RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 014847
(417 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 = 267 bits (683), Expect = 6e-80
Identities = 140/510 (27%), Positives = 201/510 (39%), Gaps = 143/510 (28%)
Query: 4 LLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLF 63
+LG++ IIP Q QA+G TN N+R+DT+ L+YPQ+PL
Sbjct: 748 ILGVAASIIPFPDHN---QSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLG 804
Query: 64 WILISDCLGRPE--------------------DSLVMNQASLECGVFRSE---SYKAEVD 100
+ L E DS++MNQ+S++ G+FRS SY +
Sbjct: 805 TTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEK 864
Query: 101 NKDIQVKSR---PSDDMLNFGKIQS----------------KSGDIVIGKYAEIGA---- 137
+ + P K + D++IGK I
Sbjct: 865 KYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEE 924
Query: 138 -----------DHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKF 186
D S L+ TE G+V +VL+++N DG F V +R +GDKF
Sbjct: 925 LGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRT----TKIPQIGDKF 980
Query: 187 SSMHGQKGVLGFL--------------------------EQTPAQLLEAALGK-GACDGL 219
+S HGQKG +G T A L+E L K A G
Sbjct: 981 ASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGN 1040
Query: 220 MSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFEC-------- 271
A+PF + E +S+LL G ++ G FE
Sbjct: 1041 EGDASPF----TDITVEG----ISKLLREHGYQSRG-------------FEVMYNGHTGK 1079
Query: 272 PMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEF 331
+ + IF T+YQ+ HM +DK+ R G Q LT +PV R R GG+ F
Sbjct: 1080 KL---------MAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRF 1130
Query: 332 GEMKCDCLIAHGASGNLHERL-------------KCKNVANVIQRVVGGPYCRICNSADD 378
GEM+ DC+IAHGA+ L ERL C + + + C+ C++ D
Sbjct: 1131 GEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKID 1190
Query: 379 IIKANVPYGAKLLSQELSFSMGITLKFDTQ 408
I + ++PY AKLL QEL +M IT + T
Sbjct: 1191 IYQIHIPYAAKLLFQEL-MAMNITPRLYTD 1219
>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 = 264 bits (676), Expect = 2e-79
Identities = 126/509 (24%), Positives = 187/509 (36%), Gaps = 139/509 (27%)
Query: 2 SFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRP 61
+LG++ IIP YQS + QA+G N +R DT L YPQRP
Sbjct: 648 PAILGITASIIP--YPEHNQSPRNTYQSAM-AKQALGLYAANYQLRTDTRAHLLHYPQRP 704
Query: 62 LFWILISDCLGRP--------------------EDSLVMNQASLECGVFRSE---SYKAE 98
L D +G EDS++MN++S+E G++RS Y E
Sbjct: 705 LVQTRALDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTE 764
Query: 99 VDNKDIQVKSR---PSDDMLNFGKIQS----------------KSGDIVIGKY------- 132
+ + P + + + K GD++IGK
Sbjct: 765 EVKYPGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQ 824
Query: 133 -------AEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDK 185
+ D SI +H E G+V VL++ +G V +R + +GDK
Sbjct: 825 EFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRD----LRIPSIGDK 880
Query: 186 FSSMHGQKGVLGFL--------------------------EQTPAQLLEAALGK-GACDG 218
F+S HGQKGV+G L T Q++E GK A G
Sbjct: 881 FASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSG 940
Query: 219 LMSYATPFATSTGGVITEQHQSFVSQLLNCIGARN------SGITFIFKHYFLFCLFECP 272
+ ATPF + + +++L + G T
Sbjct: 941 NIVDATPFYKTP-------IEQLQNEILKYGYLPDATEVTYDGRT------------GQK 981
Query: 273 MDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFG 332
+ +S I+ + +YQ+ HM DK+ R G Q LT +P R R GG+ FG
Sbjct: 982 I---------KSRIYFGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFG 1032
Query: 333 EMKCDCLIAHGASGNLHERL-------------KCKNVANVIQRVVGGPYCRICNSADDI 379
EM+ DCLI G + L +RL +C + + C I ++
Sbjct: 1033 EMERDCLIGFGTAMLLKDRLLDNSDRTTIYVCDQCGYIG-WYDKNKNKYVCPIHGDKSNL 1091
Query: 380 IKANVPYGAKLLSQELSFSMGITLKFDTQ 408
V Y KLL QEL SM I+ + +
Sbjct: 1092 FPVTVSYAFKLLIQEL-MSMIISPRLILE 1119
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 262 bits (670), Expect = 3e-78
Identities = 140/502 (27%), Positives = 194/502 (38%), Gaps = 128/502 (25%)
Query: 4 LLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLF 63
+LG+ IIP Q QA+G TN +R+DT+ L+YPQ+PL
Sbjct: 737 ILGILASIIPFPDHN---QSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLA 793
Query: 64 WILISDCLGRPE--------------------DSLVMNQASLECGVFRSE---SYKAEVD 100
+ L E DS++MNQAS++ G+FRS +Y +
Sbjct: 794 TTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEK 853
Query: 101 NKDIQVKSR---PSDDMLNFGKIQS----------------KSGDIVIGKYAEIGA---- 137
+ V P K + DI+IGK A I
Sbjct: 854 KIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEE 913
Query: 138 -----------DHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKF 186
D S L+ TE G+V +V++++N +G F V +R +GDKF
Sbjct: 914 LGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRS----TRIPQIGDKF 969
Query: 187 SSMHGQKGVLGFL--------------------------EQTPAQLLEAALGK-GACDGL 219
+S HGQKG +G T A L+E L K A G
Sbjct: 970 ASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGF 1029
Query: 220 MSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFI 279
ATPF V E VS+LL G ++ G FE
Sbjct: 1030 EGDATPF----TDVTVEA----VSKLLRSHGFQSRG-------------FEVMYHGH-TG 1067
Query: 280 CLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCL 339
+ + +F T+YQ+ H+ +DK+ R G Q LT +PV R R GG+ FGEM+ DC
Sbjct: 1068 RKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQ 1127
Query: 340 IAHGASGNLHERL-------------KCKNVANVIQRVVGGPYCRICNSADDIIKANVPY 386
I+HG S L ERL C +A + CR C + + +PY
Sbjct: 1128 ISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYK-KDSYECRSCQNRTRFSQVYLPY 1186
Query: 387 GAKLLSQELSFSMGITLKFDTQ 408
AKLL QEL SM I + T+
Sbjct: 1187 AAKLLFQEL-MSMNIAPRLFTK 1207
>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 = 50.8 bits (122), Expect = 6e-07
Identities = 77/371 (20%), Positives = 128/371 (34%), Gaps = 109/371 (29%)
Query: 123 KSGDIVIGK----------------YAEIGA------DHSIKLKHTERGLVLKVLLSSND 160
K GDI++G+ + G D S+++ E G+V++ +
Sbjct: 750 KPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRG 809
Query: 161 DGKNFAVVSIRQSVNMVHSAC-----LGDKFSSMHGQKGVLG---------FLEQ-TPA- 204
D +R+ V V+ A +GDK ++ HG KGV+ L TP
Sbjct: 810 DPGVELKPGVREVVR-VYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVD 868
Query: 205 ---------------QLLEAALGKGACDGL-MSYATP-FATSTGGVITEQHQSFVSQLLN 247
Q+LE LG A L Y +P F + I E
Sbjct: 869 VILNPLGVPSRMNLGQILETHLGL-AGYFLGQRYISPIFDGAKEPEIKEL---LAQAFEV 924
Query: 248 CIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTW-----ITFY-----QQF- 296
G R + K + + + + Y +
Sbjct: 925 YFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIE 984
Query: 297 -------------IHMSEDKVKFRNTGSF-----QPLTGRPVADRKRFGGIEFGEMKCDC 338
HM EDK+ R+TG + QPL G+ +FGG FGEM+
Sbjct: 985 GPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGK-----AQFGGQRFGEMEVWA 1039
Query: 339 LIAHGASGNLHERLKCKN-----VANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQ 393
L A+GA+ L E L K+ + ++ G +D+ + +VP ++L +
Sbjct: 1040 LEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKG---------EDVPEPSVPESFRVLVK 1090
Query: 394 ELSFSMGITLK 404
EL ++ + ++
Sbjct: 1091 ELQ-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 = 46.6 bits (110), Expect = 1e-05
Identities = 56/298 (18%), Positives = 96/298 (32%), Gaps = 88/298 (29%)
Query: 4 LLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIR--VDTLLQQLF----- 56
LLG + G + S+L+ T L + AI + + V + LF
Sbjct: 255 LLGFTPGELRSYLKGATGHSQGLV-----TAVAIAETDSWESFFVSVRKAITVLFFIGVR 309
Query: 57 ----YPQRPLFWILISDCL----GRPEDS--LV---MNQASLECGVFRSESYKAEVDNKD 103
YP L ++ D L G P S L + Q ++ V ++ S+ K
Sbjct: 310 CYEAYPNTSLPPSILEDSLENNEGVP--SPMLSISNLTQEQVQDYVNKTNSHLPA--GKQ 365
Query: 104 IQVKSRPSDDMLNF---GKIQSKSG-DIVIGKY-AEIGADHSIKLKHTERGLVLKVLLSS 158
+++ N G QS G ++ + K A G D S ++ +ER K+ S+
Sbjct: 366 VEISLVNGAK--NLVVSGPPQSLYGLNLTLRKAKAPSGLDQS-RIPFSER----KLKFSN 418
Query: 159 NDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDG 218
F V+ HS L + L++ + A D
Sbjct: 419 R-----FLPVASP-----FHSHLLVPA-------------SDLINKDLVKNNVSFNAKD- 454
Query: 219 LMSYATP-FATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDW 275
+ P + T G + S ++++CI P+ W
Sbjct: 455 I---QIPVYDTFDGSDLRVLSGSISERIVDCI-------------------IRLPVKW 490
Score = 46.2 bits (109), Expect = 2e-05
Identities = 41/254 (16%), Positives = 77/254 (30%), Gaps = 92/254 (36%)
Query: 14 SHLQTMTMQGWVLYQSQ-----------KHSPQAIGFP-----TTNPNIRVDTLLQQLFY 57
S Q M M LY++ H GF NP L F
Sbjct: 1626 SQEQGMGMD---LYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNP-----VNLTIHFG 1677
Query: 58 PQRPLFWILISDCLGRP--EDSLVMNQASLECGVFRSESYKAEVDNKDIQVKSRPSDDML 115
++ G+ E+ M ++ G ++E E++ R +L
Sbjct: 1678 GEK-----------GKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLL 1726
Query: 116 N----------------FGKIQSKSGDIVIGKY-AEIGADHS------------------ 140
+ F ++SK G I A G HS
Sbjct: 1727 SATQFTQPALTLMEKAAFEDLKSK-GLIPADATFA--G--HSLGEYAALASLADVMSIES 1781
Query: 141 -IKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFL 199
+++ RG+ ++V + ++ G R + M+ A + ++ Q+ + +
Sbjct: 1782 LVEVVF-YRGMTMQVAVPRDELG--------RSNYGMI--AINPGRVAASFSQEALQYVV 1830
Query: 200 EQTPAQ---LLEAA 210
E+ + L+E
Sbjct: 1831 ERVGKRTGWLVEIV 1844
Score = 41.6 bits (97), Expect = 5e-04
Identities = 51/307 (16%), Positives = 93/307 (30%), Gaps = 97/307 (31%)
Query: 52 LQQLF--YPQRPLFWILISDCLGRPEDSLV-MNQASLECGVFRSESYKAE--VDNKDIQV 106
L+ L+ Y L+ D + ++L + + +L+ ++ ++N
Sbjct: 173 LRDLYQTYHV------LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPS--- 223
Query: 107 KSRPSDDMLNF--------GKIQSKSGDIVIGKYA----EIGADHSIKLKHTE------R 148
+ P D L G IQ + Y +G + + +
Sbjct: 224 -NTPDKDYLLSIPISCPLIGVIQ-------LAHYVVTAKLLGFTPGELRSYLKGATGHSQ 275
Query: 149 GLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSS-MHGQKGVLGFLEQTPAQLL 207
GLV V ++ D ++F + F + E P L
Sbjct: 276 GLVTAVAIAETDSWESF----FVSVRKAITVL-----FFIGVRCY-------EAYPNTSL 319
Query: 208 EAALGKGACDGLMSYATP-FATSTGGVITEQHQSFVSQ--------------LLNCIGAR 252
++ + + + +P + S + EQ Q +V++ L+N GA+
Sbjct: 320 PPSILEDSLENNEGVPSPMLSIS--NLTQEQVQDYVNKTNSHLPAGKQVEISLVN--GAK 375
Query: 253 N---SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNT 309
N SG P +R Q I SE K+KF N
Sbjct: 376 NLVVSGP---------------PQSLYGLNLTLRK-AKAPSGLDQSRIPFSERKLKFSN- 418
Query: 310 GSFQPLT 316
F P+
Sbjct: 419 -RFLPVA 424
Score = 29.6 bits (66), Expect = 2.2
Identities = 46/334 (13%), Positives = 90/334 (26%), Gaps = 106/334 (31%)
Query: 145 HTERGLVLKVLLSSNDDGKNFAVVSIRQSVNM---VHSAC--LGDKFSSMHGQ--KGVLG 197
++ R L L G S+ + + L ++F+ + + +G
Sbjct: 4 YSTRPLTLS-------HG------SLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAA 50
Query: 198 FLEQT-PAQLLEAALG----------KGACDGLMSYATPFATST--GGVITEQHQSFVSQ 244
E T PA+L+ LG G D +++ + G + H + ++
Sbjct: 51 DDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEG--NDIH-ALAAK 107
Query: 245 LLNCIGARNSGITFIFKHYFLFC--------------LFECPMDWIAFICLV-------- 282
LL + K+Y LF + A + +
Sbjct: 108 LLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTD 167
Query: 283 ------RSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFG-GIEFGEM- 334
R L T+ I S + L + K F G+ E
Sbjct: 168 DYFEELRDLYQTYHVLVGDLIKFSAET--------LSELIRTTLDAEKVFTQGLNILEWL 219
Query: 335 -------KCDCLIAHGASGNL-------HERLKCK----NVANVIQRVVGGPYCRICNSA 376
D L++ S L H + K + + G +
Sbjct: 220 ENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGH-----S 274
Query: 377 DDIIKANVP---------YGAKLLSQELSFSMGI 401
++ 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 = 36.8 bits (84), Expect = 0.015
Identities = 61/418 (14%), Positives = 118/418 (28%), Gaps = 88/418 (21%)
Query: 12 IPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCL 71
+ LQ + Q + S+ I + + LL+ Y L L+ +
Sbjct: 198 VLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE-NCL---LVLLNV 253
Query: 72 GRPEDSLVMNQASLECGVFRSESYKAEVDNKDIQVKSRPS--DDMLNFGKIQSKSGDIVI 129
+++ N +L C + + +K D + S + + KS ++
Sbjct: 254 ---QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS---LL 307
Query: 130 GKYAEIGADHSIKLKHTERG---LVLKVLLSSNDDG----KNFAVVS-------IRQSVN 175
KY + L L ++ S DG N+ V+ I S+N
Sbjct: 308 LKYLDCRPQ---DLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN 364
Query: 176 MVHSACLGDKFSSMHGQKGVLGFLEQT--PAQLLEAALGKGACDGLMSYATPFATSTGGV 233
++ A F + V F P LL +M +
Sbjct: 365 VLEPAEYRKMFDRL----SV--FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY--SL 416
Query: 234 ITEQHQSFVSQLLNC---IGARNSGITF----IFKHYFL---FCLFECPMDWIAFICLVR 283
+ +Q + + + + + I HY + F + ++
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL------D 470
Query: 284 SLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHG 343
++ I H+ + R F F E K +
Sbjct: 471 QYFYSHIGH-----HLK----NIEHPERMTLF-------RMVFLDFRFLEQK---IRHDS 511
Query: 344 ASGNLHERLKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 401
+ N ++ N +Q++ Y I N P +L++ L F I
Sbjct: 512 TAWN-----ASGSILNTLQQLK--FY-------KPYICDNDPKYERLVNAILDFLPKI 555
Score = 33.7 bits (76), Expect = 0.13
Identities = 26/158 (16%), Positives = 55/158 (34%), Gaps = 43/158 (27%)
Query: 80 MNQASLECG----VFRSESYKAEVDNKDIQ------VKSRPSDDMLN-----------FG 118
+ + VF +++ D KD+Q + D ++ F
Sbjct: 11 TGEHQYQYKDILSVFE-DAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW 69
Query: 119 KIQSKSGDIVIGKYAE--IGADH-----SIKLKHTERGLVLKVLLSSND----DGKNFA- 166
+ SK ++V K+ E + ++ IK + + ++ ++ + D D + FA
Sbjct: 70 TLLSKQEEMV-QKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128
Query: 167 -VVSIRQSVNMVHSACLGDKFSS---MHGQKG----VL 196
VS Q + A L + + + G G +
Sbjct: 129 YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWV 166
>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 = 34.7 bits (80), Expect = 0.072
Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 12/61 (19%)
Query: 298 HMSEDKVKFRNTGSF-----QPLTGRPVADRK-RFGGIEFGEMKCDCLIAHGASGNLHER 351
H+ +DK+ R+TGS+ QPL G K +FGG FGEM+ L A+GA+ L E
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGG------KAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Query: 352 L 352
L
Sbjct: 1291 L 1291
>1k4m_A NAMN adenylyltransferase; nucleotidyltransferase; HET: NAD CIT;
1.90A {Escherichia coli} SCOP: c.26.1.3 PDB: 1k4k_A*
Length = 213
Score = 29.6 bits (67), Expect = 1.5
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 48 VDTL--LQQLFYPQRPLFWILISDCL 71
TL +Q P PL +I+ D L
Sbjct: 86 AQTLKEWRQEQGPDVPLAFIIGQDSL 111
>1yum_A 'probable nicotinate-nucleotide adenylyltransferase; alpha/beta
domain; HET: CIT NCN; 1.70A {Pseudomonas aeruginosa}
PDB: 1yul_A* 1yun_A*
Length = 242
Score = 29.6 bits (67), Expect = 1.6
Identities = 6/26 (23%), Positives = 11/26 (42%), Gaps = 2/26 (7%)
Query: 48 VDTL--LQQLFYPQRPLFWILISDCL 71
+DTL ++ LF ++ D
Sbjct: 106 IDTLESVRAELAADDQLFMLIGWDAF 131
>1sr2_A Putative sensor-like histidine kinase YOJN; four-helical bundle,
transferase; NMR {Escherichia coli} SCOP: a.24.10.4
Length = 116
Score = 27.7 bits (61), Expect = 2.8
Identities = 17/84 (20%), Positives = 27/84 (32%), Gaps = 12/84 (14%)
Query: 167 VVSIRQSVNMVHSACLGDKFSSM----HGQKGVLGFLEQTPAQLLEAALGKGACDGLMSY 222
V ++ V +++ F+++ H KGV L P GK C+ L
Sbjct: 41 VDTVPDDVKRLYTEAATSDFAALAQTAHRLKGVFAMLNLVP--------GKQLCETLEHL 92
Query: 223 ATPFATSTGGVITEQHQSFVSQLL 246
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 0.138 0.420
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: 6,154,864
Number of extensions: 361267
Number of successful extensions: 771
Number of sequences better than 10.0: 1
Number of HSP's gapped: 747
Number of HSP's successfully gapped: 18
Length of query: 417
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 321
Effective length of database: 4,021,377
Effective search space: 1290862017
Effective search space used: 1290862017
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)