RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3023
(392 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 = 441 bits (1137), Expect = e-154
Identities = 118/403 (29%), Positives = 167/403 (41%), Gaps = 59/403 (14%)
Query: 5 DSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEG-GRPKLGGLMDPRQGVIDRS 63
+ + + ++FGILSP EIR+MS E + P+T + G P GG+MD R GVID
Sbjct: 61 NLSEGGKVIGSIEFGILSPQEIRKMSAVE--VTVPDTYDDDGYPIEGGVMDKRMGVIDPG 118
Query: 64 SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPS-HPKVR 122
RC+TC G ECPGHFGHI+LA+PV HVGF +IL C C ++ ++ +
Sbjct: 119 LRCETCGGRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYM 178
Query: 123 DVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQ 182
+ + + I K ++ CG Q
Sbjct: 179 KKIELARNRRSEFNE-IIKEIHKKA----------------------KERMVCPHCGAPQ 215
Query: 183 PNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTA 242
I+ + E + +E E + L V + I L L
Sbjct: 216 YPIKFEKPTIYWEIRK-DEQGNEYRHRLMPTEVRDWLE-----------KIPDKDLPLLG 263
Query: 243 --------EWK-----HVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSG 289
EW V + I L DDLTHKL DII+ NN L +N +G
Sbjct: 264 LDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDLTHKLVDIIRINNRLKQNIEAG 323
Query: 290 AATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGK 349
A +I + +LQ+HV T +N+ PG+P A KSG+PLK + RLKGKEGR RGNL G
Sbjct: 324 APQLIIEDLWDLLQYHVTTYINNEAPGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNLSGG 383
Query: 350 RVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
+ + ++ E N++
Sbjct: 384 AGSGAGSGSVLARAAF-------EITVQHLFEAAEKGEVDNLN 419
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 432 bits (1113), Expect = e-139
Identities = 191/412 (46%), Positives = 253/412 (61%), Gaps = 43/412 (10%)
Query: 1 MAMADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQG 58
+ + S PLR V++VQFGILSP+EIR MSV + I+FPETM+ G RP++GGL+DPR G
Sbjct: 4 IQFSPSSVPLRRVEEVQFGILSPEEIRSMSVAK--IEFPETMDESGQRPRVGGLLDPRLG 61
Query: 59 VIDRSSRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSH 118
IDR +CQTC M +CPGHFGHI+LAKPVFH+GF++K KIL CVC+ C KL + S+
Sbjct: 62 TIDRQFKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSN 121
Query: 119 PKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGC 178
PK D + + R ++++CK K +C+ G + +P + GHGGC
Sbjct: 122 PKFND--TQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDNFDLSNP----SANMGHGGC 175
Query: 179 GRYQPNIRRSGLDLTAEWKHV-NEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRR-- 235
G QP IR+ GL L WK +E +K L+ V I
Sbjct: 176 GAAQPTIRKDGLRLWGSWKRGKDESDLPEKRLLSPLEVH---------------TIFTHI 220
Query: 236 -----SGLDLTAEWKH----------VNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNN 280
+ L L ++ V S I + G DDLTHKL+DIIK N
Sbjct: 221 SSEDLAHLGLNEQYARPDWMIITVLPVPPPSVRPSISVDGTSRGEDDLTHKLSDIIKANA 280
Query: 281 ELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEG 340
+ R E GA H+++E ++LQFHVAT DN++ G P+A+QKSG+PLK+I+ARLKGKEG
Sbjct: 281 NVRRCEQEGAPAHIVSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEG 340
Query: 341 RIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
R+RGNLMGKRVDFSARTVIT DPNL +D++GVPRSIA+ +T+PE VTP+N+
Sbjct: 341 RLRGNLMGKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIY 392
>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 = 418 bits (1075), Expect = e-133
Identities = 185/407 (45%), Positives = 238/407 (58%), Gaps = 47/407 (11%)
Query: 6 SKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQGVIDRS 63
S APLR VK+VQFG+ SP+E+R +SV + I+FPETM+ R K+GGL DPR G IDR+
Sbjct: 7 SSAPLRTVKEVQFGLFSPEEVRAISVAK--IRFPETMDETQTRAKIGGLNDPRLGSIDRN 64
Query: 64 SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRD 123
+CQTC M ECPGHFGHIDLAKPVFHVGF+ K K+ CVC +C KLL+ + +R
Sbjct: 65 LKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQ 124
Query: 124 VVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQP 183
+ S++R A I+ LCK K +CE + + + GGCG QP
Sbjct: 125 ALAIK--DSKKRFAAIWTLCKTKMVCETDVPSEDDP----------TQLVSRGGCGNTQP 172
Query: 184 NIRRSGLDLTAEWKH---VNEDSQEKKIPLTGKGVL---------------LNKKQGHGG 225
IR+ GL L WK + + + L+ + +L N+
Sbjct: 173 TIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSR-- 230
Query: 226 CGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRN 285
P + V I DDLT KLADI+K N L
Sbjct: 231 -----PE------WMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETL 279
Query: 286 ESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGN 345
E +GA H I E +LQFHVAT DND+ G P+A+QKSG+P+K+I+ARLKGKEGRIRGN
Sbjct: 280 EHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGN 339
Query: 346 LMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
LMGKRVDFSARTVI+ DPNL +DQVGVP+SIA+ +T+PE+VTP+N+D
Sbjct: 340 LMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNID 386
>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 = 365 bits (939), Expect = e-119
Identities = 143/396 (36%), Positives = 200/396 (50%), Gaps = 50/396 (12%)
Query: 9 PLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETM-EGGRPKLGGLMDPRQGVIDRSSRCQ 67
+ +K ++FGILSPDEIR+MSVT I P+ E G P G +MDPR GVI+ +C
Sbjct: 2 SEKNIKGIKFGILSPDEIRKMSVTA--IITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCP 59
Query: 68 TCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLK 127
TC + CPGHFGHI+L +PV HVGFV + L+ C C ++ +S +
Sbjct: 60 TCGNTLGNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIE------- 112
Query: 128 TKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQPNIRR 187
+ + IY+ K + + K A K Q CG Q I+
Sbjct: 113 -------KYSRIYNAIKKRWPSAARRLTEYVKKTAM-------KAQVCPHCGEKQFKIKL 158
Query: 188 SGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHV 247
E + ++ K P + L + Y P R EW +
Sbjct: 159 EKPYNFYEER---KEGVAKLTPSDIRERLEKVPESDVEILGYDPTTSR------PEWMIL 209
Query: 248 NEDSQEKKIP-----------LTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIA 296
+P + DDLTHKL DI++ N L + +GA +I
Sbjct: 210 ------TVLPVPPITIRPSIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQLIIE 263
Query: 297 ENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSAR 356
+ +LQ+HVAT DN++PGLP + +SG+PL+ + RLKGKEGR RGNL GKRVDFS+R
Sbjct: 264 DLWDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSR 323
Query: 357 TVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
TVI+PDPN+ ID+VGVP IA+ +T PE +TP+N++
Sbjct: 324 TVISPDPNISIDEVGVPEIIARTLTVPERITPWNIE 359
>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 = 91.4 bits (227), Expect = 6e-20
Identities = 47/123 (38%), Positives = 66/123 (53%), Gaps = 2/123 (1%)
Query: 256 IPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIK-MLQFHVATLTDNDM 314
+ + G DL +I NN L + + GA +I N K MLQ V L DN
Sbjct: 528 VQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGA-PEIIIRNEKRMLQEAVDALLDNGR 586
Query: 315 PGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPR 374
G P S +PL+++ L GK+GR R NL+GKRVD+S R+VI P L++ Q G+P+
Sbjct: 587 RGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPK 646
Query: 375 SIA 377
+A
Sbjct: 647 RMA 649
Score = 38.6 bits (90), Expect = 0.004
Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 22/102 (21%)
Query: 14 KKVQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPR--------------- 56
+KV+ + SP++IR S E ++ PET+ +P+ GL D R
Sbjct: 6 RKVRIALASPEKIRSWSYGE--VEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 57 QGVIDRSSRCQTCAGNMTECP---GHFGHIDLAKPVFHVGFV 95
+ C+ C +T+ GHI+LA P H+ FV
Sbjct: 64 KRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFV 105
>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 = 89.3 bits (222), Expect = 2e-19
Identities = 43/104 (41%), Positives = 61/104 (58%), Gaps = 2/104 (1%)
Query: 275 IIKCNNELIRNESSGAATHVIAENIK-MLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKA 333
+I NN L + + GA +I N K MLQ V + DN G P S +PL+++
Sbjct: 287 LINRNNRLKKLLAQGA-PEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTD 345
Query: 334 RLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIA 377
L GK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A
Sbjct: 346 ILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMA 389
Score = 39.6 bits (93), Expect = 0.002
Identities = 34/149 (22%), Positives = 57/149 (38%), Gaps = 34/149 (22%)
Query: 14 KKVQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPR--------------- 56
+KV+ + SP++IR S E ++ PET+ +P+ GL D R
Sbjct: 6 RKVRIALASPEKIRSWSYGE--VEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 57 QGVIDRSSRCQTCAGNMTECP---GHFGHIDLAKPVFHVGFVTK-----------TIKIL 102
+ C+ C +T GHI+LA P H+ FV L
Sbjct: 64 KRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLFATEL 123
Query: 103 RCVCFYCSKLLVSPSHPKVRDVVLKTKGQ 131
V ++ +++ P + V ++ K Q
Sbjct: 124 EQVLYFNKYIVLDPKGAVLDGVPVE-KRQ 151
>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 = 88.5 bits (220), Expect = 5e-19
Identities = 49/105 (46%), Positives = 63/105 (60%), Gaps = 5/105 (4%)
Query: 275 IIKCNNELIRNESSGAATHVIAENIK-MLQFHVATLTDNDMPGLPRAMQKSGK-PLKAIK 332
+I NN L R A +I N K MLQ V L DN G RA+ S K PLK++
Sbjct: 272 VINRNNRLKRLLDLAAP-DIIVRNEKRMLQEAVDALLDNGRRG--RAITGSNKRPLKSLA 328
Query: 333 ARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIA 377
+KGK+GR R NL+GKRVD+S R+VIT P LR+ Q G+P+ +A
Sbjct: 329 DMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMA 373
Score = 38.0 bits (89), Expect = 0.005
Identities = 29/120 (24%), Positives = 46/120 (38%), Gaps = 32/120 (26%)
Query: 1 MAMADSKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPR-- 56
+ ++ ++ + SPD IR S E +K PET+ +P+ GL R
Sbjct: 5 LKFLKAQTKTEEFDAIKIALASPDMIRSWSFGE--VKKPETINYRTFKPERDGLFCARIF 62
Query: 57 ------------------QGVIDRSSRCQTCAGNMTECP---GHFGHIDLAKPVFHVGFV 95
+GVI C+ C +T+ GHI+LA P H+ F+
Sbjct: 63 GPVKDYECLCGKYKRLKHRGVI-----CEKCGVEVTQTKVRRERMGHIELASPTAHIWFL 117
>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 = 38.3 bits (88), Expect = 0.004
Identities = 45/343 (13%), Positives = 88/343 (25%), Gaps = 107/343 (31%)
Query: 79 HFGHIDLA--------KPVFHVGFVTKTIKILRCVCFYCSKLLVSP-SHPKVRDVVLKTK 129
H H+D K + V F + C + S S ++ +++
Sbjct: 3 HHHHMDFETGEHQYQYKDILSV-FEDAFVDNFDC--KDVQDMPKSILSKEEIDHIIMSKD 59
Query: 130 GQSRRRQAFIYDLCKGKNICEG--GDEMDIN--------KDGAEDP-----------NSL 168
S + F L K + + + + + IN K P + L
Sbjct: 60 AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL 119
Query: 169 QNKKQGHGGCGRYQP-NIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCG 227
N Q + N+ R L + + E K VL+ G G G
Sbjct: 120 YNDNQ------VFAKYNVSRLQPYLKLR-QALLELRPAK-------NVLI---DGVLGSG 162
Query: 228 R-------YQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNN 280
+ + +D W ++ + + + +L L +++ +
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLE-----MLQKLLYQIDPNWTSRS 217
Query: 281 ELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPL--------KAIK 332
+ N H I ++ L + L KA
Sbjct: 218 DHSSNIKLR--IHSIQAELRRLLKS---------KPYENCL------LVLLNVQNAKAWN 260
Query: 333 ARLKGKEGRIRGNLMGKRVDFSART-VITPDPNLRIDQVGVPR 374
A + S + + T + D +
Sbjct: 261 A-----------------FNLSCKILLTTRFKQV-TDFLSAAT 285
Score = 33.3 bits (75), Expect = 0.14
Identities = 27/179 (15%), Positives = 39/179 (21%), Gaps = 65/179 (36%)
Query: 110 SKLLVSPSHPK----VRDV----VLKTKGQSRRRQAFIYDL-CK------GKNICEGGDE 154
+LL S + + +V AF +L CK K +
Sbjct: 235 RRLLKSKPYENCLLVLLNVQNAKAWN---------AF--NLSCKILLTTRFKQV------ 277
Query: 155 MDINKDGAEDPNSLQNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDS---QEKKI-PL 210
D SL + L ++ + P
Sbjct: 278 TDFLSAATTTHISLDHHSMTLT---------PDEVKSLLLKYLDCRPQDLPREVLTTNPR 328
Query: 211 TGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLT 269
R GL WKHVN D I + L+ L
Sbjct: 329 R-----------LSIIAESI----RDGLATWDNWKHVNCDKLTTIIESS-----LNVLE 367
>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 = 37.0 bits (85), Expect = 0.012
Identities = 29/160 (18%), Positives = 49/160 (30%), Gaps = 51/160 (31%)
Query: 225 GCGRYQPNIRRSGLDLTAEWKHVNEDSQE--KKIP---LTGKGVLLDDLTHKLADIIKCN 279
G R + L + + EDS E + +P L+ + + + + K N
Sbjct: 307 GV-RCYEAYPNTSLPPS-----ILEDSLENNEGVPSPMLSISNLTQEQV---QDYVNKTN 357
Query: 280 NELIRNES---S---GAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKA 333
+ L + S GA V++ G P+++ L+ KA
Sbjct: 358 SHLPAGKQVEISLVNGAKNLVVS-------------------GPPQSLYGLNLTLRKAKA 398
Query: 334 RLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVP 373
+ RI FS R + R V P
Sbjct: 399 PSGLDQSRIP---------FSER---KLKFSNRFLPVASP 426
Score = 31.6 bits (71), Expect = 0.57
Identities = 43/209 (20%), Positives = 58/209 (27%), Gaps = 78/209 (37%)
Query: 27 RRMSVTEGGIKFPETMEGGRPKLGGLMDPR---QGVIDRSSRCQTCAGNMTECPGHFGHI 83
+ + V+ G P+++ G L P Q I S R
Sbjct: 375 KNLVVS--G--PPQSLYGLNLTLRKAKAPSGLDQSRIPFSER------------------ 412
Query: 84 DLAKPVFHVGF--VTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTKGQSRRRQAF--- 138
K F F V F+ S LLV S +D L S +
Sbjct: 413 ---KLKFSNRFLPVA--------SPFH-SHLLVPASDLINKD--LVKNNVSFNAKDIQIP 458
Query: 139 IYDLCKGKNICEGGDEM--DINKDGAEDP---NSLQNKKQGH------GGCGRYQPNIRR 187
+YD G ++ + I P + K H GG
Sbjct: 459 VYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGA--------- 509
Query: 188 SGL-DLTAEWKHVNEDSQEKKIPLTGKGV 215
SGL LT H N+D G GV
Sbjct: 510 SGLGVLT----HRNKD---------GTGV 525
>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 = 30.3 bits (67), Expect = 0.62
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 18/43 (41%)
Query: 297 ENIKMLQFHVATL---TDNDMPGLPRAMQKSGKPLKAIKARLK 336
+ +K LQ A+L D+ P L AIKA ++
Sbjct: 20 QALKKLQ---ASLKLYADDSAPAL------------AIKATME 47
>2a2c_A N-acetylgalactosamine kinase; galactokinase, , transferase; HET:
NG1 ADP; 1.65A {Homo sapiens} PDB: 2a2d_A*
Length = 478
Score = 30.2 bits (68), Expect = 1.2
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 291 ATHVIAENIKMLQFHVA--TLTDNDMPGLPRAMQKS 324
A HV +E ++LQF +N + L M +S
Sbjct: 352 AKHVYSEAARVLQFKKICEEAPENMVQLLGELMNQS 387
>2ida_A Hypothetical protein; zinc binding protein, structural genomics,
PSI-2, protein structure initiative; NMR
{Rhodopseudomonas palustris} SCOP: g.44.1.5
Length = 102
Score = 26.1 bits (57), Expect = 8.4
Identities = 5/11 (45%), Positives = 6/11 (54%)
Query: 174 GHGGCGRYQPN 184
GH GC P+
Sbjct: 41 GHVGCCDDSPH 51
Score = 26.1 bits (57), Expect = 8.4
Identities = 5/11 (45%), Positives = 6/11 (54%)
Query: 222 GHGGCGRYQPN 232
GH GC P+
Sbjct: 41 GHVGCCDDSPH 51
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
0.319 0.137 0.415
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: 6,108,106
Number of extensions: 371655
Number of successful extensions: 644
Number of sequences better than 10.0: 1
Number of HSP's gapped: 629
Number of HSP's successfully gapped: 27
Length of query: 392
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 297
Effective length of database: 4,049,298
Effective search space: 1202641506
Effective search space used: 1202641506
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 (21.7 bits)
S2: 58 (26.3 bits)