RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14291
(538 letters)
>3q8k_A Flap endonuclease 1; helix-3 turn-helix, hydrophobic wedge, 3' flap
binding site, hydrolase-DNA complex, DNA repair,
replication; HET: DNA; 2.20A {Homo sapiens} PDB: 3q8l_A*
3q8m_A*
Length = 341
Score = 194 bits (494), Expect = 1e-57
Identities = 52/234 (22%), Positives = 103/234 (44%), Gaps = 29/234 (12%)
Query: 310 KKRRPYVSRKML-EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFG 368
KR V+++ E + LL L G+P++ AP EAEA CA+L T+D D FG
Sbjct: 126 TKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFG 185
Query: 369 ARTVYKNFFD---KKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTA 425
+ + ++ KK + + I L +E+ + L +L+GSDY ++G+GP A
Sbjct: 186 SPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRA 245
Query: 426 LEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEA 485
++++ K +S+ L P + +++ + +
Sbjct: 246 VDLIQKH------------KSIEEIVRRLDPNKYP------------VPENWLHKEAHQL 281
Query: 486 YLKPD-INTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKISQRS 538
+L+P+ ++ +L W P+ + L +F + +S+ R+ + + K +
Sbjct: 282 FLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGST 335
Score = 38.7 bits (90), Expect = 0.003
Identities = 6/32 (18%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 111 GVNGLWKLLE----ASGKPVPVETLENKVLAV 138
G+ GL KL+ ++ + +++ + +A+
Sbjct: 1 GIQGLAKLIADVAPSAIRENDIKSYFGRKVAI 32
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap
DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A
{Homo sapiens} SCOP: a.60.7.1 c.120.1.2
Length = 379
Score = 190 bits (483), Expect = 2e-55
Identities = 52/234 (22%), Positives = 103/234 (44%), Gaps = 29/234 (12%)
Query: 310 KKRRPYVSRKML-EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFG 368
KR V+++ E + LL L G+P++ AP EAEA CA+L T+D D FG
Sbjct: 126 TKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFG 185
Query: 369 ARTVYKNFFD---KKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTA 425
+ + ++ KK + + I L +E+ + L +L+GSDY ++G+GP A
Sbjct: 186 SPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRA 245
Query: 426 LEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEA 485
++++ K + IV + K + +++ + +
Sbjct: 246 VDLIQKHKSIEE-----IVRRLDPNKYP-------------------VPENWLHKEAHQL 281
Query: 486 YLKPD-INTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKISQRS 538
+L+P+ ++ +L W P+ + L +F + +S+ R+ + + K +
Sbjct: 282 FLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGST 335
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA
replication, RTH, RAD27, DNA repair; 2.00A
{Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2
PDB: 1a77_A
Length = 326
Score = 184 bits (469), Expect = 5e-54
Identities = 48/230 (20%), Positives = 99/230 (43%), Gaps = 37/230 (16%)
Query: 311 KRRPYVSRKML-EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA 369
KR Y++ KM+ + LL L G+P++ AP E EAQ + + V++ D D L+GA
Sbjct: 122 KRVSYLTPKMVENCKYLLSLMGIPYVEAPSEGEAQASYMAKKGDVWAVVSQDYDALLYGA 181
Query: 370 RTVYKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTP-GLQGVGPVTALEI 428
V +N K ++ ++ + LI +A+ +G+DY P G++G+G A E+
Sbjct: 182 PRVVRNLTTTKEMPELIELNEVLEDLRISLDDLIDIAIFMGTDYNPGGVKGIGFKRAYEL 241
Query: 429 LAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLK 488
+ ++ + + + + ++ F V + Y
Sbjct: 242 VRSG-----VAKDVLKKEVEYYD--------------------EIKRIFKEPKVTDNY-- 274
Query: 489 PDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKISQRS 538
L+ PD +G+ +F ++ ++ +RV + + + I+ ++
Sbjct: 275 --------SLSLKLPDKEGIIKFLVDENDFNYDRVKKHVDKLYNLIANKT 316
Score = 34.4 bits (79), Expect = 0.068
Identities = 27/145 (18%), Positives = 48/145 (33%), Gaps = 43/145 (29%)
Query: 110 MGVNGLWKLLEASGKPVPVETLENKVLAV---GILY-----FTQGRASALLDRRKEDN-- 159
MGV + + E L+ K +A+ LY S L +R+ E
Sbjct: 1 MGVQ-FGDFIPK--NIISFEDLKGKKVAIDGMNALYQFLTSIRLRDGSPLRNRKGEITSA 57
Query: 160 --------------------IID---AEEKDILEMIRAE--EENEIEFEEEIAGGKEEKT 194
+ D + K+ +R E E+ E++ +E I E+
Sbjct: 58 YNGVFYKTIHLLENDITPIWVFDGEPPKLKEKTRKVRREMKEKAELKMKEAIKKEDFEEA 117
Query: 195 EK-----IKLTREMLAEQQKILDSL 214
K LT +M+ + +L +
Sbjct: 118 AKYAKRVSYLTPKMVENCKYLLSLM 142
>3ory_A Flap endonuclease 1; hydrolase; 2.00A {Desulfurococcus
amylolyticus}
Length = 363
Score = 184 bits (469), Expect = 1e-53
Identities = 49/243 (20%), Positives = 96/243 (39%), Gaps = 43/243 (17%)
Query: 310 KKRRPYVSRKML-EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFG 368
++ +M+ +A+ LL G+P++ AP E EAQ A + + D D LFG
Sbjct: 135 AMMSAKLTEEMVRDAKSLLDAMGIPWVQAPAEGEAQAAYIVKKGDAYASASQDYDSLLFG 194
Query: 369 ARTVYKNFFDKKS------------HVLRYTAPDIRYYFELTREKLIQLALLVGSDYTP- 415
+ + +N + +T E LI + +L+G+DY P
Sbjct: 195 SPKLVRNLTISGRRKLPRKNEYVEVKPELIELDKLLVQLGITLENLIDIGILLGTDYNPD 254
Query: 416 GLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLND 475
G +G+GP AL+++ + +E + +
Sbjct: 255 GFEGIGPKKALQLVKAYG---------GIEKIPKPILK-------------------SPI 286
Query: 476 DFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKIS 535
+ +++ + +L+P + N + + W TPD D ++R ++ +S +RV L +K
Sbjct: 287 EVDVIAIKKYFLQPQVTDNYR-IEWHTPDPDAVKRILVDEHDFSIDRVSTALERYVKAFK 345
Query: 536 QRS 538
+
Sbjct: 346 ENI 348
Score = 36.0 bits (83), Expect = 0.023
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 106 NIYIMGVNGLWKLLEASGKPV--PVETLENKVLAV 138
N MGV+ L ++ K V + L K++ +
Sbjct: 7 NGVDMGVD-LKDIIPGEAKTVIEDLRILHGKIIVI 40
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3
turn-helix, hydrophobic wedge, 3' FLA site,
hydrolase-DNA complex; 2.00A {Archaeoglobus fulgidus}
SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A
Length = 336
Score = 181 bits (461), Expect = 9e-53
Identities = 55/243 (22%), Positives = 95/243 (39%), Gaps = 45/243 (18%)
Query: 310 KKRRPYVSRKML-EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFG 368
+ V ++ A+ LL G+PF+ AP E EAQ A + + + D D LFG
Sbjct: 120 AQAAGRVDEYIVDSAKTLLSYMGIPFVDAPSEGEAQAAYMAAKGDVEYTGSQDYDSLLFG 179
Query: 369 ARTVYKNFFDKKS------------HVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPG 416
+ + +N LTRE+LI +A+LVG+DY G
Sbjct: 180 SPRLARNLAITGKRKLPGKNVYVDVKPEIIILESNLKRLGLTREQLIDIAILVGTDYNEG 239
Query: 417 LQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDD 476
++GVG AL + + + R L+ +K+N D
Sbjct: 240 VKGVGVKKALNYIKTYGD-----------------------------IFRALKALKVNID 270
Query: 477 FPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMK-KIS 535
+ +L P + T+ ++ + PD + F + +S+ RV++ L + K +
Sbjct: 271 HVE-EIRNFFLNPPV-TDDYRIEFREPDFEKAIEFLCEEHDFSRERVEKALEKLKALKST 328
Query: 536 QRS 538
Q +
Sbjct: 329 QAT 331
Score = 37.5 bits (87), Expect = 0.007
Identities = 21/144 (14%), Positives = 42/144 (29%), Gaps = 42/144 (29%)
Query: 110 MGVNGLWKLLEASGKPVPVETLENKVLAV--------GILYFTQGRASALLDRRKEDN-- 159
MG + + L E + V +E K +AV I Q + L D +
Sbjct: 1 MGAD-IGDLFER--EEVELEYFSGKKIAVDAFNTLYQFISIIRQPDGTPLKDSQGRITSH 57
Query: 160 --------------------IIDA---EEKDILEMIRAE--EENEIEFEEEIAGGKEEKT 194
+ D E K R + E E + + G ++
Sbjct: 58 LSGILYRVSNMVEVGIRPVFVFDGEPPEFKKAEIEERKKRRAEAEEMWIAALQAGDKDAK 117
Query: 195 EK----IKLTREMLAEQQKILDSL 214
+ ++ ++ + +L +
Sbjct: 118 KYAQAAGRVDEYIVDSAKTLLSYM 141
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication,
transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1
c.120.1.2 PDB: 1mc8_A
Length = 340
Score = 177 bits (450), Expect = 4e-51
Identities = 68/241 (28%), Positives = 104/241 (43%), Gaps = 47/241 (19%)
Query: 312 RRPYVSRKML-EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGAR 370
R V+ ++ +A++LL+L G+P + AP E EAQ A + + D D LFGA
Sbjct: 123 RATRVNEMLIEDAKKLLELMGIPIVQAPSEGEAQAAYMAAKGSVYASASQDYDSLLFGAP 182
Query: 371 TVYKNFFDKKSHVL------------RYTAPDIRYYFELTREKLIQLALLVGSDYTP-GL 417
+ +N L ++ +LTREKLI+LA+LVG+DY P G+
Sbjct: 183 RLVRNLTITGKRKLPGKNVYVEIKPELIILEEVLKELKLTREKLIELAILVGTDYNPGGI 242
Query: 418 QGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDF 477
+G+G ALEI+ R K+ LAK K D
Sbjct: 243 KGIGLKKALEIV------------------RHSKDPLAKFQKQ--------------SDV 270
Query: 478 PNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKISQR 537
++ E +L P + N L W PD +G+ +F ++ +S+ RV L + K I
Sbjct: 271 DLYAIKEFFLNPPVTDNYN-LVWRDPDEEGILKFLCDEHDFSEERVKNGLERLKKAIKSG 329
Query: 538 S 538
Sbjct: 330 K 330
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair,
DNA-binding, endonuclease, metal-BIND excision repair,
DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus
solfataricus}
Length = 346
Score = 177 bits (449), Expect = 6e-51
Identities = 51/241 (21%), Positives = 96/241 (39%), Gaps = 40/241 (16%)
Query: 311 KRRPYVSRKML-EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA 369
+ +S M+ E+++LL+ G+P + AP E EA+ A L + + D D LFGA
Sbjct: 119 QAILRLSNIMVEESKKLLRAMGIPIVQAPSEGEAEAAYLNKLGLSWAAASQDYDAILFGA 178
Query: 370 RTVYKNFFDKKSHVL------------RYTAPDIRYYFELTREKLIQLALLVGSDYTP-G 416
+ + +N L + +TRE+LI + +L+G+DY P G
Sbjct: 179 KRLVRNLTITGKRKLPNKDVYVEIKPELIETEILLKKLGITREQLIDIGILIGTDYNPDG 238
Query: 417 LQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDD 476
++G+GP AL+I+ K+ + + + K ++R
Sbjct: 239 IRGIGPERALKIIKKYG------------KIEKAMEYGEISKKDINFNIDEIR------- 279
Query: 477 FPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKISQ 536
+L P + + L P+ + + + +S+ RV + + K I +
Sbjct: 280 -------GLFLNPQVVKPEEALDLNEPNGEDIINILVYEHNFSEERVKNGIERLTKAIKE 332
Query: 537 R 537
Sbjct: 333 A 333
Score = 29.2 bits (65), Expect = 3.3
Identities = 3/21 (14%), Positives = 11/21 (52%)
Query: 118 LLEASGKPVPVETLENKVLAV 138
L++ + + L+ K +++
Sbjct: 3 LVKDVKRELSFSELKGKRVSI 23
>3qe9_Y Exonuclease 1; exonuclease, hydrolase-DNA complex; HET: DNA; 2.51A
{Homo sapiens} PDB: 3qeb_Z* 3qea_Z*
Length = 352
Score = 132 bits (332), Expect = 2e-34
Identities = 62/406 (15%), Positives = 126/406 (31%), Gaps = 97/406 (23%)
Query: 110 MGVNGLWKLLEASGKPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDIL 169
MG+ GL + ++ + +P+ V + +V+AV + A A ++ + D +
Sbjct: 1 MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCM 60
Query: 170 EMIRAEEENEIEFEEEIAGG-KEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVD 228
+ + + I+ G K E + RE ++
Sbjct: 61 KFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRE------------RRQANLLK------ 102
Query: 229 LTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLASTITEQMSREAQELLQLFGV 288
+ R+ + E + + IT M+ + + + GV
Sbjct: 103 --------------------GKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGV 142
Query: 289 PFIVAPGEAEAQCASLELGTDKKRRPYVSRKMLEAQELLQLFGVPFIVAPGEAEAQCASL 348
+VAP EA+AQ A Y+++
Sbjct: 143 DCLVAPYEADAQLA------------YLNKA----------------------------- 161
Query: 349 ELGNHTQGVITDDSDIWLFGARTVYKNFFD--KKSHVLRYTAPDIR-YYFELTREKLIQL 405
Q +IT+DS + FG + V + + R T EK +
Sbjct: 162 ---GIVQAIITEDSALLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYM 218
Query: 406 ALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLT 465
+L G DY L+G+G A ++L + D IV+ +++ ++L
Sbjct: 219 CILSGCDYLSSLRGIGLAKACKVLRLANNPD------IVKVIKKIGHYLKMNITVPEDYI 272
Query: 466 RKLRNVKLNDDF-----PNVSVIEAYLKPDINTNVQKLAWGTPDLD 506
+ P + + + + + L++ +D
Sbjct: 273 NGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVD 318
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 80.3 bits (197), Expect = 7e-16
Identities = 93/580 (16%), Positives = 162/580 (27%), Gaps = 174/580 (30%)
Query: 3 IENLYQSPWTNMSQWRYVLPSVALPIQRVGAQR----------KTLKSKAASNADKVRSD 52
I+++ S +S + L Q Q+ K L S + S
Sbjct: 51 IDHIIMSK-DAVSGTLRLF-WTLLSKQEEMVQKFVEEVLRINYKFLMSPIK-TEQRQPSM 107
Query: 53 LLKNLLEQQLLNDVLGKNEMALPPPSVSREVDMFELPPAPAQTVQDEEEDTLENIYIMGV 112
+ + +EQ+ D L + +VSR +L A ++ +N+ I GV
Sbjct: 108 MTRMYIEQR---DRLYNDNQVFAKYNVSRLQPYLKLRQA-LLELRPA-----KNVLIDGV 158
Query: 113 NGLWKLLEASGKPVPV-ETLEN-KVLAV---GILYFTQGRASALLDRRKEDNIIDAEEKD 167
G SGK + + KV I + + +++ +K
Sbjct: 159 LG-------SGKTWVALDVCLSYKVQCKMDFKIFWLNLKN------CNSPETVLEMLQK- 204
Query: 168 ILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQK-----ILDSLVKKKAKSD 222
+L I + + I ++ R +L + +L
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAEL---RRLLKSKPYENCLLVL----------L 251
Query: 223 DVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRL---ASTITEQMSREA 279
+V + F+ C ++ ++ ++ D L L + T+T E
Sbjct: 252 NVQNAKAWNA-----FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP---DEV 303
Query: 280 QELLQLF-GVPFIVAPGEAE-------AQCASL------------ELGTDKKRRPY-VSR 318
+ LL + P E + A + DK S
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL 363
Query: 319 KMLEAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDI--------WLFGAR 370
+LE E ++F L V + I W +
Sbjct: 364 NVLEPAEYRKMF-----------------DRL-----SVFPPSAHIPTILLSLIWFDVIK 401
Query: 371 TVYK---NFFDKKSHVLR------YTAPDIRYYFELTREKLIQLAL---LVGSDYTPGLQ 418
+ N K S V + + P I Y EL + + AL +V Y
Sbjct: 402 SDVMVVVNKLHKYSLVEKQPKESTISIPSI--YLELKVKLENEYALHRSIVDH-Y----- 453
Query: 419 GVGPVTALEILAKFSPSD-SPNQ--NYIVESMRRFKNWLAK--KNKPDTHLTRKLRNVKL 473
I F D P Y F + + KN R V L
Sbjct: 454 --------NIPKTFDSDDLIPPYLDQY-------FYSHIGHHLKNIEHPERMTLFRMVFL 498
Query: 474 NDDFPNVSVIEAYLKPDINTNVQKLAWGTPD--LDGLRRF 511
+ F +E ++ D AW L+ L++
Sbjct: 499 DFRF-----LEQKIRHD------STAWNASGSILNTLQQL 527
Score = 34.1 bits (77), Expect = 0.13
Identities = 24/189 (12%), Positives = 56/189 (29%), Gaps = 53/189 (28%)
Query: 18 RYVLPSVALPIQRVGAQRKTLKSKAASNADKVRSDLLKNLLEQQLLNDVLGKNEMALPPP 77
+PS+ L ++ L +++++ + +++ P
Sbjct: 425 TISIPSIYLELKVKLENEYALH---------------RSIVDHYNIPKTFDSDDLIPPY- 468
Query: 78 SVSREVDM-------FELPPAPAQTVQDEEEDTLENIYIMGVNGLW---KLLEASGKPVP 127
+D L E ++ ++ + K+
Sbjct: 469 -----LDQYFYSHIGHHL----KNIEHPERMTLFRMVF---LDFRFLEQKI-RHDSTAWN 515
Query: 128 VETLENKVLAVGILY----------FTQGRASALLD--RRKEDNIIDAEEKDILEMIRAE 175
L Y + + +A+LD + E+N+I ++ D+L +
Sbjct: 516 ASGSILNTLQQLKFYKPYICDNDPKYER-LVNAILDFLPKIEENLICSKYTDLLRIALMA 574
Query: 176 EENEIEFEE 184
E+ I FEE
Sbjct: 575 EDEAI-FEE 582
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 69.3 bits (169), Expect = 2e-12
Identities = 94/539 (17%), Positives = 152/539 (28%), Gaps = 209/539 (38%)
Query: 68 GKNEMALPPP-------SVSREVDMFE--LPPAPAQTVQDEEEDTLENIYIMGVNGLWKL 118
G E L P S + + F LP D+E T
Sbjct: 14 GSLEHVLLVPTASFFIASQLQ--EQFNKILPEPTEGFAADDEPTT--------------- 56
Query: 119 LEASGKPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEEN 178
P E L L + + E + + + +L +
Sbjct: 57 --------PAE------LVGKFLGY--------VSSLVEPSKVGQFD-QVLNLCLT---- 89
Query: 179 EIEFEEEIAGGKEEKTEKI-KLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGF 237
EFE G + I L ++L E L K+ ++I +
Sbjct: 90 --EFENCYLEGND-----IHALAAKLLQENDTTL-------VKTKELI---------KNY 126
Query: 238 FDYGCDVIKSSTLEKDRDQLLLERGKQTRLASTITE---QMSREA--QELLQLFGV---- 288
+ K +K L R A + Q + + +EL L+
Sbjct: 127 IT-ARIMAKRPFDKKSNSALF--RAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVL 183
Query: 289 --PFIVAPGEAEAQCASLELGTDK---------------KRRP---Y-----VSRKMLEA 323
I E ++ L +K P Y +S ++
Sbjct: 184 VGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI-- 241
Query: 324 QELLQLFGVPFIVA-------PGEAEAQCASLELGNHTQGVIT----DDSDIWLFGARTV 372
++QL ++V PGE + G H+QG++T ++D W
Sbjct: 242 -GVIQL--AHYVVTAKLLGFTPGELRSYLKGA-TG-HSQGLVTAVAIAETDSW------- 289
Query: 373 YKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGL--QGVGPVTALEILA 430
++FF + F + G+ P T+L
Sbjct: 290 -ESFFVSVRKAI-------TVLFFI------------------GVRCYEAYPNTSLP--- 320
Query: 431 KFSPS---DSPNQNYIVES-MRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAY 486
PS DS N V S M L+ N + + K N P +E
Sbjct: 321 ---PSILEDSLENNEGVPSPM------LSISNLTQEQVQDYVN--KTNSHLPAGKQVEIS 369
Query: 487 LKPDINT---NVQKLAWGTP-DLDG----LRRFAANKFGWSQNRVDQTLIPIMKKISQR 537
L +N V ++ G P L G LR+ A + +DQ+ IP S+R
Sbjct: 370 L---VNGAKNLV--VS-GPPQSLYGLNLTLRKAKA------PSGLDQSRIP----FSER 412
Score = 44.7 bits (105), Expect = 9e-05
Identities = 43/257 (16%), Positives = 88/257 (34%), Gaps = 92/257 (35%)
Query: 72 MALPPPSVSREVDMFELPPAPAQTVQDEEEDTLE------N--------IYIMGVNG--- 114
+LPP + ++ E P+P ++ + ++ ++ N + I VNG
Sbjct: 317 TSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN 376
Query: 115 --LWKLLEASGKPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEK------ 166
+ SG P ++L L + +A + LD+ + I +E K
Sbjct: 377 LVV------SG---PPQSLYGLNLT-----LRKAKAPSGLDQSR---IPFSERKLKFSNR 419
Query: 167 --------------DILEMIRAE-EENEIEFEEE--------IAGGKEEKTEKIKLTREM 203
++I + +N + F + G + + ++ E
Sbjct: 420 FLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS-ER 478
Query: 204 LAEQQKIL------DSLVKKKAKSDDVID---------VDLTETSTSGFFDYGCDVIKSS 248
+ + I+ ++ + KA ++D LT + G G VI +
Sbjct: 479 IVDC--IIRLPVKWETTTQFKATH--ILDFGPGGASGLGVLTHRNKDG---TGVRVIVAG 531
Query: 249 TLEKDRDQLLLERG-KQ 264
TL+ + D + G KQ
Sbjct: 532 TLDINPDD---DYGFKQ 545
Score = 42.0 bits (98), Expect = 6e-04
Identities = 31/188 (16%), Positives = 60/188 (31%), Gaps = 58/188 (30%)
Query: 290 FIVAPGEAEAQCA-SLEL-------GTDKKRRPYVSRKMLEAQELLQLFGVPFIVAPGEA 341
+V+ G ++ +L L G D+ R P+ RK+ + L + PF
Sbjct: 377 LVVS-GPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVA-SPF------- 427
Query: 342 EAQCASLELGNHTQGVITDDSDIWL-FGAR----TVYKNFFDKKSHVLRYTAPDIRYYFE 396
S L + + D + F A+ VY + D+R
Sbjct: 428 ----HSHLLVPASDLINKDLVKNNVSFNAKDIQIPVY--------DT--FDGSDLRVLSG 473
Query: 397 LTREKLIQLAL--------LVGSDYT------PG-LQGVGPVTA-------LEILAKFSP 434
E+++ + T PG G+G +T + ++ +
Sbjct: 474 SISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTL 533
Query: 435 SDSPNQNY 442
+P+ +Y
Sbjct: 534 DINPDDDY 541
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition,
helix-coil dynamics, inhibitor design, complex
(polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP:
a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A*
1taq_A*
Length = 832
Score = 39.1 bits (92), Expect = 0.004
Identities = 46/202 (22%), Positives = 85/202 (42%), Gaps = 43/202 (21%)
Query: 324 QELLQLFGVPFIVAPG-EAE------AQCASLELGNHTQGVITDDSDIW-LFGAR-TVYK 374
+EL+ L G+ + PG EA+ A+ A + G + ++T D D++ L R V
Sbjct: 100 KELVDLLGLARLEVPGYEADDVLASLAKKAE-KEGYEVR-ILTADKDLYQLLSDRIHVL- 156
Query: 375 NFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKF 432
+ ++ T + + L ++ L G SD PG++G+G TA ++L ++
Sbjct: 157 ---HPEGYL--ITPAWLWEKYGLRPDQWADYRALTGDESDNLPGVKGIGEKTARKLLEEW 211
Query: 433 SPSDSPNQNYIVESMRRFKNWLAKK---NKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKP 489
+ +++++ R K + +K + D L+ L K+ D P L+
Sbjct: 212 GSLE-----ALLKNLDRLKPAIREKILAHMDDLKLSWDL--AKVRTDLP--------LEV 256
Query: 490 DINTNVQKLAWGTPDLDGLRRF 511
D PD + LR F
Sbjct: 257 DF------AKRREPDRERLRAF 272
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 35.5 bits (81), Expect = 0.019
Identities = 12/76 (15%), Positives = 28/76 (36%), Gaps = 16/76 (21%)
Query: 154 RRKEDNII---DAEEKDILEMIRAEEENEI-EFEEEIAGGKEEKTEKIKLTREMLAEQQK 209
R ++ + DA K + + R + + ++ E+ + + E+ EK K +
Sbjct: 91 REEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQR----QSEQVEKNK--INNRIADKA 144
Query: 210 ILDSLVKKKAKSDDVI 225
+ D+I
Sbjct: 145 FY------QQPDADII 154
Score = 32.1 bits (72), Expect = 0.27
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 163 AEEKDILEMIRA-EEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKILDSLVKKKAKS 221
+E E IR EE +E A K + E + ++ L E + V+K +
Sbjct: 81 TQEP---ESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKIN 137
Query: 222 D 222
+
Sbjct: 138 N 138
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage
T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A
Length = 290
Score = 33.8 bits (78), Expect = 0.11
Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 385 RYTAPDIRYYFELTR-EKLIQLALLVG--SDYTPGLQGVGPVTALEILAKF 432
Y D+ + + E+ I L ++G D G++G+G I+ +F
Sbjct: 173 EYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREF 223
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 32.8 bits (75), Expect = 0.39
Identities = 21/143 (14%), Positives = 51/143 (35%), Gaps = 12/143 (8%)
Query: 144 TQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREM 203
Q ++ +R+ + + ++ I E +I + + E+ K + +
Sbjct: 893 LQCCYRRMMAKRELKKLKIEARS-----VERYKKLHIGLENKIMQLQRKIDEQNKEYKSL 947
Query: 204 LAEQQKILDSLVKKKAK-SDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERG 262
L + + + + K DV + ++E + + +L+++ +L E
Sbjct: 948 LEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATN------RVLSLQEEIAKLRKELH 1001
Query: 263 KQTRLASTITEQMSREAQELLQL 285
+ TI E + E QL
Sbjct: 1002 QTQTEKKTIEEWADKYKHETEQL 1024
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin
subfragment 2, heavy meromyosin, essential light chain,
motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP:
i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 31.3 bits (71), Expect = 1.1
Identities = 27/143 (18%), Positives = 52/143 (36%), Gaps = 26/143 (18%)
Query: 147 RASALLDRRKEDNIIDAEEK-DILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREM-- 203
+A A L ++ + EEK + E ++AE E E EE +K E ++ EM
Sbjct: 875 KAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEA 934
Query: 204 -LAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERG 262
+ E+++ L +K K + LE+ ++ R
Sbjct: 935 RIEEEEERSQQLQAEKKKMQQ----------------------QMLDLEEQLEEEEAARQ 972
Query: 263 KQTRLASTITEQMSREAQELLQL 285
K T ++ + ++L +
Sbjct: 973 KLQLEKVTADGKIKKMEDDILIM 995
Score = 31.0 bits (70), Expect = 1.2
Identities = 32/184 (17%), Positives = 67/184 (36%), Gaps = 28/184 (15%)
Query: 148 ASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQ 207
+A + E D + K + + I E+ + +E ++ E++ LAE+
Sbjct: 968 EAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKE----RKLLEERVSDLTTNLAEE 1023
Query: 208 QKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGK---Q 264
++ +L K K K + +I +L + EK R +L + K +
Sbjct: 1024 EEKAKNLTKLKNKHESMIS-ELEV--------------RLKKEEKSRQELEKIKRKLEGE 1068
Query: 265 TRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKMLEAQ 324
+ ++ + EL +A E E Q A L + ++ +K+ E +
Sbjct: 1069 SSDLHEQIAELQAQIAELKAQ------LAKKEEELQAALARLEDETSQKNNALKKIRELE 1122
Query: 325 ELLQ 328
+
Sbjct: 1123 SHIS 1126
Score = 28.3 bits (63), Expect = 9.4
Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 3/81 (3%)
Query: 145 QGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKT---EKIKLTR 201
Q + + + A+++++ E++ E E EE + EK +++
Sbjct: 902 QAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLE 961
Query: 202 EMLAEQQKILDSLVKKKAKSD 222
E L E++ L +K +D
Sbjct: 962 EQLEEEEAARQKLQLEKVTAD 982
>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme
kinase, structural genomics, joint center for structural
GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}
Length = 192
Score = 30.2 bits (69), Expect = 1.3
Identities = 12/100 (12%), Positives = 30/100 (30%), Gaps = 28/100 (28%)
Query: 152 LDRRKEDNII--DAEEKDILE-----MIRAEEENEIEFEEEIA---------GGKEEK-- 193
++R+K I+ E LE +++ + I + G ++
Sbjct: 72 VNRKKLAGIVFESRENLKKLELLVHPLMKKRVQEIINKTSGLIVIEAALLKRMGLDQLCD 131
Query: 194 -------TEKIKLTREMLAEQQKILDSLVKKKAKSDDVID 226
+ + L R A+++ + V+
Sbjct: 132 HVITVVASRETILKRNREADRRL---KFQEDIVPQGIVVA 168
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 30.9 bits (71), Expect = 1.3
Identities = 16/104 (15%), Positives = 38/104 (36%), Gaps = 13/104 (12%)
Query: 117 KLLEASGK------PVPVETLENKVLAVGILYFTQGRASALLDRRKE--DNIIDAEEKDI 168
L E + K P + ++ K+ A+A ++K+ + A +K
Sbjct: 235 DLAEHAAKEPFAFEPEDTDAIKAKMKD----LVGADIAAAYKIQKKQDRYEAVGAAKKKA 290
Query: 169 LEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKILD 212
+ + +EN ++ G ++ E + R + + +D
Sbjct: 291 IAALGLSDENPTGYDPLKLGAIFKELEA-DVVRRGILDTGLRID 333
>2fxo_A Myosin heavy chain, cardiac muscle beta isoform; coiled coil
(dimeric, parallel), familial hypertrophic
cardiomyopathy, FHC-associated mutant E924K; 2.50A {Homo
sapiens} SCOP: h.1.26.1 PDB: 2fxm_A
Length = 129
Score = 28.7 bits (64), Expect = 2.3
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 161 IDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTE---KIKLTREMLAEQQKILDSLVKK 217
+ E+ D+ ++AE++N + EE + K + K+K + L +++++ L K
Sbjct: 46 LLQEKNDLQLQVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAK 105
Query: 218 KAKSDDVID 226
K K +D
Sbjct: 106 KRKLEDECS 114
>1mpy_A Catechol 2,3-dioxygenase; extradiol dioxygenase, non heme iron
dioxygenase, metapyrocatechase, oxidoreductase; 2.80A
{Pseudomonas putida} SCOP: d.32.1.3 d.32.1.3
Length = 307
Score = 29.4 bits (66), Expect = 2.5
Identities = 4/29 (13%), Positives = 6/29 (20%), Gaps = 3/29 (10%)
Query: 492 NTNVQKLAW---GTPDLDGLRRFAANKFG 517
N V + D+ G
Sbjct: 2 NKGVMRPGHVQLRVLDMSKALEHYVELLG 30
>3doa_A Fibrinogen binding protein; structural genomics, MCSG., protein
structure initiative, midwest center for structural
genomics; 2.81A {Staphylococcus aureus subsp}
Length = 288
Score = 29.6 bits (66), Expect = 2.8
Identities = 16/103 (15%), Positives = 44/103 (42%), Gaps = 11/103 (10%)
Query: 351 GNHTQGVITDDSDIWLFGARTVYKNFFDKKSHV--LRYTAPDIRYY---FELTREKLIQL 405
G H+ ++ D++ + G + + N ++ + Y AP ++ +++T ++++
Sbjct: 123 GKHSNLILVDENRKIIEGFKHLTPNTNHYRTVMPGFNYEAPPTQHKINPYDITGAEVLKY 182
Query: 406 ALLVGSDYTPGL----QGVGPVTALEIL--AKFSPSDSPNQNY 442
+ L +G P+ EI+ +F S + + +
Sbjct: 183 IDFNAGNIAKQLLNQFEGFSPLITNEIVSRRQFMTSSTLPEAF 225
>3hpy_A Catechol 2,3-dioxygenase; repeated motifs, aromatic hydrocarbons
catabolism, iron, oxidoreductase; 1.94A {Pseudomonas SP}
PDB: 3hpv_A 3hq0_A*
Length = 309
Score = 29.4 bits (66), Expect = 3.1
Identities = 6/28 (21%), Positives = 9/28 (32%), Gaps = 3/28 (10%)
Query: 493 TNVQKLAW---GTPDLDGLRRFAANKFG 517
T V + +L+ F N G
Sbjct: 4 TGVLRPGHAQVRVLNLEEGIHFYRNVLG 31
>1lgt_A Biphenyl-2,3-DIOL 1,2-dioxygenase; extradiol dioxygenase,
2,3-dihydroxybiphenyl, non-heme iron, anaerobic, PCB
biodegradation; HET: BP3; 1.70A {Burkholderia
xenovorans} SCOP: d.32.1.3 d.32.1.3 PDB: 1kmy_A* 1knd_A
1knf_A 1han_A* 1lkd_A*
Length = 297
Score = 29.1 bits (65), Expect = 3.2
Identities = 6/27 (22%), Positives = 11/27 (40%), Gaps = 3/27 (11%)
Query: 494 NVQKLAW---GTPDLDGLRRFAANKFG 517
+++ L + D+ R F K G
Sbjct: 1 SIRSLGYMGFAVSDVAAWRSFLTQKLG 27
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 29.2 bits (66), Expect = 4.0
Identities = 13/100 (13%), Positives = 32/100 (32%)
Query: 158 DNIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKILDSLVKK 217
+ +D + ++++ + +++ K K L ++ + D L
Sbjct: 207 ETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADRKQWLEQKGNLADITVEDKLTMT 266
Query: 218 KAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQL 257
+ + E + + +Y VI L D L
Sbjct: 267 SLAHHATENRSVAEFTEQAYLNYAMYVIMDRALPHISDGL 306
>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination,
branch migration, DNA BIND oligomerization, acidic PIN;
2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A
2h5x_A 1bvs_A
Length = 212
Score = 28.4 bits (64), Expect = 4.5
Identities = 7/19 (36%), Positives = 8/19 (42%)
Query: 418 QGVGPVTALEILAKFSPSD 436
GVGP A+ LA
Sbjct: 94 SGVGPRLAMAALAVHDAPA 112
>1f1u_A Homoprotocatechuate 2,3-dioxygenase; extradiol, manganese,
biodegradation, aromatic, oxidoreductase; 1.50A
{Arthrobacter globiformis} SCOP: d.32.1.3 d.32.1.3 PDB:
1f1r_A 1f1v_A* 1f1x_A
Length = 323
Score = 28.8 bits (64), Expect = 4.5
Identities = 6/27 (22%), Positives = 11/27 (40%), Gaps = 3/27 (11%)
Query: 494 NVQKLAW---GTPDLDGLRRFAANKFG 517
++ + A+ DL R F + G
Sbjct: 14 DIVRCAYMEIVVTDLAKSREFYVDVLG 40
>3hv0_A Tryptophanyl-tRNA synthetase; tRNA-ligase, ATP-binding,
aminoacyl-tRNA synthetase, ligase, nucleotide-binding;
HET: TRP; 2.42A {Cryptosporidium parvum iowa II}
Length = 393
Score = 28.7 bits (64), Expect = 4.6
Identities = 17/124 (13%), Positives = 38/124 (30%), Gaps = 8/124 (6%)
Query: 304 LELGTDKKRRPYVSRKMLEAQELLQLFGVPFIVAPGEAEAQCASLELGN--HTQGVITDD 361
+ G D + + A+ + + ++ + ++ + N
Sbjct: 143 IACGFDPELTFIFTNLEYIAELYPDILRIEKKISCSQIKSIFGFKDSCNVGKFAFPAVQA 202
Query: 362 SDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLAL----LVGSDYTPGL 417
+ + ++ H L A D YF + R+ +L + S + P L
Sbjct: 203 APAFSSSFPHIFGG--RTDIHCLVPHAIDQDPYFRMVRDVAPRLGYLKPSSIHSIFLPSL 260
Query: 418 QGVG 421
QG
Sbjct: 261 QGSQ 264
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex,
octameric RUVA, AAA-ATPase domain, complex with
nucleotide, hydrolase; HET: ANP; 3.30A {Thermus
thermophilus} SCOP: a.60.2.1 b.40.4.2
Length = 191
Score = 28.3 bits (64), Expect = 4.7
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 418 QGVGPVTALEILAKFSPSD 436
GVGP AL +L+ P
Sbjct: 78 SGVGPKVALALLSALPPRL 96
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA
recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1
a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A
Length = 203
Score = 28.1 bits (63), Expect = 5.5
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 418 QGVGPVTALEILAKFSPSD 436
GVGP AL IL+ S
Sbjct: 79 NGVGPKLALAILSGMSAQQ 97
>3eck_A Protein (homoprotocatechuate 2,3-dioxygenase); oxidoreductase,
extradiol, FEII, crystal packing; HET: XXG; 1.60A
{Brevibacterium fuscum} SCOP: d.32.1.3 d.32.1.3 PDB:
3ecj_A* 3ojn_A* 1q0o_A 1q0c_A 2iga_A* 2ig9_A 3ojj_A*
3bza_A* 3ojk_A* 3ojt_A*
Length = 365
Score = 28.5 bits (63), Expect = 6.0
Identities = 6/27 (22%), Positives = 11/27 (40%), Gaps = 3/27 (11%)
Query: 494 NVQKLAW---GTPDLDGLRRFAANKFG 517
++ + A+ DL R F + G
Sbjct: 14 DILRCAYAELVVTDLAKSRNFYVDVLG 40
>2qag_C Septin-7; cell cycle, cell division, GTP-binding,
nucleotide-binding, phosphorylation, acetylation,
alternative splicing, coiled coil; HET: GDP GTP; 4.00A
{Homo sapiens}
Length = 418
Score = 28.2 bits (62), Expect = 8.0
Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 12/70 (17%)
Query: 154 RRKEDNIIDAEE---KDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKI 210
+ E + E K++ + EE +FE+E A + ++ + EQQ
Sbjct: 354 KDSEAELQRRHEQMKKNLEAQHKELEEKRRQFEDEKANWEAQQR---------ILEQQNS 404
Query: 211 LDSLVKKKAK 220
+L K K K
Sbjct: 405 SRTLEKNKKK 414
>3v6i_A V-type ATP synthase subunit E; peripheral stator stalk, right
handed coiled-coil, ATPase/SY ATP binding, membrane,
hydrolase; 2.25A {Thermus thermophilus} PDB: 3k5b_E
3j0j_J
Length = 187
Score = 27.6 bits (61), Expect = 9.3
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 156 KEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQK 209
K + I+ E + ++ + E E + E + EEK + + RE E Q
Sbjct: 2 KLEAILSQEVEAEIQALLQEAEAKAE---AVKREAEEKAKALLQARERALEAQY 52
>2xcs_B DNA gyrase subunit B, DNA gyrase subunit A; isomerase, type IIA
topoisomerase; HET: DNA 5UA RXV; 2.10A {Staphylococcus
aureus} PDB: 2xct_B* 2xcr_B* 2xcq_A* 2xco_A*
Length = 692
Score = 28.0 bits (63), Expect = 9.7
Identities = 16/106 (15%), Positives = 34/106 (32%), Gaps = 6/106 (5%)
Query: 152 LDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREMLAEQQKIL 211
++ + E L ++ E+ E + E+ G + + + +
Sbjct: 144 MNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFA 203
Query: 212 DSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQL 257
+ + + ++T F DY VI + L RD L
Sbjct: 204 E------LPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGL 243
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.315 0.133 0.376
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,169,285
Number of extensions: 512010
Number of successful extensions: 1401
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1342
Number of HSP's successfully gapped: 98
Length of query: 538
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 440
Effective length of database: 3,965,535
Effective search space: 1744835400
Effective search space used: 1744835400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 60 (27.6 bits)