RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7582
(661 letters)
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 935 bits (2417), Expect = 0.0
Identities = 379/685 (55%), Positives = 477/685 (69%), Gaps = 59/685 (8%)
Query: 1 LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVET 60
L QE CW VI+++F+E L RQQL SFDEF+Q ++Q IV+D + L AQHT + +
Sbjct: 12 LTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDV 71
Query: 61 PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGE--- 117
RY + F QIYLS+PT E DGS + M P EARLRNLTYS+PLYVD+ K V+ +
Sbjct: 72 TRRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNV 131
Query: 118 ---------EPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIIN 168
E + K FIGKIPIMLRST+C+LNG++D +L +LNECP D GGYFIIN
Sbjct: 132 PIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIIN 191
Query: 169 GSEKVLIAQEKMATNTVYVFS-MKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSL 227
GSEKV+IAQE+ A N V VF S AY EIRS LE SR S++ + +MAR
Sbjct: 192 GSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMAR----- 246
Query: 228 KKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDE 287
GQ I A LPYI+ +IPI+IVFRALG V DRDILEHI YD +D +M+EM+KP ++E
Sbjct: 247 NTENSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEE 306
Query: 288 AFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGY 347
AFVIQ++++AL++IG RG+ GVT+E+R++YA +ILQKE+LPH+ + ET+KA+FLGY
Sbjct: 307 AFVIQDKDIALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGY 366
Query: 348 MVHRLLLASLGRRELDDRDHY--------------------------VRMYAQKFIDRGK 381
M+HR+LL +L RRE DDRDH+ V Y QK ++ +
Sbjct: 367 MIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNR 426
Query: 382 DFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNS 441
+FNL LA+K+ IIT+GLRYSLATGNWGDQK++ R GVSQVLNR TFAS+LSHLRR N+
Sbjct: 427 EFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNT 486
Query: 442 PIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEE 501
PIGRDGKLAKPRQLHNT WGM+CPAETPEG A GLVKNL+LM+Y+SVGS +PI+EFLEE
Sbjct: 487 PIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEE 546
Query: 502 WSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDI 561
W +E LE+ PSA +ATK+FVNG W+G+HRDP L TLR LRR+ I +EVSI+RDI
Sbjct: 547 WGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRR-LDISAEVSIVRDI 605
Query: 562 RDREIRIHTDAGRICRPLLIAEN-------GSLLLKKRHIDNLKER-------DYNNYGW 607
R++E+R+ TDAGRICRPL I +N G L ++K HI L E +GW
Sbjct: 606 REKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRFGW 665
Query: 608 QVLVQSGVVEYIDTLEEETTMIAMW 632
LV SG++EY+D EEET MIAM
Sbjct: 666 TALVSSGLIEYLDAEEEETVMIAMS 690
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 917 bits (2371), Expect = 0.0
Identities = 339/689 (49%), Positives = 447/689 (64%), Gaps = 64/689 (9%)
Query: 1 LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVET 60
+ E W VI+A+F EKGLV QQLDSF++F+ ++Q I+ + + L+ AQHT+
Sbjct: 25 ITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNI 84
Query: 61 PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQG---- 116
+Y + F +IY++KP E DG + P EARLRNLTYS+ L+VD+ K
Sbjct: 85 SRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPG 144
Query: 117 ----------EEPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFI 166
E ++ K FIG++PIMLRS C L+ T+ DL +L ECP D GGYFI
Sbjct: 145 RELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFI 204
Query: 167 INGSEKVLIAQEKMATNTVYVFSM-KDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQ 225
INGSEKVLIAQE+ A N V VF S ++ EIRS LE SR STL V +
Sbjct: 205 INGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLY----- 259
Query: 226 SLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSL 285
++ + + I A LPYIKQ+IPI+I+FRALG + D +ILEHI YD +D +M+EM+KP +
Sbjct: 260 -GREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCV 318
Query: 286 DEAFVIQEQNVALNFIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFL 345
++ FVIQ++ AL+FIG RG G+ KE+RI+YA++ILQKE LPH+ + E++KA+FL
Sbjct: 319 EDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFL 378
Query: 346 GYMVHRLLLASLGRRELDDRDHY--------------------------VRMYAQKFIDR 379
GYM++RLLL +L R++ DDRDH+ + Y Q+ ++
Sbjct: 379 GYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEE 438
Query: 380 GKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRV 439
DFN++LAI K IT GL+Y+LATGNWG+QKKA +RAGVSQVLNR T++S+LSHLRR
Sbjct: 439 AHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRT 498
Query: 440 NSPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFL 499
N+PIGRDGKLAKPRQLHNT WG++CPAETPEG A GLVKNL+LM+ ISVG+ P PI+ FL
Sbjct: 499 NTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFL 558
Query: 500 EEWSMENLEEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIR 559
EW ME LE+ P DAT++FVNG W G+HR+P +LM TLR LRR+ I EVS+IR
Sbjct: 559 SEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRK-GDINPEVSMIR 617
Query: 560 DIRDREIRIHTDAGRICRPLLIAEN------GSLLLKKRHIDNLKER----------DYN 603
DIR++E++I TDAGR+ RPL I E+ L ++K HI L D
Sbjct: 618 DIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVE 677
Query: 604 NYGWQVLVQSGVVEYIDTLEEETTMIAMW 632
Y W L+ G+VEYID EEE+ +IAM
Sbjct: 678 EYTWSSLLNEGLVEYIDAEEEESILIAMQ 706
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 764 bits (1973), Expect = 0.0
Identities = 228/670 (34%), Positives = 346/670 (51%), Gaps = 83/670 (12%)
Query: 1 LWQEACWIVINAYFDEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVET 60
L + W VI AYF KGLVRQ LDS+++F++ +Q I+++ +I +
Sbjct: 8 LSIDERWKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTE------------ 55
Query: 61 PPRYLLKFEQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPV 120
P ++ +I + KP E D + P EARLRNLTY+APL++ + E
Sbjct: 56 IPGLKVRLGKIRIGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAE-- 113
Query: 121 TTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKM 180
++ +IG +PIML+S ++ T L E+ E P DPGGYFI+NGSE+V++ QE +
Sbjct: 114 ---PEEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDL 170
Query: 181 ATNTVYVFSM-KDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAI 239
A N V V + S + +I S P + + G
Sbjct: 171 APNRVLVDTGKTGSNITHTAKIISSTAGYRVPVTI----ERLKDG----------TFHVS 216
Query: 240 LPYIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALN 299
P + +IP +I+ RALG + DRDI+ + D PE+ + PSL++A I + AL+
Sbjct: 217 FPAVPGKIPFVILMRALGILTDRDIVYAVSLD---PEIQNELFPSLEQASSIANVDDALD 273
Query: 300 FIGARGARPGVTKERRIKYAREILQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLASLGR 359
FIG+R G +E RI+ A++I+ K LPH+G S KKAY+L Y + +++ LGR
Sbjct: 274 FIGSRV-AIGQKRENRIEKAQQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGR 332
Query: 360 RELDDRDHY--------------------------VRMYAQKFIDRGKDFNLELAIKTKI 393
RE DD+DHY + +K RG+ L+ ++ I
Sbjct: 333 REPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDI 392
Query: 394 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPR 453
+T+ +R++LATGNW R GVSQ+L+R + S LSHLRRV S + R + R
Sbjct: 393 VTERIRHALATGNWVGG------RTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEAR 446
Query: 454 QLHNTLWGMICPAETPEGAAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEIA-- 511
LH T WG +CP ETPEG GLVKNLALMA I+VG + + L E + +EE+
Sbjct: 447 DLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVEEVIRR 506
Query: 512 -------PSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRRQMDIIVSEVSIIRDIRD- 563
+ +K+ +NG VG +RD E+L +R+ RR+ + I EV++ + D
Sbjct: 507 VTEGGEDQNEYLKWSKVILNGRLVGYYRDGEELAKKIRERRRKGE-ISDEVNVGHIVTDF 565
Query: 564 -REIRIHTDAGRICRPLLIAENGSLLLKKRHIDNLKERDYNNYGWQVLVQSGVVEYIDTL 622
E+ ++ D+GR+ RPL+I NG+ L+ + I+ L + + LV+ G +EY+D
Sbjct: 566 INEVHVNCDSGRVRRPLIIVSNGNPLVTREDIEKLDS---GSITFDDLVRQGKIEYLDAE 622
Query: 623 EEETTMIAMW 632
EEE +A+
Sbjct: 623 EEENAYVALE 632
>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 = 73.2 bits (179), Expect = 2e-13
Identities = 97/562 (17%), Positives = 178/562 (31%), Gaps = 195/562 (34%)
Query: 205 LEHS-SRPTSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEI--------PIMIVFRA 255
LEH PT+ + L++ + ILP + P +V +
Sbjct: 16 LEHVLLVPTA-SFFI-----ASQLQE-----QFNKILPEPTEGFAADDEPTTPAELVGKF 64
Query: 256 LGFVADR----------DILEHIIYDFD-------DPEMMEMVKPSLDEAFVIQEQNVAL 298
LG+V+ +L + +F+ D + ++ +++ + +
Sbjct: 65 LGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIK 124
Query: 299 NFIGARGA--RPGVTKER------------RIKYAREIL--QKEMLPHVGVSD--FCETK 340
N+I AR RP K ++ A I Q G +D F E +
Sbjct: 125 NYITARIMAKRPFDKKSNSALFRAVGEGNAQL-VA--IFGGQ-------GNTDDYFEELR 174
Query: 341 KAY-----FLGYMVHRL--LLASLGRRELDDRDHYVRMYAQKFIDRGKDFNLELAIKTKI 393
Y +G ++ L+ L R LD + + N+ ++
Sbjct: 175 DLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVF-----------TQGLNILEWLENPS 223
Query: 394 ITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPR 453
T Y L + +S L + L+H +G P
Sbjct: 224 NTPDKDY-LLS-------------IPISCPLIGVI---QLAHYVVTAKLLGFT-----PG 261
Query: 454 QLHNTLWGM------------ICPAETPEGAAVGLVKNLALMAYISVGSQ---PSPILE- 497
+L + L G I ++ E V + K + ++ +I V P+ L
Sbjct: 262 ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP 321
Query: 498 -FLEEWSMENLEEIAPS---AIADATK-------------------IF---VNG--CWV- 528
LE+ S+EN E PS +I++ T+ + VNG V
Sbjct: 322 SILED-SLEN-NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVV 379
Query: 529 -GIHRDPEQLMG---TLRKLRRQMDIIVSEVSIIRDIRDREIRI-----------HTDAG 573
G P+ L G TLRK + + S + +R+++ H+
Sbjct: 380 SG---PPQSLYGLNLTLRKAKAPSGLDQSRIP----FSERKLKFSNRFLPVASPFHS--- 429
Query: 574 RICRPLLIAENGSLL--LKKRHIDNLKERD-----YNNYGWQVL--VQSGVVEYI-DTLE 623
LL+ + + L K ++ +D Y+ + L + + E I D +
Sbjct: 430 ----HLLVPASDLINKDLVKNNVS-FNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCI- 483
Query: 624 EETTMIAMWQVLVQSGVVEYID 645
+ W+ Q +D
Sbjct: 484 --IRLPVKWETTTQFKATHILD 503
Score = 54.7 bits (131), Expect = 1e-07
Identities = 99/637 (15%), Positives = 178/637 (27%), Gaps = 244/637 (38%)
Query: 22 QQL-DSFDEFIQMSVQRIVED---SPQIDLQAE-AQHTSTEVE----TPPRYLLK----- 67
QL + F++ + + D + +L + + S+ VE +L
Sbjct: 31 SQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTE 90
Query: 68 FEQIYLS-KPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVR-------QGEEP 119
FE YL H A L + TK +++ + P
Sbjct: 91 FENCYLEGNDIH--------------ALAAKLLQENDTTLVKTKELIKNYITARIMAKRP 136
Query: 120 VTTQHQKSFI-----GKIPIM---------------LRSTY----CLLNGLTDR---DLT 152
+ + G ++ LR Y L+ L L+
Sbjct: 137 FDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLS 196
Query: 153 ELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIRSCLEH-SSRP 211
EL LD F + L I LE+ S+ P
Sbjct: 197 ELIRTTLDAEKVF-----TQGL-------------------------NILEWLENPSNTP 226
Query: 212 TSTLWVNMMARGGQSLKKSAIGQRIIAILPYIKQEIPIMIVFRALGFVAD--RDIL---- 265
+ + S IG +I + Y+ + + LGF R L
Sbjct: 227 D----KDYLLSIPISCP--LIG--VIQLAHYV-------VTAKLLGFTPGELRSYLKGAT 271
Query: 266 ---EHIIYDFDDPEMMEMVKPSLD-EAFVIQEQNV--ALNFIGARG--ARPGVTKERRIK 317
+ ++ + + E+F + + L FIG R A P +
Sbjct: 272 GHSQGLV-------TAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTS------ 318
Query: 318 YAREILQKEMLPHVGVSDFCETKKAYFLG---YMVHRLLLASLGRRELDDRDHYVRMYAQ 374
LP + D E + G M L +++L + ++ Q
Sbjct: 319 ----------LPPSILEDSLENNE----GVPSPM---LSISNLTQEQV-----------Q 350
Query: 375 KFIDRGKDFNLELAIKTKI------------ITDGLRYSLATGNWGDQK-KA----HQAR 417
++++ N L ++ ++ G SL N +K KA Q+R
Sbjct: 351 DYVNK---TNSHLPAGKQVEISLVNGAKNLVVS-GPPQSLYGLNLTLRKAKAPSGLDQSR 406
Query: 418 AGVSQ----VLNR-LT----FASSLSHLRRVNSPIGRD----------GKLAKPRQLHNT 458
S+ NR L F S L L + I +D + P +++T
Sbjct: 407 IPFSERKLKFSNRFLPVASPFHSHL--LVPASDLINKDLVKNNVSFNAKDIQIP--VYDT 462
Query: 459 LWGMICPAETPEGAAVGLVKNLALMAYI-------SVGSQPSPILEFLEEWSMENLEEIA 511
G + + + + + + + IL+F
Sbjct: 463 FDG-----SDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDF------------G 505
Query: 512 P---SAIADATKIFVNGCWVGI------HRDPEQLMG 539
P S + T +G V + +P+ G
Sbjct: 506 PGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDYG 542
Score = 48.5 bits (115), Expect = 7e-06
Identities = 76/479 (15%), Positives = 149/479 (31%), Gaps = 161/479 (33%)
Query: 10 INAYFDEKGLVRQQL-DSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKF 68
+ YF+E L + L ++ V +++ S + L + T + +
Sbjct: 166 TDDYFEE--L--RDLYQTYHVL----VGDLIKFSAET-LSELIRTTL---DAEKVFTQGL 213
Query: 69 EQIYLSKPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSF 128
I W ++ PS P++ L ++ S PL I Q V T
Sbjct: 214 -NIL-----EWLEN--PSN-TPDKDYLLSIPISCPL---IGVI---QLAHYVVTAKL--- 255
Query: 129 IGKIPIMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVF 188
+G P LRS L G T S+ ++ A
Sbjct: 256 LGFTPGELRS---YLKGATGH--------------------SQGLVTAV---------AI 283
Query: 189 SMKDSKYAYKTEIRSCLE---------HSSRPTSTLWVNMMARGGQSLKKSAIGQRIIAI 239
+ DS ++ +R + + + P ++L +++ SL+ +
Sbjct: 284 AETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILE---DSLENN--------- 331
Query: 240 LPYIKQEIPI-MIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVAL 298
+ +P M+ L ++ ++ + L ++ ++L
Sbjct: 332 -----EGVPSPMLSISNL----TQEQVQDYV---------NKTNSHLPAGKQVE---ISL 370
Query: 299 -----NFI--GARGARPGVTKE-RRIKYAREILQKEMLPHVGVSDFCETKKAY---FL-- 345
N + G + G+ R+ K + Q + P F E K + FL
Sbjct: 371 VNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRI-P------FSERKLKFSNRFLPV 423
Query: 346 ------GYM--VHRLLLASLGRRELDDRDHYVRM--YAQKFIDRGKDFNLELAIKTKIIT 395
+ L+ L + + +++ Y D G D L + + I+
Sbjct: 424 ASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYD--TFD-GSD----LRVLSGSIS 476
Query: 396 DGLRYSLATG--NWGDQKKAHQARAGVSQVLNRLTF----ASSLSHLRRVNSPIGRDGK 448
+ + + W + Q +A + + L F AS L L N +DG
Sbjct: 477 ERIVDCIIRLPVKW---ETTTQFKA--THI---LDFGPGGASGLGVLTHRN----KDGT 523
Score = 38.1 bits (88), Expect = 0.011
Identities = 28/182 (15%), Positives = 53/182 (29%), Gaps = 58/182 (31%)
Query: 508 EEIAPSAIADATKIFVNGCWVGIHRDPEQLMGTLRKLRR----QMDIIVSEVSIIRDIRD 563
E+I +T R + L L Q + + E + D++
Sbjct: 1704 EKIFKEINEHSTSY--------TFRSEKGL------LSATQFTQPALTLMEKAAFEDLKS 1749
Query: 564 REIRIHTD--AGRICRPL-----LIAENGSL-------LLKKR--HIDNLKERDYN---N 604
+ + AG L L + + ++ R + RD N
Sbjct: 1750 KGLIPADATFAG---HSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSN 1806
Query: 605 YG------WQV---LVQSGVVEYIDTLEEETTM---IA-----MWQVLVQSGVVEYIDTL 647
YG +V Q + ++ + + T I Q V +G + +DT+
Sbjct: 1807 YGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQY-VAAGDLRALDTV 1865
Query: 648 EE 649
Sbjct: 1866 TN 1867
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C*
3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
Length = 1119
Score = 63.1 bits (154), Expect = 2e-10
Identities = 53/313 (16%), Positives = 104/313 (33%), Gaps = 85/313 (27%)
Query: 23 QLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTS---TEVETPPRYLLKFEQIYLSKPTHW 79
Q++S+ +Q V E + +QA + T E + +L F + L +P
Sbjct: 22 QVESYRRALQADVPP--EKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFP 79
Query: 80 EKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRST 139
+ E R ++LTY APLY + G + + F+G IP+M
Sbjct: 80 QD----------ECREKDLTYQAPLYARLQLIHKDTGL----IKEDEVFLGHIPLM---- 121
Query: 140 YCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFSM-KDSKYAYK 198
T+ G FIING+++V+++Q + + + +Y
Sbjct: 122 -------TED-------------GSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIAS 161
Query: 199 TEIRSCLEHSSRPTSTLWVNMMARGGQSL----KKSAIGQRIIAILPYIKQEIPIMIVFR 254
+ RG + ++ K++ P++++ R
Sbjct: 162 IIP-----------------LPKRGPWIDLEVEPNGVVSMKV------NKRKFPLVLLLR 198
Query: 255 ALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQEQNVALNFIGARGARPG--VTK 312
LG+ + E Y +M+ ++ + L RPG +
Sbjct: 199 VLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFTLL--------RPGDPPKR 250
Query: 313 ERRIKYAREILQK 325
++ A +
Sbjct: 251 DK----AVAYVYG 259
Score = 38.8 bits (91), Expect = 0.006
Identities = 18/34 (52%), Positives = 24/34 (70%)
Query: 453 RQLHNTLWGMICPAETPEGAAVGLVKNLALMAYI 486
R +H T +G ICP ETPEGA +GL+ +LA A +
Sbjct: 428 RDVHRTHYGRICPVETPEGANIGLITSLAAYARV 461
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 62.8 bits (153), Expect = 3e-10
Identities = 39/162 (24%), Positives = 67/162 (41%), Gaps = 43/162 (26%)
Query: 19 LVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLSKPTH 78
L+ QLDSF +FI+ + Q L+A + L++ L +P
Sbjct: 27 LLSIQLDSFQKFIEQ------DPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVF 80
Query: 79 WEKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQH---QKSFIGKIPIM 135
+ E ++R +TYSAPL V + + + T + Q+ ++G+IP+M
Sbjct: 81 DVQ----------ECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLM 130
Query: 136 LRSTYCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQ 177
TD G F+ING+E+V+++Q
Sbjct: 131 -----------TDN-------------GTFVINGTERVIVSQ 148
Score = 47.4 bits (113), Expect = 1e-05
Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 4/71 (5%)
Query: 420 VSQVLNRLTFASSLSHLRRVNS--PIG--RDGKLAKPRQLHNTLWGMICPAETPEGAAVG 475
+SQ + + S ++H RR+++ P G R+ + R +H T +G +CP ETPEG +G
Sbjct: 511 LSQFMVQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Query: 476 LVKNLALMAYI 486
L+ +L++ A
Sbjct: 571 LINSLSVYAQT 581
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor,
transferase-transcription complex; 2.91A {Thermus
aquaticus}
Length = 188
Score = 54.1 bits (131), Expect = 1e-08
Identities = 33/158 (20%), Positives = 64/158 (40%), Gaps = 43/158 (27%)
Query: 23 QLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTS---TEVETPPRYLLKFEQIYLSKPTHW 79
Q++S+ + +Q V E + +QA + T + +L F + + P
Sbjct: 7 QVESYKKALQADVP--PEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFS 64
Query: 80 EKDGSPSPMMPNEARLRNLTYSAPLYVDITKTVVRQGEEPVTTQHQKSFIGKIPIMLRST 139
+ E R ++LTY APLY + + + + + + F+G +P+M
Sbjct: 65 QD----------ECREKDLTYQAPLYARL-QLIHKDTGL---IKEDEVFLGHLPLM---- 106
Query: 140 YCLLNGLTDRDLTELNECPLDPGGYFIINGSEKVLIAQ 177
T+ G FIING+++V+++Q
Sbjct: 107 -------TED-------------GSFIINGADRVIVSQ 124
>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 = 53.3 bits (127), Expect = 2e-07
Identities = 72/408 (17%), Positives = 133/408 (32%), Gaps = 138/408 (33%)
Query: 262 RDILEH----IIYDFDDPEMMEMVKPSLDEA---FVIQEQNVALNFIGARGARPGVTKER 314
+DIL + +FD ++ +M K L + +I ++ V+
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDA-------------VSGTL 65
Query: 315 RIKYAREILQKEMLPHVGVSDFCET--KKAYFLGYMVHRLLLASLGRRELDDRDHYVRMY 372
R+ + Q+E V F E + Y +++ + + E RMY
Sbjct: 66 RLFWTLLSKQEE-----MVQKFVEEVLRINY--KFLMSPI------KTEQRQPSMMTRMY 112
Query: 373 AQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTFASS 432
++ R + +N D ++ K + +R Q +L +
Sbjct: 113 IEQ---RDRLYN-----------DNQVFA----------KYNVSRL---QPYLKLR--QA 143
Query: 433 LSHLRRVNSPIGRDGKLAKPRQLHNTLWGMICPAETPEGAAVGLVKN-LALMAYISVGSQ 491
L LR + + G++ G+ G K +AL +S Q
Sbjct: 144 LLELRP-AKNVL----------ID----GVL-------GS--G--KTWVALDVCLSYKVQ 177
Query: 492 PSPILEFLEEWSMENLEEIAPSAIADATKIFVNGCW--VGIHRDPEQLMGTLRKLRRQMD 549
M+ KIF W + PE ++ L+KL Q+D
Sbjct: 178 CK----------MDF-------------KIF----WLNLKNCNSPETVLEMLQKLLYQID 210
Query: 550 I-IVSEVSIIRDIRDREIRIHTDAGRICRPLLIAENG--SLL-LKKRHIDNLKERDYNNY 605
S +I+ +RIH+ + R LL ++ LL L ++ N K + N
Sbjct: 211 PNWTSRSDHSSNIK---LRIHSIQAEL-RRLLKSKPYENCLLVL--LNVQNAKAWNAFNL 264
Query: 606 GWQVLVQSGVVEYIDTLEEETTMIAMWQVLVQSGVVEYIDTLEEETTM 653
++L+ + + D L TT + + TL +
Sbjct: 265 SCKILLTTRFKQVTDFLSAATT--------THISLDHHSMTLTPDEVK 304
Score = 50.2 bits (119), Expect = 2e-06
Identities = 63/420 (15%), Positives = 121/420 (28%), Gaps = 122/420 (29%)
Query: 54 TSTEVETPPRYLLKFEQIY--LSKPTHWEKDGSPSPMMPNE---ARLRNLTYSAP----L 104
+P L +++ + D S + + A LR L S P L
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL 247
Query: 105 YV--DI-TKTVVRQGEEPVTTQHQKSFIGKIPIMLRSTYCLLNGLTDRDLTELNECPLDP 161
V ++ +F I+L T R +
Sbjct: 248 LVLLNVQNAKAW------------NAFNLSCKILL----------TTRFKQVTDFLSAAT 285
Query: 162 GGYFIINGSEKVLIAQEKMATNTVYVFSMKDSKYAYKTEIR-SCLEHSSRPTSTLWVNMM 220
+ ++ L E + + KY + R L T+ ++++
Sbjct: 286 TTHISLDHHSMTLTPDEVKS-----LLL----KYL---DCRPQDLPREVLTTNPRRLSII 333
Query: 221 A---RGGQSL----------KKSAIGQRIIAIL-PYIKQEIPIMIVFRALG-FVADRDIL 265
A R G + K + I + + +L P ++ +F L F I
Sbjct: 334 AESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK-----MFDRLSVFPPSAHIP 388
Query: 266 EHII------YDFDDPEMM--EMVKPSLDEAFVIQEQNVALNFIGARGARPGVTKERRIK 317
++ D ++ ++ K SL V ++ + I P + E ++K
Sbjct: 389 TILLSLIWFDVIKSDVMVVVNKLHKYSL----VEKQPKESTISI------PSIYLELKVK 438
Query: 318 YAREI-LQKEMLPHVGVSD-FCETKKA------YFLGYMVHRLLLASLGRRELDDRDHYV 369
E L + ++ H + F YF ++ H L + +
Sbjct: 439 LENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNI--------EHPERM 490
Query: 370 RMYAQKFIDRGKDFNLELAIKTKIITDGLRYSLATGNWGDQKKAHQARAGVSQVLNRLTF 429
++ F+ DF ++ KI D A A + L +L F
Sbjct: 491 TLFRMVFL----DFRF---LEQKIRHDST--------------AWNASGSILNTLQQLKF 529
Score = 49.1 bits (116), Expect = 4e-06
Identities = 100/699 (14%), Positives = 188/699 (26%), Gaps = 236/699 (33%)
Query: 15 DEKGLVRQQLDSFDEFIQMSVQRIVEDSPQIDLQAEAQHTSTEVETPPRYLLKFEQIYLS 74
D + + + VQ+ VE+ +I+ Y KF L
Sbjct: 59 DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRIN-----------------Y--KF----LM 95
Query: 75 KPTHWEKDGSPSPMMPNEARLRNLTYSAPLYVDITK-TVVRQGEEPVTTQHQKSFIGKIP 133
P E PS M R+ Y+ K V R +P
Sbjct: 96 SPIKTE-QRQPSMMTRMYIEQRDRLYNDN--QVFAKYNVSR--LQPYLK----------- 139
Query: 134 IMLRSTYCLLNGLTDRDLTELNECPLDPGGYFIIN---GSEK-VLIAQ-------EKMAT 182
LR LL L P +I+ GS K + +
Sbjct: 140 --LRQ--ALLE--------------LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMD 181
Query: 183 NTVYVFSMKDSKYAYKTEIRSCLEHSSRPTSTLWVNMMARGGQSLKKSA-IGQRIIAILP 241
++ ++ + LE L + S+ I RI +I
Sbjct: 182 FKIFWLNL-----KNCNSPETVLE----MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232
Query: 242 YIKQEIPIMIVFRALGFVADRDILEHIIYDFDDPEMMEMVKPSLDEAFVIQ--------E 293
+++ + L +L ++ + + AF +
Sbjct: 233 ELRRLLKSKPYENCL------LVLLNV----QNAKAW--------NAFNLSCKILLTTRF 274
Query: 294 QNVALNFIGARGA--------RPGVTKERRIKYAREILQK------EMLPHVGVSDFCET 339
+ V +F+ A +T + + +L K + LP E
Sbjct: 275 KQVT-DFLSAATTTHISLDHHSMTLTPD----EVKSLLLKYLDCRPQDLPR-------EV 322
Query: 340 KKAYFLGYMVHRLLLASLGRRELDDRDHYVRMYAQKFIDRGKDFNLELAIKTKIITDGLR 399
+ L+ + D + + D+ L I++
Sbjct: 323 LT-------TNPRRLSIIAESIRDGLATWDN-WKHVNCDK-----LTTIIES-------- 361
Query: 400 YSLATGNWGDQKKAHQARAGVSQVLNRLTFASSLSHLRRVNSPIGRDGKLAKPRQLHNTL 459
SL + +K + F ++ I P L + +
Sbjct: 362 -SLNVLEPAEYRKMFDRLS---------VF--------PPSAHI--------PTILLSLI 395
Query: 460 WGMICPAETPEGAAVGLVKNLAL-----MAYISVGSQPSPILEFLEEWSMENLEEIAPSA 514
W + L K + + IS+ PS LE + +EN + S
Sbjct: 396 WFDV-IKSDVMVVVNKLHKYSLVEKQPKESTISI---PSIYLELKVK--LENEYALHRSI 449
Query: 515 IA-----------DATKIFVNGCW---VGIH---RDPEQLMGTLRKLRRQMDIIVSEVSI 557
+ D +++ + +G H + + M R +
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM-------------V 496
Query: 558 IRDIR--DREIRIHTDAGRICRPLLIAENGSLLLKKRHI-DNLKERDYNNYGWQVLVQSG 614
D R +++IR H ++ L K +I DN + Y
Sbjct: 497 FLDFRFLEQKIR-HDSTAWNASGSILNTLQQLKFYKPYICDN--DPKYERL--------- 544
Query: 615 VVEYIDTLE--EETTMIAMWQVLVQSGVVEYIDTLEEET 651
V +D L EE + + + L++ ++ + + EE
Sbjct: 545 VNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEA 583
>2xap_A Ribonucleoside-diphosphate reductase 1 subunit alpha;
oxidoreductase, DNA replication, allosteric enzyme,
nucleotide-binding; HET: NIY; 2.10A {Escherichia coli}
PDB: 2xo5_A* 2x0x_A 2r1r_A 3r1r_A* 3uus_A* 1r1r_A
2xav_A* 7r1r_A 2xax_A* 6r1r_A 2xaw_A* 5r1r_A 2xo4_A*
2xak_A* 4r1r_A* 2xaz_A* 2xay_A* 1rlr_A 1qfn_B
Length = 761
Score = 29.2 bits (66), Expect = 5.1
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 361 ELDDRDHYVRMYA--QKFIDRGKDFNLELA 388
E+ D Y+++ QKFID+ N
Sbjct: 671 EMPGNDGYLQLVGIMQKFIDQSISANTNYD 700
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
0.320 0.136 0.401
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 10,417,261
Number of extensions: 661659
Number of successful extensions: 1561
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1518
Number of HSP's successfully gapped: 25
Length of query: 661
Length of database: 6,701,793
Length adjustment: 100
Effective length of query: 561
Effective length of database: 3,909,693
Effective search space: 2193337773
Effective search space used: 2193337773
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.1 bits)