RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 019610
(338 letters)
>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 = 225 bits (576), Expect = 1e-66
Identities = 115/414 (27%), Positives = 164/414 (39%), Gaps = 120/414 (28%)
Query: 1 MNQASLECGVFRSE---SYKAEVDNKDIQVKSR---PSDDMLNFGKIQS----------- 43
MNQ+S++ G+FRS SY + + + P K +
Sbjct: 841 MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIA 900
Query: 44 -----KSGDIVIGKYAEIGA---------------DHSIKLKHTERGLVLKVLLSSNDDG 83
D++IGK I D S L+ TE G+V +VL+++N DG
Sbjct: 901 PGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG 960
Query: 84 KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFL----------------------- 120
F V +R +GDKF+S HGQKG +G
Sbjct: 961 LKFVKVRVRT----TKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHA 1016
Query: 121 ---EQTPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSG 176
T A L+E L K A G A+PF + E +S+LL G ++ G
Sbjct: 1017 IPSRMTVAHLIECLLSKVAALSGNEGDASPF----TDITVEG----ISKLLREHGYQSRG 1068
Query: 177 ITFIFKHYFLFCLFEC--------PMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFR 228
FE + + IF T+YQ+ HM +DK+ R
Sbjct: 1069 -------------FEVMYNGHTGKKL---------MAQIFFGPTYYQRLRHMVDDKIHAR 1106
Query: 229 NTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KC 275
G Q LT +PV R R GG+ FGEM+ DC+IAHGA+ L ERL C
Sbjct: 1107 ARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGIC 1166
Query: 276 KNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQ 329
+ + + C+ C++ DI + ++PY AKLL QEL +M IT + T
Sbjct: 1167 GLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQEL-MAMNITPRLYTD 1219
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 223 bits (570), Expect = 1e-65
Identities = 116/406 (28%), Positives = 159/406 (39%), Gaps = 105/406 (25%)
Query: 1 MNQASLECGVFRSE---SYKAEVDNKDIQVKSR---PSDDMLNFGKIQS----------- 43
MNQAS++ G+FRS +Y + + V P K +
Sbjct: 830 MNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIA 889
Query: 44 -----KSGDIVIGKYAEIGA---------------DHSIKLKHTERGLVLKVLLSSNDDG 83
DI+IGK A I D S L+ TE G+V +V++++N +G
Sbjct: 890 PGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEG 949
Query: 84 KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFL----------------------- 120
F V +R +GDKF+S HGQKG +G
Sbjct: 950 LKFVKVRMRS----TRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHA 1005
Query: 121 ---EQTPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSG 176
T A L+E L K A G ATPF V E VS+LL G ++ G
Sbjct: 1006 IPSRMTVAHLVECQLSKVSALSGFEGDATPF----TDVTVEA----VSKLLRSHGFQSRG 1057
Query: 177 ITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPL 236
FE + + +F T+YQ+ H+ +DK+ R G Q L
Sbjct: 1058 -------------FEVMYHGH-TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQIL 1103
Query: 237 TGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNVANVIQ 283
T +PV R R GG+ FGEM+ DC I+HG S L ERL C +A
Sbjct: 1104 TRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASY 1163
Query: 284 RVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQ 329
+ CR C + + +PY AKLL QEL SM I + T+
Sbjct: 1164 K-KDSYECRSCQNRTRFSQVYLPYAAKLLFQEL-MSMNIAPRLFTK 1207
>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 = 222 bits (566), Expect = 3e-65
Identities = 99/411 (24%), Positives = 151/411 (36%), Gaps = 116/411 (28%)
Query: 1 MNQASLECGVFRSE---SYKAEVDNKDIQVKSR---PSDDMLNFGKIQS----------- 43
MN++S+E G++RS Y E + + P + + +
Sbjct: 743 MNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVS 802
Query: 44 -----KSGDIVIGKY--------------AEIGADHSIKLKHTERGLVLKVLLSSNDDGK 84
K GD++IGK + D SI +H E G+V VL++ +G
Sbjct: 803 PEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGN 862
Query: 85 NFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFL------------------------ 120
V +R + +GDKF+S HGQKGV+G L
Sbjct: 863 KLVKVRVRD----LRIPSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHAL 918
Query: 121 --EQTPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARN--- 174
T Q++E GK A G + ATPF + + +++L +
Sbjct: 919 PSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTP-------IEQLQNEILKYGYLPDATE 971
Query: 175 ---SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTG 231
G T + +S I+ + +YQ+ HM DK+ R G
Sbjct: 972 VTYDGRT------------GQKI---------KSRIYFGVVYYQKLHHMVADKIHARARG 1010
Query: 232 SFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNV 278
Q LT +P R R GG+ FGEM+ DCLI G + L +RL +C +
Sbjct: 1011 PVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSDRTTIYVCDQCGYI 1070
Query: 279 ANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFDTQ 329
+ C I ++ V Y KLL QEL SM I+ + +
Sbjct: 1071 G-WYDKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQEL-MSMIISPRLILE 1119
>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 = 50.4 bits (121), Expect = 5e-07
Identities = 34/118 (28%), Positives = 58/118 (49%), Gaps = 25/118 (21%)
Query: 218 IHMSEDKVKFRNTGSF-----QPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHER 272
HM EDK+ R+TG + QPL G+ +FGG FGEM+ L A+GA+ L E
Sbjct: 998 YHMVEDKMHARSTGPYSLITQQPLGGK-----AQFGGQRFGEMEVWALEAYGAAHTLQEM 1052
Query: 273 LKCKN-----VANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLK 325
L K+ + ++ G +D+ + +VP ++L +EL ++ + ++
Sbjct: 1053 LTLKSDDIEGRNAAYEAIIKG---------EDVPEPSVPESFRVLVKELQ-ALALDVQ 1100
>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 = 38.9 bits (90), Expect = 0.002
Identities = 35/188 (18%), Positives = 58/188 (30%), Gaps = 57/188 (30%)
Query: 69 RGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSS-MHGQKGVLGFLEQTPAQL 127
+GLV V ++ D ++F + F + E P
Sbjct: 275 QGLVTAVAIAETDSWESF----FVSVRKAITVL-----FFIGVRCY-------EAYPNTS 318
Query: 128 LEAALGKGACDGLMSYATP-FATSTGGVITEQHQSFVSQ--------------LLNCIGA 172
L ++ + + + +P + S + EQ Q +V++ L+N GA
Sbjct: 319 LPPSILEDSLENNEGVPSPMLSIS--NLTQEQVQDYVNKTNSHLPAGKQVEISLVN--GA 374
Query: 173 RN---SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRN 229
+N SG P +R Q I SE K+KF N
Sbjct: 375 KNLVVSGP---------------PQSLYGLNLTLRK-AKAPSGLDQSRIPFSERKLKFSN 418
Query: 230 TGSFQPLT 237
F P+
Sbjct: 419 --RFLPVA 424
Score = 36.2 bits (83), Expect = 0.015
Identities = 34/202 (16%), Positives = 64/202 (31%), Gaps = 61/202 (30%)
Query: 1 MNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDMLNF---GKIQSKSG-DIVIGKY-AE 55
+ Q ++ V ++ S+ K +++ N G QS G ++ + K A
Sbjct: 344 LTQEQVQDYVNKTNSHLPA--GKQVEISLVNGAK--NLVVSGPPQSLYGLNLTLRKAKAP 399
Query: 56 IGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKG 115
G D S ++ +ER K+ S+ F V+ HS L
Sbjct: 400 SGLDQS-RIPFSER----KLKFSNR-----FLPVASP-----FHSHLLVPA--------- 435
Query: 116 VLGFLEQTPAQLLEAALGKGACDGLMSYATP-FATSTGGVITEQHQSFVSQLLNCIGARN 174
+ L++ + A D + P + T G + S ++++CI
Sbjct: 436 ----SDLINKDLVKNNVSFNAKD-I---QIPVYDTFDGSDLRVLSGSISERIVDCI---- 483
Query: 175 SGITFIFKHYFLFCLFECPMDW 196
P+ W
Sbjct: 484 ---------------IRLPVKW 490
Score = 30.8 bits (69), Expect = 0.79
Identities = 46/334 (13%), Positives = 90/334 (26%), Gaps = 106/334 (31%)
Query: 66 HTERGLVLKVLLSSNDDGKNFAVVSIRQSVNM---VHSAC--LGDKFSSMHGQ--KGVLG 118
++ R L L G S+ + + L ++F+ + + +G
Sbjct: 4 YSTRPLTLS-------HG------SLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAA 50
Query: 119 FLEQT-PAQLLEAALG----------KGACDGLMSYATPFATST--GGVITEQHQSFVSQ 165
E T PA+L+ LG G D +++ + G + H + ++
Sbjct: 51 DDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEG--NDIH-ALAAK 107
Query: 166 LLNCIGARNSGITFIFKHYFLFC--------------LFECPMDWIAFICLV-------- 203
LL + K+Y LF + A + +
Sbjct: 108 LLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTD 167
Query: 204 ------RSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFG-GIEFGEM- 255
R L T+ I S + L + K F G+ E
Sbjct: 168 DYFEELRDLYQTYHVLVGDLIKFSAET--------LSELIRTTLDAEKVFTQGLNILEWL 219
Query: 256 -------KCDCLIAHGASGNL-------HERLKCK----NVANVIQRVVGGPYCRICNSA 297
D L++ S L H + K + + G +
Sbjct: 220 ENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGH-----S 274
Query: 298 DDIIKANVP---------YGAKLLSQELSFSMGI 322
++ A + + + + F +G+
Sbjct: 275 QGLVTAVAIAETDSWESFFVSVRKAITVLFFIGV 308
>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 = 35.2 bits (80), Expect = 0.028
Identities = 46/376 (12%), Positives = 96/376 (25%), Gaps = 126/376 (33%)
Query: 1 MNQASLECG----VFRSESYKAEVDNKDIQ------VKSRPSDDMLN-----------FG 39
+ + VF +++ D KD+Q + D ++ F
Sbjct: 11 TGEHQYQYKDILSVFE-DAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW 69
Query: 40 KIQSKSGDIVIGKYAE--IGADH-----SIKLKHTERGLVLKVLLSSND----DGKNFA- 87
+ SK ++V K+ E + ++ IK + + ++ ++ + D D + FA
Sbjct: 70 TLLSKQEEMV-QKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128
Query: 88 -VVSIRQSVNMVHSACLGDKFSS---MHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSY 143
VS Q + A L + + + G G GK
Sbjct: 129 YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS----------------GK--------- 163
Query: 144 ATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAF--IC 201
+ + + C + + W+
Sbjct: 164 ----------------TWVALDVC-----LSYKVQ---------CKMDFKIFWLNLKNCN 193
Query: 202 LVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLI 261
+++ Q + + L + R + + +CL+
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSDHSSN---IKLRIHSIQAELRR--LLKSKPYENCLL 248
Query: 262 AHGASGNLHERLKCKNV--ANVIQRVVGGPYCRI-----CNSADDIIKANVPYGAKLLSQ 314
L NV A C+I D + A L
Sbjct: 249 V------L------LNVQNAKAWNAFNLS--CKILLTTRFKQVTDFLSAATTTHISLDHH 294
Query: 315 ELSF----SMGITLKF 326
++ + LK+
Sbjct: 295 SMTLTPDEVKSLLLKY 310
>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 = 34.3 bits (79), Expect = 0.067
Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 12/61 (19%)
Query: 219 HMSEDKVKFRNTGSF-----QPLTGRPVADRK-RFGGIEFGEMKCDCLIAHGASGNLHER 272
H+ +DK+ R+TGS+ QPL G K +FGG FGEM+ L A+GA+ L E
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGG------KAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Query: 273 L 273
L
Sbjct: 1291 L 1291
>1sr2_A Putative sensor-like histidine kinase YOJN; four-helical bundle,
transferase; NMR {Escherichia coli} SCOP: a.24.10.4
Length = 116
Score = 28.1 bits (62), Expect = 1.8
Identities = 17/84 (20%), Positives = 27/84 (32%), Gaps = 12/84 (14%)
Query: 88 VVSIRQSVNMVHSACLGDKFSSM----HGQKGVLGFLEQTPAQLLEAALGKGACDGLMSY 143
V ++ V +++ F+++ H KGV L P GK C+ L
Sbjct: 41 VDTVPDDVKRLYTEAATSDFAALAQTAHRLKGVFAMLNLVP--------GKQLCETLEHL 92
Query: 144 ATPFATSTGGVITEQHQSFVSQLL 167
S+V LL
Sbjct: 93 IREKDVPGIEKYISDIDSYVKSLL 116
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
0.323 0.137 0.412
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: 4,974,095
Number of extensions: 294172
Number of successful extensions: 655
Number of sequences better than 10.0: 1
Number of HSP's gapped: 632
Number of HSP's successfully gapped: 14
Length of query: 338
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 244
Effective length of database: 4,077,219
Effective search space: 994841436
Effective search space used: 994841436
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.4 bits)