXXXXXXXXXXXXXXXNDRYSQKL 518
+ ++ KH ++I+DE D M+AG + + ++ ++ +
Sbjct: 99 KKL---HLPPGKHK--IVILDEADSMTAGAQQALR--RTMELYSNSTRFAFACNQSNKII 151
Query: 519 KSLVNYCSDLRFRKPRKQEIAKRLMQIANAEGLEVNEIALEELADRVNGDIRMAINQLQ 577
+ L + C+ LR+ K +++ KRL+QI E ++ LE + GD+R AIN LQ
Sbjct: 152 EPLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQ 210
>pdb|1L7B|A Chain A, Solution Nmr Structure Of Brct Domain Of T. Thermophilus:
Northeast Structural Genomics Consortium Target Wr64tt
Length = 92
Score = 67.8 bits (164), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 40/83 (48%), Positives = 56/83 (67%), Gaps = 2/83 (2%)
Query: 203 DCLGGLTFVISGTLDSLEREEAEDLIKRHGGRVTGSVSKKTNYLLCDEDIAGAKSTKAKE 262
+ L GLTFVI+G L S REE + L++R G +VT SVS+KT+YL+ E+ G+K KA+
Sbjct: 6 EALKGLTFVITGEL-SRPREEVKALLRRLGAKVTDSVSRKTSYLVVGEN-PGSKLEKARA 63
Query: 263 LGTPFLTEDGLFDMIRASKPMKA 285
LG P LTE+ L+ ++ A KA
Sbjct: 64 LGVPTLTEEELYRLLEARTGKKA 86
>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 = 63.5 bits (153), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 67/260 (25%), Positives = 111/260 (42%), Gaps = 50/260 (19%)
Query: 330 SPAKRKGQNIQQSSLTWTEKYRPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGK 389
S KR +N L W EKYRP+T +E+ G +++ + KF+D G +
Sbjct: 4 STEKRSKEN-----LPWVEKYRPETLDEVYGQNEVITTVR--------KFVDEGKLPH-- 48
Query: 390 KQNDASAEKAAILSGSPGMGKT-TAAKLVCQMLG----FQAIEVNASDSRGKADAKISKG 444
+ G PG GKT T L ++ G +E+NASD RG +
Sbjct: 49 ----------LLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVR---- 94
Query: 445 IGGSNANSIKELVSNEALSANMDRSKHPKTVLIMDEVDGMSAGDRGGIADLXXXXXXXXX 504
N IK+ S + SK K ++I+DE D M+ + + +
Sbjct: 95 ------NQIKDFASTRQIF-----SKGFK-LIILDEADAMTNAAQNALRRVIERYTKNTR 142
Query: 505 XXXXXXNDRYSQKLK-SLVNYCSDLRFRKPRKQEIAKRLMQIANAEGLEVNEIALEELAD 563
Y+ KL +L++ C+ RF+ ++ I +R+ + E L+++ A + L +
Sbjct: 143 FCVLA---NYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIE 199
Query: 564 RVNGDIRMAINQLQYMSLSL 583
NGD+R +N LQ +L
Sbjct: 200 LSNGDMRRVLNVLQSCKATL 219
>pdb|1DGS|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase From T.
Filiformis
pdb|1DGS|B Chain B, Crystal Structure Of Nad+-Dependent Dna Ligase From T.
Filiformis
Length = 667
Score = 60.5 bits (145), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 36/80 (45%), Positives = 51/80 (63%), Gaps = 2/80 (2%)
Query: 199 EGAPDCLGGLTFVISGTLDSLEREEAEDLIKRHGGRVTGSVSKKTNYLLCDEDIAGAKST 258
E D L GLTFV++G L S REE + L+ R G +VT SVS+KT+YL+ E+ G+K
Sbjct: 582 EEVSDLLSGLTFVLTGEL-SRPREEVKALLGRLGAKVTDSVSRKTSYLVVGEN-PGSKLE 639
Query: 259 KAKELGTPFLTEDGLFDMIR 278
KA+ LG LTE+ + ++
Sbjct: 640 KARALGVAVLTEEEFWRFLK 659
>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 = 56.6 bits (135), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 60/246 (24%), Positives = 92/246 (37%), Gaps = 50/246 (20%)
Query: 346 WTEKYRPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGS 405
W EKYRPK +E+ V L KK ++ + G
Sbjct: 27 WVEKYRPKNLDEVTAQDHAVTVL--------------------KKTLKSANLPHMLFYGP 66
Query: 406 PGMGKT-TAAKLVCQMLG-----FQAIEVNASDSRGKADAKISKGIGGSNANSIKELVSN 459
PG GKT T L ++ G + +E+NASD RG + ++E V N
Sbjct: 67 PGTGKTSTILALTKELYGPDLMKSRILELNASDERG--------------ISIVREKVKN 112
Query: 460 EALSANMDRSKH--------PKTVLIMDEVDGMSAGDRGGIADLXXXXXXXXXXXXXXXN 511
A SKH P ++I+DE D M+A + +
Sbjct: 113 FARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALR--RTMETYSGVTRFCLIC 170
Query: 512 DRYSQKLKSLVNYCSDLRFRKPRKQEIAKRLMQIANAEGLEVNEIALEELADRVNGDIRM 571
+ ++ + L + CS RF+ RL I+ E ++ ++ LE + D GD+R
Sbjct: 171 NYVTRIIDPLASQCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRR 230
Query: 572 AINQLQ 577
I LQ
Sbjct: 231 GITLLQ 236
>pdb|2OWO|A Chain A, Last Stop On The Road To Repair: Structure Of E.Coli Dna
Ligase Bound To Nicked Dna-Adenylate
Length = 671
Score = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 205 LGGLTFVISGTLDSLEREEAEDLIKRHGGRVTGSVSKKTNYLLCDEDIAGAKSTKAKELG 264
G T V++G+L + R++A+ + G +V GSVSKKT+ ++ E AG+K KA+ELG
Sbjct: 598 FAGKTVVLTGSLSQMSRDDAKARLVELGAKVAGSVSKKTDLVIAGE-AAGSKLAKAQELG 656
Query: 265 TPFLTEDGLFDMI 277
+ E + ++
Sbjct: 657 IEVIDEAEMLRLL 669
>pdb|1HQC|A Chain A, Structure Of Ruvb From Thermus Thermophilus Hb8
pdb|1HQC|B Chain B, Structure Of Ruvb From Thermus Thermophilus Hb8
Length = 324
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 57/228 (25%), Positives = 89/228 (39%), Gaps = 33/228 (14%)
Query: 351 RPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGSPGMGK 410
RPKT +E +G ++L ++L +L K E +L G PG+GK
Sbjct: 7 RPKTLDEYIGQERLKQKLRVYL--------------EAAKARKEPLEHL-LLFGPPGLGK 51
Query: 411 TTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIKE---LVSNEA--LSAN 465
TT A ++ LG VN + G A K + ANS++E L +E LS
Sbjct: 52 TTLAHVIAHELG-----VNLRVTSGPAIEK-PGDLAAILANSLEEGDILFIDEIHRLSRQ 105
Query: 466 MDRSKHPKTV-LIMDEVDGMSAGDRGGIADLXXXXXXXXXXXXXXXNDRYSQKLKSLVNY 524
+ +P +MD V G R + + L S
Sbjct: 106 AEEHLYPAMEDFVMDIVIGQGPAAR----TIRLELPRFTLIGATTRPGLITAPLLSRFGI 161
Query: 525 CSDLRFRKPRKQEIAKRLMQIANAEGLEVNEIALEELADRVNGDIRMA 572
L + P +E+A+ +M+ A G+ + E A E+ R G +R+A
Sbjct: 162 VEHLEYYTP--EELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVA 207
>pdb|1IXS|B Chain B, Structure Of Ruvb Complexed With Ruva Domain Iii
Length = 318
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 57/228 (25%), Positives = 89/228 (39%), Gaps = 33/228 (14%)
Query: 351 RPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGSPGMGK 410
RPKT +E +G ++L ++L +L K E +L G PG+GK
Sbjct: 7 RPKTLDEYIGQERLKQKLRVYL--------------EAAKARKEPLEHL-LLFGPPGLGK 51
Query: 411 TTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIKE---LVSNEA--LSAN 465
TT A ++ LG VN + G A K + ANS++E L +E LS
Sbjct: 52 TTLAHVIAHELG-----VNLRVTSGPAIEK-PGDLAAILANSLEEGDILFIDEIHRLSRQ 105
Query: 466 MDRSKHPKTV-LIMDEVDGMSAGDRGGIADLXXXXXXXXXXXXXXXNDRYSQKLKSLVNY 524
+ +P +MD V G R + + L S
Sbjct: 106 AEEHLYPAMEDFVMDIVIGQGPAAR----TIRLELPRFTLIGATTRPGLITAPLLSRFGI 161
Query: 525 CSDLRFRKPRKQEIAKRLMQIANAEGLEVNEIALEELADRVNGDIRMA 572
L + P +E+A+ +M+ A G+ + E A E+ R G +R+A
Sbjct: 162 VEHLEYYTP--EELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVA 207
>pdb|1IXR|C Chain C, Ruva-Ruvb Complex
Length = 312
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 57/228 (25%), Positives = 89/228 (39%), Gaps = 33/228 (14%)
Query: 351 RPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGSPGMGK 410
RPKT +E +G ++L ++L +L K E +L G PG+GK
Sbjct: 7 RPKTLDEYIGQERLKQKLRVYL--------------EAAKARKEPLEHL-LLFGPPGLGK 51
Query: 411 TTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIKE---LVSNEA--LSAN 465
TT A ++ LG VN + G A K + ANS++E L +E LS
Sbjct: 52 TTLAHVIAHELG-----VNLRVTSGPAIEK-PGDLAAILANSLEEGDILFIDEIHRLSRQ 105
Query: 466 MDRSKHPKTV-LIMDEVDGMSAGDRGGIADLXXXXXXXXXXXXXXXNDRYSQKLKSLVNY 524
+ +P +MD V G R + + L S
Sbjct: 106 AEEHLYPAMEDFVMDIVIGQGPAAR----TIRLELPRFTLIGATTRPGLITAPLLSRFGI 161
Query: 525 CSDLRFRKPRKQEIAKRLMQIANAEGLEVNEIALEELADRVNGDIRMA 572
L + P +E+A+ +M+ A G+ + E A E+ R G +R+A
Sbjct: 162 VEHLEYYTP--EELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVA 207
>pdb|3E1S|A Chain A, Structure Of An N-Terminal Truncation Of Deinococcus
Radiodurans Recd2
pdb|3GP8|A Chain A, Crystal Structure Of The Binary Complex Of Recd2 With Dna
pdb|3GPL|A Chain A, Crystal Structure Of The Ternary Complex Of Recd2 With Dna
And Adpnp
pdb|3GPL|B Chain B, Crystal Structure Of The Ternary Complex Of Recd2 With Dna
And Adpnp
Length = 574
Score = 36.6 bits (83), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 8/95 (8%)
Query: 395 SAEKAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIK 454
+ + +L+G PG GK+T K V + +EV GKA ++ + + G A+++
Sbjct: 202 AGHRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGE-VTGRTASTVH 260
Query: 455 ELVSNEALSANMDRSKH----PKTVLIMDEVDGMS 485
L+ R H P +LI+DEV M
Sbjct: 261 RLLG---YGPQGFRHNHLEPAPYDLLIVDEVSMMG 292
>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 36.6 bits (83), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 38/87 (43%), Gaps = 16/87 (18%)
Query: 398 KAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIKELV 457
K +L G PG GKT AK V +G I AS G D I G +A I+E+
Sbjct: 216 KGVLLYGPPGTGKTLLAKAVAATIGANFIFSPAS---GIVDKYI-----GESARIIREMF 267
Query: 458 SNEALSANMDRSKHPKTVLIMDEVDGM 484
+ +H ++ MDEVD +
Sbjct: 268 AYA--------KEHEPCIIFMDEVDAI 286
>pdb|3J04|A Chain A, Em Structure Of The Heavy Meromyosin Subfragment Of Chick
Smooth Muscle Myosin With Regulatory Light Chain In
Phosphorylated State
pdb|3J04|D Chain D, Em Structure Of The Heavy Meromyosin Subfragment Of Chick
Smooth Muscle Myosin With Regulatory Light Chain In
Phosphorylated State
Length = 909
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 42/100 (42%), Gaps = 14/100 (14%)
Query: 397 EKAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGS-------- 448
+++ + +G G GKT K V Q L V AS +GK D I++G S
Sbjct: 169 DQSILCTGESGAGKTENTKKVIQYLA-----VVASSHKGKKDTSITQGPSFSYGELEKQL 223
Query: 449 -NANSIKELVSNEALSANMDRSKHPKTVLIMDEVDGMSAG 487
AN I E N N + S+ K + I +V G G
Sbjct: 224 LQANPILEAFGNAKTVKNDNSSRFGKFIRINFDVTGYIVG 263
>pdb|3U5Z|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|C Chain C, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|D Chain D, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|E Chain E, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|L Chain L, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|M Chain M, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|N Chain N, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U5Z|O Chain O, Structure Of T4 Bacteriophage Clamp Loader Bound To The T4
Clamp, Primer-Template Dna, And Atp Analog
pdb|3U60|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|C Chain C, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|D Chain D, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U60|E Chain E, Structure Of T4 Bacteriophage Clamp Loader Bound To Open
Clamp, Dna And Atp Analog
pdb|3U61|B Chain B, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|C Chain C, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|D Chain D, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
pdb|3U61|E Chain E, Structure Of T4 Bacteriophage Clamp Loader Bound To Closed
Clamp, Dna And Atp Analog And Adp
Length = 324
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 44/189 (23%), Positives = 78/189 (41%), Gaps = 33/189 (17%)
Query: 403 SGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIKELVSNEAL 462
S SPG GKTT AK +C + + VN SD + + ++ ++N A
Sbjct: 54 SPSPGTGKTTVAKALCHDVNADMMFVNGSDCK---------------IDFVRGPLTNFAS 98
Query: 463 SANMD-RSKHPKTVLIMDEVD--GMSAGDRGGIADLXXXXXXXXXXXXXXXNDRYSQKLK 519
+A+ D R K V+++DE D G++ R + + D +K
Sbjct: 99 AASFDGRQK----VIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGI---IK 151
Query: 520 SLVNYCSDLRFRKPRKQ-------EIAKRLMQIANAEGLEVNEI-ALEELADRVNGDIRM 571
L + C + F +P + ++ +RL +I EG+ + ++ + L + D R
Sbjct: 152 PLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRK 211
Query: 572 AINQLQYMS 580
I +L S
Sbjct: 212 TIGELDSYS 220
>pdb|3DTP|A Chain A, Tarantula Heavy Meromyosin Obtained By Flexible Docking To
Tarantula Muscle Thick Filament Cryo-Em 3d-Map
Length = 971
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 42/100 (42%), Gaps = 14/100 (14%)
Query: 397 EKAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGS-------- 448
+++ + +G G GKT K V Q L V AS +GK D I++G S
Sbjct: 169 DQSILCTGESGAGKTENTKKVIQYLA-----VVASSHKGKKDTSITQGPSFSYGELEKQL 223
Query: 449 -NANSIKELVSNEALSANMDRSKHPKTVLIMDEVDGMSAG 487
AN I E N N + S+ K + I +V G G
Sbjct: 224 LQANPILEAFGNAKTVKNDNSSRFGKFIRINFDVTGYIVG 263
>pdb|1BR2|A Chain A, Smooth Muscle Myosin Motor Domain Complexed With
Mgadp.Alf4
pdb|1BR2|B Chain B, Smooth Muscle Myosin Motor Domain Complexed With
Mgadp.Alf4
pdb|1BR2|C Chain C, Smooth Muscle Myosin Motor Domain Complexed With
Mgadp.Alf4
pdb|1BR2|D Chain D, Smooth Muscle Myosin Motor Domain Complexed With
Mgadp.Alf4
pdb|1BR2|E Chain E, Smooth Muscle Myosin Motor Domain Complexed With
Mgadp.Alf4
pdb|1BR2|F Chain F, Smooth Muscle Myosin Motor Domain Complexed With
Mgadp.Alf4
Length = 791
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 42/100 (42%), Gaps = 14/100 (14%)
Query: 397 EKAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGS-------- 448
+++ + +G G GKT K V Q L V AS +GK D I++G S
Sbjct: 169 DQSILCTGESGAGKTENTKKVIQYLA-----VVASSHKGKKDTSITQGPSFSYGELEKQL 223
Query: 449 -NANSIKELVSNEALSANMDRSKHPKTVLIMDEVDGMSAG 487
AN I E N N + S+ K + I +V G G
Sbjct: 224 LQANPILEAFGNAKTVKNDNSSRFGKFIRINFDVTGYIVG 263
>pdb|1BR1|A Chain A, Smooth Muscle Myosin Motor Domain-Essential Light Chain
Complex With Mgadp.Alf4 Bound At The Active Site
pdb|1BR1|C Chain C, Smooth Muscle Myosin Motor Domain-Essential Light Chain
Complex With Mgadp.Alf4 Bound At The Active Site
pdb|1BR1|E Chain E, Smooth Muscle Myosin Motor Domain-Essential Light Chain
Complex With Mgadp.Alf4 Bound At The Active Site
pdb|1BR1|G Chain G, Smooth Muscle Myosin Motor Domain-Essential Light Chain
Complex With Mgadp.Alf4 Bound At The Active Site
pdb|1BR4|A Chain A, Smooth Muscle Myosin Motor Domain-Essential Light Chain
Complex With Mgadp.Bef3 Bound At The Active Site
pdb|1BR4|C Chain C, Smooth Muscle Myosin Motor Domain-Essential Light Chain
Complex With Mgadp.Bef3 Bound At The Active Site
pdb|1BR4|E Chain E, Smooth Muscle Myosin Motor Domain-Essential Light Chain
Complex With Mgadp.Bef3 Bound At The Active Site
pdb|1BR4|G Chain G, Smooth Muscle Myosin Motor Domain-Essential Light Chain
Complex With Mgadp.Bef3 Bound At The Active Site
Length = 820
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 42/100 (42%), Gaps = 14/100 (14%)
Query: 397 EKAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGS-------- 448
+++ + +G G GKT K V Q L V AS +GK D I++G S
Sbjct: 169 DQSILCTGESGAGKTENTKKVIQYLA-----VVASSHKGKKDTSITQGPSFSYGELEKQL 223
Query: 449 -NANSIKELVSNEALSANMDRSKHPKTVLIMDEVDGMSAG 487
AN I E N N + S+ K + I +V G G
Sbjct: 224 LQANPILEAFGNAKTVKNDNSSRFGKFIRINFDVTGYIVG 263
>pdb|1I84|S Chain S, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
Chicken Gizzard Smooth Muscle Myosin With Regulatory
Light Chain In The Dephosphorylated State. Only C Alphas
Provided For Regulatory Light Chain. Only Backbone Atoms
Provided For S2 Fragment.
pdb|1I84|V Chain V, Cryo-Em Structure Of The Heavy Meromyosin Subfragment Of
Chicken Gizzard Smooth Muscle Myosin With Regulatory
Light Chain In The Dephosphorylated State. Only C Alphas
Provided For Regulatory Light Chain. Only Backbone Atoms
Provided For S2 Fragment
Length = 1184
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 42/100 (42%), Gaps = 14/100 (14%)
Query: 397 EKAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGS-------- 448
+++ + +G G GKT K V Q L V AS +GK D I++G S
Sbjct: 169 DQSILCTGESGAGKTENTKKVIQYLA-----VVASSHKGKKDTSITQGPSFSYGELEKQL 223
Query: 449 -NANSIKELVSNEALSANMDRSKHPKTVLIMDEVDGMSAG 487
AN I E N N + S+ K + I +V G G
Sbjct: 224 LQANPILEAFGNAKTVKNDNSSRFGKFIRINFDVTGYIVG 263
>pdb|3DTP|B Chain B, Tarantula Heavy Meromyosin Obtained By Flexible Docking To
Tarantula Muscle Thick Filament Cryo-Em 3d-Map
Length = 973
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 42/100 (42%), Gaps = 14/100 (14%)
Query: 397 EKAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGS-------- 448
+++ + +G G GKT K V Q L V AS +GK D I++G S
Sbjct: 169 DQSILCTGESGAGKTENTKKVIQYLA-----VVASSHKGKKDTSITQGPSFSYGELEKQL 223
Query: 449 -NANSIKELVSNEALSANMDRSKHPKTVLIMDEVDGMSAG 487
AN I E N N + S+ K + I +V G G
Sbjct: 224 LQANPILEAFGNAKTVKNDNSSRFGKFIRINFDVTGYIVG 263
>pdb|2XNK|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|B Chain B, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|C Chain C, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|D Chain D, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 292
Score = 34.3 bits (77), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 35/85 (41%), Gaps = 6/85 (7%)
Query: 207 GLTFVISGTLDSLEREEAEDLIKRHGGRVTGSVSKKTNYLLCDEDIAGAKSTKAKELGTP 266
G ++G L L+R+E + L +HGG+ G + L ++ G K AK
Sbjct: 204 GCIICVTG-LCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKRWNVH 262
Query: 267 FLTEDGLFDMIRASKPMKALAQAES 291
+T FD I K Q ES
Sbjct: 263 CVTTQWFFDSIE-----KGFCQDES 282
>pdb|2XNH|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 287
Score = 33.9 bits (76), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 35/85 (41%), Gaps = 6/85 (7%)
Query: 207 GLTFVISGTLDSLEREEAEDLIKRHGGRVTGSVSKKTNYLLCDEDIAGAKSTKAKELGTP 266
G ++G L L+R+E + L +HGG+ G + L ++ G K AK
Sbjct: 202 GCIICVTG-LCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKRWNVH 260
Query: 267 FLTEDGLFDMIRASKPMKALAQAES 291
+T FD I K Q ES
Sbjct: 261 CVTTQWFFDSIE-----KGFCQDES 280
>pdb|3OLC|X Chain X, Crystal Structure Of The N-Terminal Region Of Topbp1
Length = 298
Score = 33.9 bits (76), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 35/85 (41%), Gaps = 6/85 (7%)
Query: 207 GLTFVISGTLDSLEREEAEDLIKRHGGRVTGSVSKKTNYLLCDEDIAGAKSTKAKELGTP 266
G ++G L L+R+E + L +HGG+ G + L ++ G K AK
Sbjct: 202 GCIICVTG-LCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKRWNVH 260
Query: 267 FLTEDGLFDMIRASKPMKALAQAES 291
+T FD I K Q ES
Sbjct: 261 CVTTQWFFDSIE-----KGFCQDES 280
>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 = 33.9 bits (76), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 44/89 (49%), Gaps = 8/89 (8%)
Query: 402 LSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIKELVSNEA 461
L+G PG+GKT+ AK + + LG + + ++ R +++ I G + +
Sbjct: 113 LAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESE------IRGHRRTYVGAMPGR-- 164
Query: 462 LSANMDRSKHPKTVLIMDEVDGMSAGDRG 490
+ M ++ V ++DE+D MS+ RG
Sbjct: 165 IIQGMKKAGKLNPVFLLDEIDKMSSDFRG 193
>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating
Nucleotidase
pdb|3H4M|B Chain B, Aaa Atpase Domain Of The Proteasome- Activating
Nucleotidase
pdb|3H4M|C Chain C, Aaa Atpase Domain Of The Proteasome- Activating
Nucleotidase
Length = 285
Score = 33.1 bits (74), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 16/89 (17%)
Query: 398 KAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIKELV 457
K +L G PG GKT AK V A E NA+ R + K I G A+ +K++
Sbjct: 52 KGILLYGPPGTGKTLLAKAV-------ATETNATFIRVVGSELVKKFI-GEGASLVKDIF 103
Query: 458 SNEALSANMDRSKHPKTVLIMDEVDGMSA 486
+ + K P +++ +DE+D ++A
Sbjct: 104 -------KLAKEKAP-SIIFIDEIDAIAA 124
>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 405
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 43/98 (43%), Gaps = 20/98 (20%)
Query: 398 KAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIKELV 457
K IL G PG GKT A+ V + I V+ A++ + G + ++EL
Sbjct: 183 KGVILYGPPGTGKTLLARAVAHHTDCKFIRVSG--------AELVQKYIGEGSRMVRELF 234
Query: 458 SNEALSANMDRSKHPKTVLIMDEVDGMSA----GDRGG 491
M R +H +++ MDE+D + + G GG
Sbjct: 235 V-------MAR-EHAPSIIFMDEIDSIGSTRVEGSGGG 264
>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp
Length = 262
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 33/110 (30%), Positives = 45/110 (40%), Gaps = 30/110 (27%)
Query: 377 EKFLDTGTKRNGKKQNDASAEKAAILSGSPGMGKTTAAKLVCQ--MLGFQAIEVNASDSR 434
E+FL G K K A+L G PG GKT AK V + F A+
Sbjct: 29 ERFLQLGAK----------VPKGALLLGPPGCGKTLLAKAVATEAQVPFLAM-------- 70
Query: 435 GKADAKISKGIGGSNANSIKELVSNEALSANMDRSKHPKTVLIMDEVDGM 484
A A+ + IGG A ++ L R++ P V I DE+D +
Sbjct: 71 --AGAEFVEVIGGLGAARVRSLFKEA-------RARAPCIVYI-DEIDAV 110
>pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v
Length = 334
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 15/71 (21%)
Query: 351 RPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGSPGMGK 410
RPK+ +E +G + + K+L L K G+ + +L+G PG+GK
Sbjct: 20 RPKSLDEFIGQENVKKKLSLALE---------AAKMRGEVLDHV------LLAGPPGLGK 64
Query: 411 TTAAKLVCQML 421
TT A ++ L
Sbjct: 65 TTLAHIIASEL 75
>pdb|1IN7|A Chain A, Thermotoga Maritima Ruvb R170a
Length = 334
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 15/71 (21%)
Query: 351 RPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGSPGMGK 410
RPK+ +E +G + + K+L L K G+ + +L+G PG+GK
Sbjct: 20 RPKSLDEFIGQENVKKKLSLALE---------AAKMRGEVLDHV------LLAGPPGLGK 64
Query: 411 TTAAKLVCQML 421
TT A ++ L
Sbjct: 65 TTLAHIIASEL 75
>pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junction Branch
Migration Motor
Length = 334
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 15/71 (21%)
Query: 351 RPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGSPGMGK 410
RPK+ +E +G + + K+L L K G+ + +L+G PG+GK
Sbjct: 20 RPKSLDEFIGQENVKKKLSLALE---------AAKMRGEVLDHV------LLAGPPGLGK 64
Query: 411 TTAAKLVCQML 421
TT A ++ L
Sbjct: 65 TTLAHIIASEL 75
>pdb|1J7K|A Chain A, Thermotoga Maritima Ruvb P216g Mutant
Length = 334
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 15/71 (21%)
Query: 351 RPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGSPGMGK 410
RPK+ +E +G + + K+L L K G+ + +L+G PG+GK
Sbjct: 20 RPKSLDEFIGQENVKKKLSLALE---------AAKMRGEVLDHV------LLAGPPGLGK 64
Query: 411 TTAAKLVCQML 421
TT A ++ L
Sbjct: 65 TTLAHIIASEL 75
>pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant
Length = 334
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 15/71 (21%)
Query: 351 RPKTPNEIVGNQQLVKQLHTWLAHWNEKFLDTGTKRNGKKQNDASAEKAAILSGSPGMGK 410
RPK+ +E +G + + K+L L K G+ + +L+G PG+GK
Sbjct: 20 RPKSLDEFIGQENVKKKLSLALE---------AAKMRGEVLDHV------LLAGPPGLGK 64
Query: 411 TTAAKLVCQML 421
TT A ++ L
Sbjct: 65 TTLAHIIASEL 75
>pdb|1WKR|A Chain A, Crystal Structure Of Aspartic Proteinase From Irpex
Lacteus
Length = 340
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 27/70 (38%), Gaps = 9/70 (12%)
Query: 2 PQDIRKWFLKPHSKDK-----DN----ATIPANTALSNLETTNSEPGCGGHESMGRRKTS 52
P D+ L PH+ DN TIP N + E T SE G + G +S
Sbjct: 109 PVDLTVGTLSPHTSTSIPTVTDNLFSQGTIPTNLLAVSFEPTTSESSTNGELTFGATDSS 168
Query: 53 KYFATDKQKP 62
KY + P
Sbjct: 169 KYTGSITYTP 178
>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer
Length = 331
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 43/90 (47%), Gaps = 17/90 (18%)
Query: 401 ILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIKELVSNE 460
+L G PG GK+ AK V V++SD +SK +G S +K+L +
Sbjct: 64 LLYGPPGTGKSYLAKAVATEANSTFFSVSSSD-------LVSKWMGESE-KLVKQLFA-- 113
Query: 461 ALSANMDRSKHPKTVLIMDEVDGMSAGDRG 490
M R P +++ +DEVD ++ G RG
Sbjct: 114 -----MARENKP-SIIFIDEVDALT-GTRG 136
>pdb|1Y63|A Chain A, Initial Crystal Structural Analysis Of A Probable Kinase
From Leishmania Major Friedlin
Length = 184
Score = 30.0 bits (66), Expect = 5.7, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 22/29 (75%), Gaps = 1/29 (3%)
Query: 401 ILSGSPGMGKTTAAKLVCQML-GFQAIEV 428
+++G+PG GKT+ A+++ L GFQ +EV
Sbjct: 14 LITGTPGTGKTSMAEMIAAELDGFQHLEV 42
>pdb|1YE8|A Chain A, Crystal Structure Of Thep1 From The Hyperthermophile
Aquifex Aeolicus
Length = 178
Score = 29.6 bits (65), Expect = 6.7, Method: Composition-based stats.
Identities = 29/105 (27%), Positives = 47/105 (44%), Gaps = 24/105 (22%)
Query: 401 ILSGSPGMGKTTAAKLVCQMLGFQAI-----EVNASDSRGKADAKI-------------- 441
I++G PG+GKTT K + + LG +AI EV +++ + +I
Sbjct: 4 IITGEPGVGKTTLVKKIVERLGKRAIGFWTEEVRDPETKKRTGFRIITTEGKKKIFSSKF 63
Query: 442 --SKGIGGS---NANSIKELVSNEALSANMDRSKHPKTVLIMDEV 481
SK + GS N +EL A + K + V+I+DE+
Sbjct: 64 FTSKKLVGSYGVNVQYFEELAIPILERAYREAKKDRRKVIIIDEI 108
>pdb|2AR7|A Chain A, Crystal Structure Of Human Adenylate Kinase 4, Ak4
pdb|2AR7|B Chain B, Crystal Structure Of Human Adenylate Kinase 4, Ak4
pdb|2BBW|A Chain A, Crystal Structure Of Human Adenylate Kinase 4 (Ak4) In
Complex With Diguanosine Pentaphosphate
pdb|2BBW|B Chain B, Crystal Structure Of Human Adenylate Kinase 4 (Ak4) In
Complex With Diguanosine Pentaphosphate
Length = 246
Score = 29.6 bits (65), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 380 LDTGTKRNGKKQNDASAEKAAILSGSPGMGKTTAAKLVCQMLGFQAI 426
+D GT+ N Q+ AS A++ G PG GK T + + Q G Q +
Sbjct: 11 VDLGTE-NLYFQSMASKLLRAVILGPPGSGKGTVCQRIAQNFGLQHL 56
>pdb|4F7C|A Chain A, Crystal Structure Of Bovine Cd1d With Bound
C12-Di-Sulfatide
pdb|4F7C|C Chain C, Crystal Structure Of Bovine Cd1d With Bound
C12-Di-Sulfatide
pdb|4F7E|A Chain A, Crystal Structure Of Bovine Cd1d With Bound
C16:0-Alpha-Galactosyl Ceramide
Length = 283
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 358 IVGNQQLVKQLHTWLAH--WNEKFLDTGTKRNGKKQNDASAEKAAILSG--SPGMGKTTA 413
++ Q K+ WL H W E L G + GK + + + A LS SPG G+
Sbjct: 147 VLNQNQGTKETVHWLLHDIWPE--LVRGVLQTGKSELEKQVKPEAWLSSGPSPGPGRLL- 203
Query: 414 AKLVCQMLGFQAIEVNASDSRGKAD 438
LVC + GF V RG+ +
Sbjct: 204 --LVCHVSGFYPKPVRVMWMRGEQE 226
>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound
State
Length = 322
Score = 29.3 bits (64), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 43/90 (47%), Gaps = 17/90 (18%)
Query: 401 ILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSIKELVSNE 460
+L G PG GK+ AK V V++SD +SK +G S +K+L +
Sbjct: 55 LLYGPPGTGKSYLAKAVATEANSTFFSVSSSD-------LVSKWMGESE-KLVKQLFA-- 104
Query: 461 ALSANMDRSKHPKTVLIMDEVDGMSAGDRG 490
M R P +++ +D+VD ++ G RG
Sbjct: 105 -----MARENKP-SIIFIDQVDALT-GTRG 127
>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|B Chain B, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|C Chain C, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|D Chain D, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|E Chain E, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|2DHR|F Chain F, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
Length = 499
Score = 29.3 bits (64), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 16/91 (17%)
Query: 394 ASAEKAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSI 453
A K +L G PG+GKT A+ V I + SD ++ G+G + +
Sbjct: 61 ARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDF-----VEMFVGVGAARVRDL 115
Query: 454 KELVSNEALSANMDRSKHPKTVLIMDEVDGM 484
E +H ++ +DE+D +
Sbjct: 116 FETA-----------KRHAPCIVFIDEIDAV 135
>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|B Chain B, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|C Chain C, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|D Chain D, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|E Chain E, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
pdb|4EIW|F Chain F, Whole Cytosolic Region Of Atp-Dependent Metalloprotease
Ftsh (G399l)
Length = 508
Score = 29.3 bits (64), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 36/91 (39%), Gaps = 16/91 (17%)
Query: 394 ASAEKAAILSGSPGMGKTTAAKLVCQMLGFQAIEVNASDSRGKADAKISKGIGGSNANSI 453
A K +L G PG+GKT A+ V I + SD ++ G+G + +
Sbjct: 70 ARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDF-----VEMFVGVGAARVRDL 124
Query: 454 KELVSNEALSANMDRSKHPKTVLIMDEVDGM 484
E +H ++ +DE+D +
Sbjct: 125 FETA-----------KRHAPCIVFIDEIDAV 144
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
0.312 0.130 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,657,295
Number of Sequences: 62578
Number of extensions: 795425
Number of successful extensions: 1819
Number of sequences better than 100.0: 71
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 46
Number of HSP's that attempted gapping in prelim test: 1769
Number of HSP's gapped (non-prelim): 77
length of query: 790
length of database: 14,973,337
effective HSP length: 107
effective length of query: 683
effective length of database: 8,277,491
effective search space: 5653526353
effective search space used: 5653526353
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: 55 (25.8 bits)