RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13848
(409 letters)
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase
subunit A', DNA-directed...; transcription, fusion
protein, chimera protein, multiprotein; 3.30A
{Pyrococcus furiosus}
Length = 436
Score = 183 bits (466), Expect = 1e-53
Identities = 33/114 (28%), Positives = 48/114 (42%), Gaps = 8/114 (7%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDF 59
+I++ W+ LQ H +IN+E G+P + + L QRLKGK+GRFRGNLSG
Sbjct: 328 IIEDLWDLLQYHVTTYINNEAPGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNLSGGAGSG 387
Query: 60 TSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG 113
+ V + E+ N + + VL G H
Sbjct: 388 AGSGSVLARAAF-------EITVQHLFEAAEKGEVDNLNGVIENVLIGQKHHHH 434
Score = 32.7 bits (75), Expect = 0.18
Identities = 7/57 (12%), Positives = 21/57 (36%), Gaps = 2/57 (3%)
Query: 333 NRDCPVNANLKTKGRAYTFK--FSIMVKDQFRERNTACKISHVTFCVDSPTEIQQQS 387
+ ++ + +++++ + I + F + SP EI++ S
Sbjct: 30 GEEERISKVEMSYAFKLLLDELKAMVIRPKLNLSEGGKVIGSIEFGILSPQEIRKMS 86
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A
2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Length = 880
Score = 185 bits (470), Expect = 1e-51
Identities = 43/134 (32%), Positives = 72/134 (53%), Gaps = 2/134 (1%)
Query: 112 PGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKA 171
+ + + + + I+ ++G L+ PG + EE+LE IL L +R AG
Sbjct: 655 DDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRSTAGDI 714
Query: 172 CLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSK 231
+ L P N VMA +G++GS +NI+QM A +GQQ++ G+R+ G+ R+LPHF +
Sbjct: 715 ASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDI 774
Query: 232 DPASKGNVK--FLR 243
P ++G + F
Sbjct: 775 SPEARGFIYSSFRT 788
Score = 171 bits (434), Expect = 7e-47
Identities = 64/114 (56%), Positives = 84/114 (73%), Gaps = 1/114 (0%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDF 59
+I++ W+ LQ H A + ++E G+P + + R L QRLKGK+GRFRGNLSGKRVDF
Sbjct: 261 IIEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDF 320
Query: 60 TSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG 113
+SRTVISPDPN+ I +VG+PE +A+ LT PER+ N E L+Q V+NGPDK PG
Sbjct: 321 SSRTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPG 374
Score = 66.4 bits (162), Expect = 7e-12
Identities = 13/49 (26%), Positives = 24/49 (48%)
Query: 306 VIIPPPAIMKPKALWTGKQIFSLILKPNRDCPVNANLKTKGRAYTFKFS 354
+ + PAI+ P+ +TGKQ+ S L + + AN+ + R +
Sbjct: 532 IDLGEPAILAPREYYTGKQVVSAFLPKDFNFHGQANVSSGPRLCKNEDC 580
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 172 bits (438), Expect = 3e-47
Identities = 55/114 (48%), Positives = 79/114 (69%), Gaps = 1/114 (0%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDF 59
++ E + LQ H A ++++E +G P +Q + + + RLKGK+GR RGNL GKRVDF
Sbjct: 294 IVSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDF 353
Query: 60 TSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG 113
++RTVI+ DPNL + ++G+P +AK LTYPE V N L++LV NGPD+HPG
Sbjct: 354 SARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPG 407
Score = 171 bits (433), Expect = 1e-46
Identities = 52/129 (40%), Positives = 75/129 (58%)
Query: 112 PGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKA 171
++ R + E + I+ + RL+ +PG + E+ EA + + L+ RD+AG++
Sbjct: 679 ADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMTLRESFEAKVSRILNQARDNAGRS 738
Query: 172 CLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSK 231
L SN M +GSKGSFINISQM ACVGQQ + GKR+P GF R+LPHF K
Sbjct: 739 AEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDD 798
Query: 232 DPASKGNVK 240
P S+G ++
Sbjct: 799 SPESRGFIE 807
Score = 44.7 bits (105), Expect = 6e-05
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 302 HETSVIIPPPAIMKPKALWTGKQIFSLILKPNRDCPVNANLKTK 345
+ I+PPP I+KPK LWTGKQI SLI+ + + K
Sbjct: 560 PDWDGILPPPVILKPKVLWTGKQILSLIIPKGI-NLIRDDDKQS 602
Score = 34.3 bits (78), Expect = 0.088
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 356 MVKDQFRERN-TACKISHVTFCVDSPTEIQQQS 387
M QF + ++ V F + SP EI+ S
Sbjct: 1 MSGIQFSPSSVPLRRVEEVQFGILSPEEIRSMS 33
>1twf_A B220, DNA-directed RNA polymerase II largest subunit;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB:
1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A
1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A*
1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 171 bits (433), Expect = 1e-46
Identities = 48/129 (37%), Positives = 71/129 (55%)
Query: 112 PGLLRAKERLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKA 171
+R ++E K + ++ L + G + E+ E +++ L+ RD AG+
Sbjct: 673 GPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRL 732
Query: 172 CLQELHPSNGPLVMALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSK 231
L N M ++GSKGSFINI+QM ACVGQQ++ GKR+ GF +R+LPHF K
Sbjct: 733 AEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDY 792
Query: 232 DPASKGNVK 240
P SKG V+
Sbjct: 793 SPESKGFVE 801
Score = 169 bits (430), Expect = 3e-46
Identities = 58/114 (50%), Positives = 80/114 (70%), Gaps = 1/114 (0%)
Query: 1 MIQEDWEWLQLHCALFINSETSGIPLNMQPKSKS-RGLIQRLKGKQGRFRGNLSGKRVDF 59
I+E LQ H A +++++ +G P +Q + + + RLKGK+GR RGNL GKRVDF
Sbjct: 288 AIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDF 347
Query: 60 TSRTVISPDPNLQIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPG 113
++RTVIS DPNL++ QVG+P+ +AK LTYPE V N + L QLV NGP++HPG
Sbjct: 348 SARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG 401
Score = 44.7 bits (105), Expect = 5e-05
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 302 HETSVIIPPPAIMKPKALWTGKQIFSLILKPNRDCPVNANLKTKGRAYT 350
+ +IP PAI+KPK LW+GKQI S+ + ++ +G
Sbjct: 554 PDWDGVIPTPAIIKPKPLWSGKQILSVAIPNG----IHLQRFDEGTTLL 598
Score = 35.8 bits (82), Expect = 0.025
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 356 MVKDQFRERNTACKISHVTFCVDSPTEIQQQS 387
MV Q+ + V F + SP E++ S
Sbjct: 1 MVGQQYSSAPLR-TVKEVQFGLFSPEEVRAIS 31
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D-
structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB:
1i6v_D* 2gho_D
Length = 1265
Score = 71.6 bits (176), Expect = 2e-13
Identities = 34/90 (37%), Positives = 49/90 (54%), Gaps = 20/90 (22%)
Query: 1 MIQE--DWEWLQLHCALFINSE----TSGIPLNMQP-KSKSRGLIQRLKGKQGRFRGNLS 53
M+QE D A+ N + P + +P +S L L GKQGRFR NL
Sbjct: 313 MLQEAVD--------AVIDNGRRGSPVTN-PGSERPLRS----LTDILSGKQGRFRQNLL 359
Query: 54 GKRVDFTSRTVISPDPNLQIYQVGIPEHVA 83
GKRVD++ R+VI P L+++Q G+P+ +A
Sbjct: 360 GKRVDYSGRSVIVVGPQLKLHQCGLPKRMA 389
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_D*
Length = 1407
Score = 71.5 bits (176), Expect = 2e-13
Identities = 23/39 (58%), Positives = 32/39 (82%)
Query: 41 LKGKQGRFRGNLSGKRVDFTSRTVISPDPNLQIYQVGIP 79
+KGKQGRFR NL GKRVD++ R+VI+ P L+++Q G+P
Sbjct: 331 IKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLP 369
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2
PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D*
2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D*
3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Length = 1524
Score = 67.1 bits (164), Expect = 5e-12
Identities = 34/85 (40%), Positives = 44/85 (51%), Gaps = 10/85 (11%)
Query: 1 MIQE--DWEWLQLHCALFINSETSGIPLNMQPKSKSRGLIQRLKGKQGRFRGNLSGKRVD 58
M+QE D AL N N R L L GKQGRFR NL GKRVD
Sbjct: 573 MLQEAVD--------ALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVD 624
Query: 59 FTSRTVISPDPNLQIYQVGIPEHVA 83
++ R+VI P L+++Q G+P+ +A
Sbjct: 625 YSGRSVIVVGPQLKLHQCGLPKRMA 649
>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 = 51.2 bits (122), Expect = 5e-07
Identities = 55/372 (14%), Positives = 111/372 (29%), Gaps = 124/372 (33%)
Query: 56 RVDFTSRTVISPDPNLQIYQ----VGIPEHVAKILTY------PERVHHANK------EH 99
+ F I P+P E V K L Y P +V ++
Sbjct: 34 QEQFNK---ILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTE 90
Query: 100 LKQLVLNGPDKH---PGLLRAKERLLSEGYSKCEGYIRAME-SGRLQTQPGCSAEETLEA 155
+ L G D H LL+ + L + + YI A + R + SA A
Sbjct: 91 FENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSA--LFRA 148
Query: 156 VILKELSVIRDHAGKAC-------------LQELHPSNGPLVMALSGSKGSFINISQMIA 202
V ++ A L++L+ + LV L ++ ++
Sbjct: 149 VGEGNAQLV------AIFGGQGNTDDYFEELRDLYQTYHVLVGDL------IKFSAETLS 196
Query: 203 CVGQQAINGKRV-PNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKIASELKS----- 256
+ + ++ ++V G + ++ ++P++ + +L S S
Sbjct: 197 ELIRTTLDAEKVFTQGLN------ILEWLENPSNTPDKDYL--------LSIPISCPLIG 242
Query: 257 -----AYLVW-RVAGSISARGELHPKQKTDKVRSRNGWLSSVLSSS-------------- 296
Y+V ++ G P + ++ G ++++
Sbjct: 243 VIQLAHYVVTAKLLG-------FTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVS 295
Query: 297 ----LRF------REHET-SVIIPPPAIMK---------P------KALWTGKQIFSLIL 330
+ R +E PP+I++ P L T +Q+ +
Sbjct: 296 VRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNL-TQEQVQDYVN 354
Query: 331 KPNRDCPVNANL 342
K N P +
Sbjct: 355 KTNSHLPAGKQV 366
Score = 39.6 bits (92), Expect = 0.002
Identities = 74/440 (16%), Positives = 116/440 (26%), Gaps = 196/440 (44%)
Query: 71 LQ-IYQVGIPEHVAKILTYPERVH---HANKEHLKQLV-------------------LNG 107
L+ +YQ TY V + E L +L+ L
Sbjct: 173 LRDLYQ-----------TYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLEN 221
Query: 108 PDKHPGLLRAKERLLSEGYS-------KCEGYIRAMESGRLQTQPGCSAEETLEAVILKE 160
P P K+ LLS S + Y+ + L PG E
Sbjct: 222 PSNTPD----KDYLLSIPISCPLIGVIQLAHYVVTAKL--LGFTPG-------------E 262
Query: 161 LSVIRDH--AGKACLQELHPSNGPLVMALSGSKGSFINISQM-------IACVGQQAI-- 209
L R + Q L + + +A + S SF + I +A
Sbjct: 263 L---RSYLKGATGHSQGLVTA---VAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPN 316
Query: 210 -------------NGKRVP------NGFD-----------NRSLPH-----------FDK 228
N + VP + N LP
Sbjct: 317 TSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN 376
Query: 229 F--SKDPAS-KGNVKFLRYGNRLKIASELKSAYLVWRVAGSISARGELHPKQKTDKVRSR 285
S P S G LR + K S L + R+ S ++ K++
Sbjct: 377 LVVSGPPQSLYGLNLTLR---KAKAPSGLDQS----RIPFS----------ER--KLKFS 417
Query: 286 NGWL-------SSVLSSSLRFREHETSVIIPPPAIMKPKALWTGKQIFSLILKPNRDCPV 338
N +L S +L + + ++K + K ++ PV
Sbjct: 418 NRFLPVASPFHSHLLVPASDLINKD---------LVKNNVSFNAKD-----IQ----IPV 459
Query: 339 -----NANLKTKGRAYTFKFSIMVKDQ-FR-----ERNTACKISHV-TFCVDSPTEIQQQ 386
++L R + S + D R E T K +H+ F
Sbjct: 460 YDTFDGSDL----RVLSGSISERIVDCIIRLPVKWETTTQFKATHILDF----------- 504
Query: 387 SGPGNKYSPS---YSNRTGT 403
GPG + N+ GT
Sbjct: 505 -GPGGASGLGVLTHRNKDGT 523
Score = 35.0 bits (80), Expect = 0.053
Identities = 40/240 (16%), Positives = 72/240 (30%), Gaps = 74/240 (30%)
Query: 72 QIYQVGIPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAKE----RLLSEGYS 127
+ Y I E + E++ EH GLL A + L +
Sbjct: 1686 ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEK---GLLSATQFTQPALTLMEKA 1742
Query: 128 KCEGYIRAMES-GRLQTQP---G----------CSA-----EETLEAV----ILKELSVI 164
++S G + G A E +E V + +++V
Sbjct: 1743 ----AFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVP 1798
Query: 165 RDHAGKAC--LQELHPSNGPLVMALSGSKGSFINISQMIA-------------CVGQQ-A 208
RD G++ + ++P +A S S+ + + + + QQ
Sbjct: 1799 RDELGRSNYGMIAINPGR----VAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYV 1854
Query: 209 INGKRVPNGFDNRSLPHFDKFSKDPASKGNVKFLRYGNRLKI-ASELKSAYLVWRVAGSI 267
G D R+L D + L + KI EL+ + + V G +
Sbjct: 1855 AAG-------DLRAL---DTVT---------NVLNFIKLQKIDIIELQKSLSLEEVEGHL 1895
>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 = 50.6 bits (120), Expect = 7e-07
Identities = 53/355 (14%), Positives = 102/355 (28%), Gaps = 108/355 (30%)
Query: 78 IPEHVAKILTYPERVHHANKEHLKQLVLNGPDKHPGLLRAKERLLSEGYSKCEGYIRAME 137
+ + IL+ KE + ++ D G LR LLS+ E + +E
Sbjct: 38 VQDMPKSILS---------KEEIDH-IIMSKDAVSGTLRLFWTLLSKQE---EMVQKFVE 84
Query: 138 SG----------RLQT---QPGCSAEETLEAV--------ILKELSVIRD---HAGKACL 173
++T QP +E + + +V R + L
Sbjct: 85 EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQAL 144
Query: 174 QELHPSNGPLV--MALSGSKGSFINISQMIACVGQQAINGKRVPNGFDNRSLPHFDKFSK 231
EL P+ L+ + SG K + + +V D
Sbjct: 145 LELRPAKNVLIDGVLGSG-K------TWVAL----DVCLSYKVQCKMDF----------- 182
Query: 232 DPASKGNVKFLRYGNRLKIASELKS-AYLVWRVAGSISARGELHPKQKTDKVRSRNGWLS 290
+ +L N + L+ L++++ + ++R + + ++ R +
Sbjct: 183 ------KIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD-----HSSNIKLRIHSIQ 231
Query: 291 SVLSSSLRFREHETSVIIPPPAIMKPKAL---WTGKQI--FSL---ILKPNRDCPVNANL 342
+ L L+ + +E +++ L K F+L IL R V L
Sbjct: 232 AELRRLLKSKPYENCLLV----------LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFL 281
Query: 343 KTKGRAYTFKFSIMVKDQFRERNTA--------CKISHVTFCVDSPTEIQQQSGP 389
T C+ D P E+ + P
Sbjct: 282 --SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ------DLPREVLTTN-P 327
Score = 35.6 bits (81), Expect = 0.032
Identities = 22/163 (13%), Positives = 53/163 (32%), Gaps = 42/163 (25%)
Query: 7 EWLQLHCALFINSETSGIPLNMQ---PKSKSRGLI-QRLKGKQGRFRG--NLSGKRVDFT 60
E L +++ +P + P+ S +I + ++ + +++ ++
Sbjct: 302 EVKSL-LLKYLDCRPQDLPREVLTTNPRRLS--IIAESIRDGLATWDNWKHVNCDKLTTI 358
Query: 61 ---SRTVISPDPNLQIYQ--------VGIPEHVAKIL------TYPERVHHANKEHLKQL 103
S V+ P +++ IP + ++ + V NK H L
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVV--VNKLHKYSL 416
Query: 104 VLNGPDKH----PGL----------LRAKERLLSEGYSKCEGY 132
V P + P + A R + + Y+ + +
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTF 459
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 33.4 bits (75), Expect = 0.051
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 5/26 (19%)
Query: 97 KEHLKQLV----LNGPDKHPGL-LRA 117
K+ LK+L L D P L ++A
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKA 44
Score = 28.4 bits (62), Expect = 2.8
Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 17/43 (39%)
Query: 276 KQKTDKVRSRNGWLSSVLSSSLRFREHETSVIIPPPAIMKPKA 318
KQ K L +SL+ +++ P AI KA
Sbjct: 19 KQALKK-----------LQASLKLYADDSA---PALAI---KA 44
>3ez9_A Para; DNA binding, winged-HTH, partition, biosynthetic protein;
2.80A {Salmonella enterica subsp} PDB: 3ezf_A
Length = 403
Score = 31.6 bits (72), Expect = 0.51
Identities = 14/101 (13%), Positives = 30/101 (29%), Gaps = 8/101 (7%)
Query: 120 RLLSEGYSKCEGYIRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPS 179
+L + I+ ME Q A+ ++ + I H +
Sbjct: 51 KLPKLSRRIVDQAIKEMEEDGYQFNKKQVGNVEQYALTIQNVIDIYAHRKIP--KYRDIH 108
Query: 180 NGPLVMALSGSKG------SFINISQMIACVGQQAINGKRV 214
P V+ + KG S + ++ + + R+
Sbjct: 109 KSPYVIFVVNLKGGVSKTVSTVTLAHALRVHQDLLRHDLRI 149
>3ez2_A Plasmid partition protein A; type IA, DNA binding, winged-HTH, DNA
bindin; HET: ADP EPE; 2.05A {Escherichia coli} PDB:
3ez6_A* 3ez7_A
Length = 398
Score = 28.2 bits (63), Expect = 6.0
Identities = 12/88 (13%), Positives = 30/88 (34%), Gaps = 8/88 (9%)
Query: 133 IRAMESGRLQTQPGCSAEETLEAVILKELSVIRDHAGKACLQELHPSNGPLVMALSGSKG 192
+ ME + A+ ++ + I +H G + + V+ +S KG
Sbjct: 61 VSEMEEKGYVFDKRPAGSSMKYAMSIQNIIDIYEHRGVP--KYRDRYSEAYVIFISNLKG 118
Query: 193 ------SFINISQMIACVGQQAINGKRV 214
S ++++ + + R+
Sbjct: 119 GVSKTVSTVSLAHAMRAHPHLLMEDLRI 146
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
0.318 0.134 0.399
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,092,040
Number of extensions: 355480
Number of successful extensions: 498
Number of sequences better than 10.0: 1
Number of HSP's gapped: 489
Number of HSP's successfully gapped: 27
Length of query: 409
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 313
Effective length of database: 4,021,377
Effective search space: 1258691001
Effective search space used: 1258691001
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: 41 (21.7 bits)
S2: 58 (26.3 bits)