RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 046830
(518 letters)
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 730 bits (1887), Expect = 0.0
Identities = 299/552 (54%), Positives = 380/552 (68%), Gaps = 45/552 (8%)
Query: 9 EEDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQH 68
+ E TQE+ W VIS++FEE L RQQL SFDEF QNTMQEIVD+ + + + +QH
Sbjct: 5 DYQYNETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQH 64
Query: 69 NPGQQSD-------FAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVI 121
Q F +IYLS+P MTE+DG T T+F + ARLRNLTYS+PLYVD+ K+V+
Sbjct: 65 TGAQGDVTRRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVM 124
Query: 122 KKGHDGEE----------------------VPIMLRSSYCTLYQNSQKALTELGECPYDE 159
+PIMLRS++C L S L +L ECPYD+
Sbjct: 125 VAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQ 184
Query: 160 GGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPML 219
GGYFIINGSEKV+IAQE+ + N V VFKK P+ AYVAE+ S E +R S++ + ++
Sbjct: 185 GGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLM 244
Query: 220 SRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLR 279
+R +SGQ I ATLPYIR++IPI+I+FRALG D DILEHICYD D QM+E+++
Sbjct: 245 AR---NTENSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMK 301
Query: 280 PSLEEAFFIQNQ----QYIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKA 335
P +EEAF IQ++ YIGKRG+T GVTREK ++YA +ILQKE+LPH+ T + ET+KA
Sbjct: 302 PCIEEAFVIQDKDIALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKA 361
Query: 336 YYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKC 395
++ G++IHR+LLCAL RR DDRDH+G KRLDLAGPLL LFR LFRK+T DV Y+QKC
Sbjct: 362 FFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKC 421
Query: 396 VDNGKDVNLQFAIKAKTITGGLKYSLATGNWG-QGNAAGTRAGVSQVLNCLTYASTFTYY 454
V+ ++ NL A+K+ IT GL+YSLATGNWG Q + R GVSQVLN T+AST ++
Sbjct: 422 VETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHL 481
Query: 455 L--------SWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIGSAAYPIL 506
KLAKPRQLHN+ WGM+CPAETPEGQACGLVKNL+LM Y+++GS + PI+
Sbjct: 482 RRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPII 541
Query: 507 EFLEEWGTENFE 518
EFLEEWG E E
Sbjct: 542 EFLEEWGLETLE 553
>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 = 719 bits (1858), Expect = 0.0
Identities = 280/559 (50%), Positives = 373/559 (66%), Gaps = 48/559 (8%)
Query: 4 EEERLEEDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIR 63
E+ EDE T E++WAVISA+F EKGLV QQLDSF++F T+Q+I+ E + + +
Sbjct: 13 EDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILE 72
Query: 64 PESQHNPGQQSD-------FAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDV 116
+QH + F +IY++KPM+ ESDG T L+ + ARLRNLTYS+ L+VDV
Sbjct: 73 QLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDV 132
Query: 117 TKRVIKKGHDGE------------------------EVPIMLRSSYCTLYQNSQKALTEL 152
KR + +PIMLRS C L + ++ L +L
Sbjct: 133 KKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKL 192
Query: 153 GECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPS 212
ECP+D GGYFIINGSEKVLIAQE+ + N V VFKK P+ ++VAE+ S E +R S
Sbjct: 193 KECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFIS 252
Query: 213 TIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDT 272
T+ V + + GSS + I ATLPYI+ +IPI+I+FRALG D +ILEHICYD D
Sbjct: 253 TLQV----KLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDW 308
Query: 273 QMMELLRPSLEEAFFIQNQQ----YIGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGD 328
QM+E+L+P +E+ F IQ+++ +IG+RG +G+ +EK I+YAK+ILQKE LPH+ +
Sbjct: 309 QMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLE 368
Query: 329 FCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDV 388
E++KA++ G++I+RLLLCAL R+ +DDRDH+G KRLDLAGPLL LF+TLF+KLT D+
Sbjct: 369 GFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDI 428
Query: 389 RSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWG-QGNAAGTRAGVSQVLNCLTY 447
Y+Q+ V+ D N++ AI AKTIT GLKY+LATGNWG Q A +RAGVSQVLN TY
Sbjct: 429 FRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTY 488
Query: 448 ASTFTYYL--------SWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITIG 499
+ST ++ KLAKPRQLHN+ WG++CPAETPEGQACGLVKNL+LM I++G
Sbjct: 489 SSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVG 548
Query: 500 SAAYPILEFLEEWGTENFE 518
+ PI+ FL EWG E E
Sbjct: 549 TDPMPIITFLSEWGMEPLE 567
>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 = 605 bits (1561), Expect = 0.0
Identities = 189/526 (35%), Positives = 273/526 (51%), Gaps = 43/526 (8%)
Query: 10 EDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHN 69
+ + +E W VI AYF+ KGLVRQ LDS+++F +N +QEI+DE +I
Sbjct: 2 NELSSNLSIDERWKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPT-----EI 56
Query: 70 PGQQSDFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEE 129
PG + +I + KP + ESD + ARLRNLTY+APL++ + + EE
Sbjct: 57 PGLKVRLGKIRIGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVENNIEAEPEE 116
Query: 130 V-----PIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVY 184
V PIML+S+ + Q + L E+GE P D GGYFI+NGSE+V++ QE ++ N V
Sbjct: 117 VYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVL 176
Query: 185 VFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEI 244
V + + + A++ S P + + H + P + +I
Sbjct: 177 VDTGKTGSNITHTAKIISSTAGYRVPVTIERL------------KDGTFHVSFPAVPGKI 224
Query: 245 PIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQ----QYIGKRGAT 300
P +IL RALG D DI+ + D ++ L PSLE+A I N +IG R A
Sbjct: 225 PFVILMRALGILTDRDIVYAVSLD---PEIQNELFPSLEQASSIANVDDALDFIGSRVA- 280
Query: 301 VGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDH 360
+G RE I+ A++I+ K LPH+GT KKAYY + I +++ LGRR DD+DH
Sbjct: 281 IGQKRENRIEKAQQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDH 340
Query: 361 YGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYS 420
Y NKRL LAG L LFR F+ D+ ++K G+ + L+ ++ +T ++++
Sbjct: 341 YANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRHA 400
Query: 421 LATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYY--------LSWKLAKPRQLHNSQWGM 472
LATGNW G R GVSQ+L+ + S ++ + R LH +QWG
Sbjct: 401 LATGNWVGG-----RTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGR 455
Query: 473 MCPAETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE 518
MCP ETPEG GLVKNLALM I +G + + L E G E
Sbjct: 456 MCPFETPEGPNSGLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVE 501
>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 = 70.4 bits (173), Expect = 7e-13
Identities = 73/385 (18%), Positives = 126/385 (32%), Gaps = 96/385 (24%)
Query: 38 QLDSFDEF-NQNTMQEIVD----ESADIEIRPESQHNPGQQS---DFAEIYLSKPMMTES 89
Q++S+ + E + ++A E P + + G+ DF E L +P +
Sbjct: 22 QVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQD 81
Query: 90 DGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKAL 149
+ R ++LTY APLY ++I K D + ++
Sbjct: 82 E----------CREKDLTYQAPLYA--RLQLIHK--DTGLI---------------KEDE 112
Query: 150 TELGECPY-DEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQN 208
LG P E G FIING+++V+++Q S + +P +Y
Sbjct: 113 VFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIP-------- 164
Query: 209 RPPSTIFVPMLSRTSAKGG------SSGQYIHATLPYIRTEIPIIILFRALGFTADEDIL 262
+ +G + + + + P+++L R LG+ +
Sbjct: 165 -----L--------PKRGPWIDLEVEPNGVVSMKV--NKRKFPLVLLLRVLGYDQETLAR 209
Query: 263 EHICYDFQDTQMMEL-----------------LRP----SLEEAF-FIQNQQYIGKRGAT 300
E Y +M+ LRP ++A ++ +R
Sbjct: 210 ELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDL 269
Query: 301 VGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAE--DDR 358
R K +E L + K F + L G DD
Sbjct: 270 GEAGRYKA----EEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDI 325
Query: 359 DHYGNKRLDLAGPLLGGLFRT-LFR 382
DH GN+R+ G L+ FR L R
Sbjct: 326 DHLGNRRIRTVGELMTDQFRVGLAR 350
Score = 41.1 bits (97), Expect = 8e-04
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 463 RQLHNSQWGMMCPAETPEGQACGLVKNLA 491
R +H + +G +CP ETPEG GL+ +LA
Sbjct: 428 RDVHRTHYGRICPVETPEGANIGLITSLA 456
>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 = 57.4 bits (139), Expect = 7e-09
Identities = 51/267 (19%), Positives = 88/267 (32%), Gaps = 107/267 (40%)
Query: 34 LVRQQLDSFDEFNQNTMQE-------------IVDESADIEIRPESQHNPGQQSDFAEIY 80
L+ QLDSF +F + + I S + E+ +
Sbjct: 27 LLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSEL------------QYVSYR 74
Query: 81 LSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCT 140
L +P+ + ++R +TYSAPL V + R++ + E
Sbjct: 75 LGEPVFDVQE----------CQIRGVTYSAPLRVKL--RLVIYEREAPE--------GTV 114
Query: 141 LYQNSQKALTELGECPY-DEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAE 199
Q+ +GE P + G F+ING+E+V++
Sbjct: 115 KDIKEQEVY--MGEIPLMTDNGTFVINGTERVIV-------------------------- 146
Query: 200 VCSMAESQ-NRPPSTIFVPMLSRTSAKGGSSGQYIHAT--LPYI---------------- 240
SQ +R P F K SSG+ ++ +PY
Sbjct: 147 ------SQLHRSPGVFF----DSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFV 196
Query: 241 ----RTEIPIIILFRALGFTADEDILE 263
R ++P I+ RAL +T ++ +
Sbjct: 197 RIDRRRKLPATIILRALNYTTEQILDL 223
Score = 55.1 bits (133), Expect = 4e-08
Identities = 37/163 (22%), Positives = 65/163 (39%), Gaps = 26/163 (15%)
Query: 341 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGK 400
++ +L+ G+ DD DH GN+R+ G + FR ++ V+ + + +
Sbjct: 428 VMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS--LGDLD 485
Query: 401 DVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLA 460
+ Q I AK I+ +K + +SQ + S T+
Sbjct: 486 TLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMVQNNPLSEITHKRRISAL 533
Query: 461 KP------------RQLHNSQWGMMCPAETPEGQACGLVKNLA 491
P R +H + +G +CP ETPEG GL+ +L+
Sbjct: 534 GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLS 576
>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 = 57.2 bits (137), Expect = 9e-09
Identities = 72/526 (13%), Positives = 138/526 (26%), Gaps = 183/526 (34%)
Query: 10 EDEEEET-TQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIE------- 61
+D + ++EE +I + G + + + +Q+ V+E I
Sbjct: 39 QDMPKSILSKEEIDHIIMSKDAVSG-TLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSP 97
Query: 62 IRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVI 121
I+ E + Q S +Y+ + R+ LY D +V
Sbjct: 98 IKTEQR----QPSMMTRMYIEQ--------------------RD-----RLYNDN--QVF 126
Query: 122 KKGHDGEEVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIING---SEK-VLIAQEK 177
K + V R Y ++AL EL +I+G S K +
Sbjct: 127 AKYN----VS---RLQ---PYLKLRQALLEL-----RPAKNVLIDGVLGSGKTWV----- 166
Query: 178 MSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIF-------------VPM---LSR 221
+VC + Q + IF + M L
Sbjct: 167 -------------------ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY 207
Query: 222 TSAKGGSSGQYIHATLPY----IRTEIPIIILF----RALGFTADEDILEHIC------- 266
+S + + I+ E+ ++ L +L ++
Sbjct: 208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL------LVLLNVQNAKAWNA 261
Query: 267 YDFQ--------DTQMMELLRPSLEEAFFIQNQQYIGKRGATVGVTREKMIKYAKEILQK 318
++ Q+ + L + + + T + ++KY Q
Sbjct: 262 FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHS----MTLTPDEVKSLLLKYLDCRPQD 317
Query: 319 EMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGN-KRLDLAGPLLGGLF 377
LP E + L + D + N K ++ L +
Sbjct: 318 --LPR-------EVLT-------TNPRRLSIIAESIRDGLATWDNWKHVNCDK--LTTII 359
Query: 378 RTLFRKLT-GDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRA 436
+ L + R + + I ++ + W ++
Sbjct: 360 ESSLNVLEPAEYRKMFDRLSVFPPSAH----IPTILLS-----LI----WFD----VIKS 402
Query: 437 GVSQVLNCLTYAS-------TFTYYL-------SWKLAKPRQLHNS 468
V V+N L S T + KL LH S
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRS 448
Score = 47.2 bits (111), Expect = 1e-05
Identities = 55/401 (13%), Positives = 112/401 (27%), Gaps = 97/401 (24%)
Query: 5 EERLEEDEEEETTQEEAWAVISAYFEEKGLVR-----------QQLDSFDEFNQNTM--- 50
R + + A + + K + ++F+ + +
Sbjct: 214 TSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-LSCKILLTT 272
Query: 51 --QEIVDE-SADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLKAARLR--N 105
+++ D SA H+ +T E +L LK R +
Sbjct: 273 RFKQVTDFLSAATTTHISLDHH-------------SMTLTPD--EVKSLLLKYLDCRPQD 317
Query: 106 LTYSA----PLYVDVTKRVIKKGHD---------GEEVPIMLRSSYCTLYQNSQKAL-TE 151
L P + + I+ G +++ ++ SS L + +
Sbjct: 318 LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377
Query: 152 LGECPYDEGGYFIINGSEKVL-IAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRP 210
L P + +L + + + V V + S+ E +
Sbjct: 378 LSVFPPS------AHIPTILLSLIWFDVIKSDVMVVVNKLHKY--------SLVE-KQPK 422
Query: 211 PSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTAD-ED--ILEHICY 267
STI +P + + +H + I I F + D HI +
Sbjct: 423 ESTISIPSIYLELKVKLENEYALHRS---IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479
Query: 268 DFQDTQMMELLRPSLEEAF----FIQNQ-QYIGKRGATVGV---TREKMIKYAKEILQKE 319
++ + E + F F++ + ++ G T +++ Y I +
Sbjct: 480 HLKNIEHPERMT-LFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDND 538
Query: 320 MLPH--VGT-GDF---CETKKAYYFGHIIH----RLLLCAL 350
V DF E ++I LL AL
Sbjct: 539 PKYERLVNAILDFLPKIEE-------NLICSKYTDLLRIAL 572
Score = 40.6 bits (94), Expect = 0.001
Identities = 37/213 (17%), Positives = 64/213 (30%), Gaps = 59/213 (27%)
Query: 249 LFRALG-FTADEDI----LEHICYD--FQDTQMM--ELLRPSL------EEAFFIQNQQY 293
+F L F I L I +D D ++ +L + SL E I Y
Sbjct: 374 MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI-PSIY 432
Query: 294 IGKRGATVGVTREKMIKYAKEILQKEMLPHVGTGDFCETKKA------YYFGHIIHRLLL 347
+ + V E + I+ +P F Y++ HI H L
Sbjct: 433 LELK-----VKLENEYALHRSIVDHYNIPK----TFDSDDLIPPYLDQYFYSHIGHHLKN 483
Query: 348 CALGRRAEDDRDHYGN--------KRLDLAGPLLGGLFRTL----------------FRK 383
R R + + + A G + TL + +
Sbjct: 484 IEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYER 543
Query: 384 LTGDVRSYVQKCVDN---GKDVNL-QFAIKAKT 412
L + ++ K +N K +L + A+ A+
Sbjct: 544 LVNAILDFLPKIEENLICSKYTDLLRIALMAED 576
>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 = 49.3 bits (117), Expect = 3e-06
Identities = 77/513 (15%), Positives = 141/513 (27%), Gaps = 195/513 (38%)
Query: 11 DEEEETTQEEAWAVISAYFEEKGLVRQQLDS----------------------------- 41
+E +TT + +I Y + + ++ D
Sbjct: 109 LQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDD 168
Query: 42 -FDEFNQNTMQEIVD----------ESADIEIRPESQHNPGQQSDFAEIY-----LSKPM 85
F+E ++++ + + + + + F + L P
Sbjct: 169 YFEE-----LRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPS 223
Query: 86 MTESDGETATLFLKAARLRNLTYSAPL--------YVDVTKRVIKKGHDGEEVPIMLRSS 137
T +L + S PL YV VT +++ GE + ++
Sbjct: 224 NTPDKD-----YLLSI-----PISCPLIGVIQLAHYV-VTAKLLGFTP-GELRSYLKGAT 271
Query: 138 YC-----------------TLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMST 180
+ + + +KA+T L F I G E
Sbjct: 272 GHSQGLVTAVAIAETDSWESFFVSVRKAITVL----------FFI-GVR----CYE---- 312
Query: 181 NHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYI 240
Y PN + + E+ PS PML S + Q + +
Sbjct: 313 --AY------PNTSLPPSILEDSLENNEGVPS----PML---SISNLTQEQ-VQDYVNKT 356
Query: 241 RTEIP----III-LF---RAL---GFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQ 289
+ +P + I L + L G L + + + PS + Q
Sbjct: 357 NSHLPAGKQVEISLVNGAKNLVVSGPPQS---LYGLNLTLR-----KAKAPSGLD----Q 404
Query: 290 NQQYIGKRGATVGVTR---------EKMIKYAKEILQKEM-------------LP--HVG 325
++ +R R ++ A +++ K++ +P
Sbjct: 405 SRIPFSER-KLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTF 463
Query: 326 TG-DFCETKKAYYFGHIIHRLLLCALGRR------AEDDRDHYGNKRLDLAGPLLGGLFR 378
G D G I R++ C + + H LD GP GG
Sbjct: 464 DGSDLRVLS-----GSISERIVDCIIRLPVKWETTTQFKATHI----LDF-GP--GGASG 511
Query: 379 --TLFRKL---TGDVRSYVQKCVDNGKDVNLQF 406
L + TG VR V +D D + F
Sbjct: 512 LGVLTHRNKDGTG-VRVIVAGTLDINPDDDYGF 543
Score = 47.7 bits (113), Expect = 9e-06
Identities = 53/356 (14%), Positives = 102/356 (28%), Gaps = 115/356 (32%)
Query: 213 TIFVPMLSRTSAKGGSSGQYIHA---------TLPYIRTEI--------PIIILFRALGF 255
+ VP + + A LP P ++ + LG+
Sbjct: 19 VLLVP-----------TASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGY 67
Query: 256 TADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQYIGKR-----GATVGVTREKMIK 310
+ +E + Q ++L L E F Y+ A + + +
Sbjct: 68 VSSL--VE----PSKVGQFDQVLNLCLTE-F---ENCYLEGNDIHALAAKLLQENDTTLV 117
Query: 311 YAKEILQKEMLPHVGTGDFCETKKAYYFGHI-----IHRLLLCALGRRAEDDRDH-Y--- 361
KE++ K Y I + AL R +
Sbjct: 118 KTKELI-----------------KNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF 160
Query: 362 ---GNKR--LD-LA------GPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIK 409
GN + L L+G L + L+ +R+ + + +N+ ++
Sbjct: 161 GGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLE 220
Query: 410 AKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLA--KPRQLHN 467
+ T Y L + +S L + + Y ++ KL P +L +
Sbjct: 221 NPSNTPDKDY-LLS------------IPISCPLIGVIQLA--HYVVTAKLLGFTPGELRS 265
Query: 468 SQWGM----------MCPAETPEGQA--CGLVKNLALMVYITIGSA---AYPILEF 508
G + AET ++ + K + ++ + IG AYP
Sbjct: 266 YLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFF--IGVRCYEAYPNTSL 319
Score = 39.6 bits (92), Expect = 0.003
Identities = 50/329 (15%), Positives = 99/329 (30%), Gaps = 139/329 (42%)
Query: 35 VRQQLDSFDEFNQNT----MQEIVDESADIEIRPESQ--HNPGQQS-DFAEIYLSKPMMT 87
+ + D ++T + +IV + P + H G++ E Y + M+
Sbjct: 1642 AQDVWNRADNHFKDTYGFSILDIVINN------PVNLTIHFGGEKGKRIRENYSA--MIF 1693
Query: 88 ES--DGETAT--LFLKA-ARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLY 142
E+ DG+ T +F + + T+ + + + +
Sbjct: 1694 ETIVDGKLKTEKIFKEINEHSTSYTFRSE----------------KGL--------LSAT 1729
Query: 143 QNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYA------Y 196
Q +Q ALT + + + + L + K F A Y
Sbjct: 1730 QFTQPALTLMEKAAF------------EDL--KSKGLIPADATF--------AGHSLGEY 1767
Query: 197 VAEVCSMAESQNRPPSTIFVPMLS----------RTSAKGGSSGQYIHATLPYIRTEI-- 244
A +A+ +S R G + +P R E+
Sbjct: 1768 AALAS-LADV------------MSIESLVEVVFYR--------GMTMQVAVP--RDELGR 1804
Query: 245 ---------PIIILFRALGFTAD--EDILEHICYDFQDTQMMELLRPSLEEA--FFIQNQ 291
P + A F+ + + ++E + + T L+ E + ++NQ
Sbjct: 1805 SNYGMIAINPGRV---AASFSQEALQYVVERVG---KRTG--WLV-----EIVNYNVENQ 1851
Query: 292 QY-IGKRGATVGVTREKMIKYAKEI-LQK 318
QY G + + + I LQK
Sbjct: 1852 QYVAA--GDLRAL--DTVTNVLNFIKLQK 1876
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor,
transferase-transcription complex; 2.91A {Thermus
aquaticus}
Length = 188
Score = 44.5 bits (106), Expect = 2e-05
Identities = 37/153 (24%), Positives = 59/153 (38%), Gaps = 50/153 (32%)
Query: 38 QLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLF 97
Q++S+ + Q ++ PE + N G Q+ F E + P+ E D L
Sbjct: 7 QVESYKKALQA------------DVPPEKRENVGIQAAFKETF---PI-EEGDKGKGGLV 50
Query: 98 L--------------KAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQ 143
L R ++LTY APLY + G E+ ++
Sbjct: 51 LDFLEYRIGDPPFSQDECREKDLTYQAPLYARLQLIHKDTGLIKED----------EVF- 99
Query: 144 NSQKALTELGECPY-DEGGYFIINGSEKVLIAQ 175
LG P E G FIING+++V+++Q
Sbjct: 100 --------LGHLPLMTEDGSFIINGADRVIVSQ 124
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 39.8 bits (92), Expect = 8e-04
Identities = 8/58 (13%), Positives = 24/58 (41%), Gaps = 9/58 (15%)
Query: 4 EEERLEEDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIE 61
+ +RL+E + E+ W EK ++ L+ +++ +++ + +
Sbjct: 94 QRKRLQELDAASKVMEQEW-------REKA--KKDLEEWNQRQSEQVEKNKINNRIAD 142
>3lti_A DNA-directed RNA polymerase subunit beta; BBM2,
nucleotidyltransferase, transcription, transferase; HET:
MLY MSE; 1.60A {Escherichia coli} PDB: 3e7h_A
Length = 296
Score = 32.9 bits (76), Expect = 0.20
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 244 IPIIILFRALGFTADEDILEH 264
+P I+ RAL +T E IL+
Sbjct: 57 LPATIILRALNYT-TEQILDL 76
>1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 KD
polypeptide; transcription, mRNA, multiprotein complex;
HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP:
a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F
1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F*
1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F
1y77_F* ...
Length = 155
Score = 29.3 bits (65), Expect = 2.0
Identities = 19/115 (16%), Positives = 38/115 (33%), Gaps = 6/115 (5%)
Query: 4 EEERLEEDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIR 63
EE + +E E E ++ Y E+ + + T ++ E
Sbjct: 5 EEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQI 64
Query: 64 PESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTK 118
+ + P MT+ E A + R ++ +AP++VD+
Sbjct: 65 RRKTLKEKAIPK--DQRATTPYMTKY--ERARIL--GTRALQISMNAPVFVDLEG 113
>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 = 28.4 bits (62), Expect = 4.1
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 8/32 (25%)
Query: 382 RKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTI 413
+KL ++ Y D+ AIKA T+
Sbjct: 23 KKLQASLKLYAD---DSAP----ALAIKA-TM 46
>1q44_A RARO47, steroid sulfotransferase, AT2G03760/; APO, structu
genomics, protein structure initiative, center for
eukaryot structural genomics; 1.90A {Arabidopsis
thaliana} SCOP: c.37.1.5 PDB: 2q3m_A
Length = 326
Score = 27.9 bits (62), Expect = 8.4
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 2 MMEEERLEEDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFN--QNTMQEIVDESAD 59
M + +E +E A+IS+ +EKG + ++ F Q +Q I+
Sbjct: 1 MSSSSSVPAYLGDEDLTQETRALISSLPKEKGWLVSEIYEFQGLWHTQAILQGILICQKR 60
Query: 60 IEIRPE 65
E +
Sbjct: 61 FEAKDS 66
>4dsg_A UDP-galactopyranose mutase; rossmann fold, flavin adenine
dinucleotide, isomerase; HET: FAD UDP; 2.25A
{Trypanosoma cruzi} PDB: 4dsh_A*
Length = 484
Score = 27.9 bits (61), Expect = 8.5
Identities = 23/182 (12%), Positives = 51/182 (28%), Gaps = 12/182 (6%)
Query: 310 KYAKEILQKEMLPHVGT--GDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLD 367
++ + I M P+ + + + L + R +++RD G
Sbjct: 146 QFGEGIADIFMRPYNFKVWAVPPCLMSTEWVEERVAPVDLERIRRNIQENRDDLGWGPNA 205
Query: 368 LAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYS------- 420
G +++ + + S + + + K T + G S
Sbjct: 206 TFRFPQRGGTGIIYQAIKEKLPSEKLTFNSGFQAIAIDADAKTITFSNGEVVSYDYLIST 265
Query: 421 ---LATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAKPRQLHNSQWGMMCPAE 477
+G + + + Y+ST + K P L + W
Sbjct: 266 VPFDNLLRMTKGTGFKGYDEWPAIADKMVYSSTNVIGIGVKGTPPPHLKTACWLYFPEDT 325
Query: 478 TP 479
+P
Sbjct: 326 SP 327
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 0.396
Gapped
Lambda K H
0.267 0.0712 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,035,398
Number of extensions: 492412
Number of successful extensions: 1206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1167
Number of HSP's successfully gapped: 29
Length of query: 518
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 420
Effective length of database: 3,965,535
Effective search space: 1665524700
Effective search space used: 1665524700
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: 59 (26.5 bits)