RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5290
(536 letters)
>3h0g_E DNA-directed RNA polymerases I, II, and III subunit rpabc1;
transcription, multi-protein complex, DNA- binding,
magnesium; 3.65A {Schizosaccharomyces pombe}
Length = 210
Score = 159 bits (402), Expect = 9e-46
Identities = 58/147 (39%), Positives = 86/147 (58%), Gaps = 3/147 (2%)
Query: 1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQM-FVFF 59
QL HDRGY V+Q ELD TLDQFK R+ L ++D ++ F
Sbjct: 19 HQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLD--RTTLSFYAKPSNDSNKGTIYIEF 76
Query: 60 PDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELL 119
EP +GIK ++T+ + + I++ MTPSA + + + ++ +E F ES+L+
Sbjct: 77 AKEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIATVTGQFTIETFQESDLI 136
Query: 120 INITEHELVPEHIVLTPEEKQELLTRY 146
+NIT HELVP+HI+L+P+EK+ELL RY
Sbjct: 137 VNITHHELVPKHILLSPDEKKELLDRY 163
>1dzf_A DNA-directed RNA polymerases I, II, and III 27 KD polypeptide; RNA
polymerase subunit; 1.9A {Saccharomyces cerevisiae}
SCOP: c.52.3.1 d.78.1.1 PDB: 1i3q_E 1i50_E 1i6h_E
1k83_E* 1nik_E 1nt9_E 1pqv_E 1r5u_E 1r9s_E* 1r9t_E*
1sfo_E* 1twa_E* 1twc_E* 1twf_E* 1twg_E* 1twh_E* 1wcm_E
1y1v_E 1y1w_E 1y1y_E ...
Length = 215
Score = 142 bits (359), Expect = 1e-39
Identities = 57/152 (37%), Positives = 88/152 (57%), Gaps = 9/152 (5%)
Query: 1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDP------TDQ 54
++ DRGY +TQ+E++ L+ FK ++ D S RP R + ++
Sbjct: 20 KEMVKDRGYFITQEEVELPLEDFKAKYCD--SMGRPQRKMMSFQANPTEESISKFPDMGS 77
Query: 55 MFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFL 114
++V F DEP +G+KT+KT+ +QE+ I V Q +TPSA + + P +E F
Sbjct: 78 LWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLV-PSIPPATIETFN 136
Query: 115 ESELLINITEHELVPEHIVLTPEEKQELLTRY 146
E+ L++NIT HELVP+HI L+ +EK+ELL RY
Sbjct: 137 EAALVVNITHHELVPKHIRLSSDEKRELLKRY 168
>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 = 85.9 bits (212), Expect = 1e-17
Identities = 95/529 (17%), Positives = 149/529 (28%), Gaps = 185/529 (34%)
Query: 7 RGYLVTQDELDQTL----------DQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQ-- 54
R ++ L+ L Q +EQF ++ P +E A +D+PT
Sbjct: 7 RPLTLSHGSLEHVLLVPTASFFIASQLQEQF----NKILPEPTEGF---AADDEPTTPAE 59
Query: 55 MFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFL 114
+ F +G Y + E +K D L F
Sbjct: 60 LVGKF-----LG------YVSSLVEP----------------SKVGQFDQVLNLCLTEF- 91
Query: 115 ESELL--INITEHELV---PEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKEC 169
E+ L +I H L + T + +EL+ Y + + + +
Sbjct: 92 ENCYLEGNDI--HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAV 149
Query: 170 SFESATVKSV--------------------YPSLKAPIFQLLQQPLFLLVKTSDRANAVF 209
+A + ++ Y L + + + L L++T+ A VF
Sbjct: 150 GEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVF 209
Query: 210 LPQG------LSTPESHP--------PVS-PSIDTMLRSYEERHSLVFSLAHFP-FKHFK 253
QG L P + P P+S P I V LAH+
Sbjct: 210 -TQGLNILEWLENPSNTPDKDYLLSIPISCPLI------------GVIQLAHYVVTAKLL 256
Query: 254 EVTLGDFLTNGKSL---KQGVPLTDIPVMAFYTKHELDELKPFFK--------FFYMG-- 300
T G+ + K QG+ V A D + FF F++G
Sbjct: 257 GFTPGELRSYLKGATGHSQGL------VTAVAIAET-DSWESFFVSVRKAITVLFFIGVR 309
Query: 301 DLEVTANSVAQPN-RKSSMETAPAMPVPMQA--GYNTGEGYKSVDGFK------------ 345
E N+ P+ + S+E +P PM + + V+
Sbjct: 310 CYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEIS 369
Query: 346 ----PDP--VSGYP---YA----------------NRLPSS--HPQKHAFFLAPVPVILP 378
VSG P Y +R+P S + FL PV P
Sbjct: 370 LVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFL---PVASP 426
Query: 379 QPKPQEH-HHDGPGQHNILNRSPSVQQESRGVTPGGDKTAADL--PVYS 424
H H P I A D+ PVY
Sbjct: 427 -----FHSHLLVPASDLINKDLVKNNVSFN---------AKDIQIPVYD 461
>4ayb_H DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_H
2y0s_H 2waq_H 4b1o_H 4b1p_Z 2pmz_H 3hkz_H
Length = 84
Score = 56.3 bits (136), Expect = 2e-10
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 115 ESELLINITEHELVPEHIVLTPEEKQELLTRY 146
S I+ H LVP+H VL+ +E ++L
Sbjct: 4 SSNRKIDPRIHYLVPKHEVLSIDEAYKILKEL 35
>1eik_A RNA polymerase subunit RPB5; RPBH, OCSP, NESG, protein structure
initiative, structural genomics, PSI; NMR
{Methanothermobacterthermautotrophicus} SCOP: d.78.1.1
Length = 77
Score = 52.8 bits (127), Expect = 3e-09
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 118 LLINITEHELVPEHIVLTPEEKQELLTRY 146
+ I +H+LVPEH++L E + +L
Sbjct: 1 MKREILKHQLVPEHVILNESEAKRVLKEL 29
>1hmj_A RPB5, protein (subunit H); RNA polymerase, archaea; NMR
{Methanocaldococcus jannaschii} SCOP: d.78.1.1
Length = 78
Score = 52.4 bits (126), Expect = 4e-09
Identities = 12/27 (44%), Positives = 20/27 (74%)
Query: 120 INITEHELVPEHIVLTPEEKQELLTRY 146
+ +T+H LVP+H ++ EE +E+L RY
Sbjct: 1 MKVTDHILVPKHEIVPKEEVEEILKRY 27
>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 = 58.3 bits (140), Expect = 5e-09
Identities = 51/297 (17%), Positives = 93/297 (31%), Gaps = 80/297 (26%)
Query: 13 QDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTD-----QMFVFFPDEPKIGI 67
+D L T D +K DK + S L VL +P + FP I
Sbjct: 338 RDGLA-TWDNWKHVNCDKLTTII--ESSLNVL-----EPAEYRKMFDRLSVFPPSAHIPT 389
Query: 68 KTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPK----YILEYFLESELLI-NI 122
+ + + V + K SLV+ PK I +LE ++ + N
Sbjct: 390 ILLSLIWFDVIKS-------DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENE 442
Query: 123 TE-HELVPEHIVLTPEEKQELLT-----RYWRSCVTIFWTQKRTGEEHF---LKECSFES 173
H + +H + + L +Y+ + H LK
Sbjct: 443 YALHRSIVDHYNIPKTFDSDDLIPPYLDQYF------YS--------HIGHHLKNIE--- 485
Query: 174 ATVKSVYPSLKAPIFQLLQQPLFLLVKTSDRANAVFLPQGL-STPESHPPVSPSIDTM-- 230
+ +F++ +FL + FL Q + + ++T+
Sbjct: 486 -------HPERMTLFRM----VFL--------DFRFLEQKIRHDSTAWNASGSILNTLQQ 526
Query: 231 LRSYEERHSLVFSLAHFPFKHFKEVTLGDFLTN-GKSLKQGVPLTDIPVMAFYTKHE 286
L+ Y+ + + P + DFL ++L TD+ +A + E
Sbjct: 527 LKFYKP-----YICDNDPKYERLVNAILDFLPKIEENLICS-KYTDLLRIALMAEDE 577
Score = 55.2 bits (132), Expect = 4e-08
Identities = 67/448 (14%), Positives = 124/448 (27%), Gaps = 150/448 (33%)
Query: 32 SEKRPARSELIVLVA--HNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIH-RAIIV 88
+ L +L + DP K+ I +I+ +R+ + + ++V
Sbjct: 190 KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV 249
Query: 89 VQTGMTPSAKQSLVDMAPKYILEYF-LESELLI--------------NITEHELVPEHIV 133
L+++ F L ++L+ T L +
Sbjct: 250 ------------LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT 297
Query: 134 LTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQ 193
LTP+E + LL + + R + L E V + P + I + ++
Sbjct: 298 LTPDEVKSLLLK---------YLDCRPQD---LPR---E---VLTTNPRRLSIIAESIRD 339
Query: 194 PLFLLVKTSDRANAVFLPQGLSTPESHPPVSPSIDTMLRSYEERHSLVFSLAHFPFKHFK 253
L T D V + + ES S++ L E R + L+ FP
Sbjct: 340 GL----ATWDNWKHVNCDKLTTIIES------SLNV-LEPAEYRK-MFDRLSVFP-PSAH 386
Query: 254 --EVTLG------------DFLT--NGKSL--KQGVPLTDIPVMAFYTKHELDELKPFFK 295
+ L + + SL KQ T + +
Sbjct: 387 IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKEST-------ISIPSI-------- 431
Query: 296 FFYMGDLEVTANSVAQPNRKSSMETAPAMPVPMQAGYNTGEGYKSVDGFKPDPVSGYPYA 355
Y+ +L+V + +R + YN + + S D P + Y Y
Sbjct: 432 --YL-ELKVKLENEYALHRS------------IVDHYNIPKTFDS-DDLIPPYLDQYFY- 474
Query: 356 NRLPSSHPQKHAFFLAPVPVILPQPKPQEHHHDGPGQHNILNRSPSV-------QQESRG 408
+ HH + V +Q+ R
Sbjct: 475 ------------SHIG-------------HHLKNIEHPERMTLFRMVFLDFRFLEQKIRH 509
Query: 409 VTPGGDKTAADLPVYS----YKGVPLYI 432
+ + + + L YK YI
Sbjct: 510 DSTAWNASGSILNTLQQLKFYKP---YI 534
Score = 44.1 bits (103), Expect = 1e-04
Identities = 40/237 (16%), Positives = 73/237 (30%), Gaps = 73/237 (30%)
Query: 103 DMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGE 162
+ K + + +++ E+ +HI+++ + T +FWT E
Sbjct: 32 NFDCKDVQDMPKSI-----LSKEEI--DHIIMSKDAVSG--TLR------LFWTLLSKQE 76
Query: 163 E---HFLKECSFESATVKSVYPSLKAPIFQLLQQP---LFLLVKTSDR---ANAVFLPQG 213
E F++E ++ Y L +PI +QP + ++ DR N VF
Sbjct: 77 EMVQKFVEE------VLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN 130
Query: 214 LSTPESHPPVSPSIDTMLRS--YEERHS---LVF--------SLA-----------HFPF 249
+S + + LR E R + L+ +A F
Sbjct: 131 VSRLQPY--------LKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182
Query: 250 KHF-----KEVTLGDFLTNGKSL-----KQGVPLTDIPVMAFYTKHEL-DELKPFFK 295
K F + L + L +D H + EL+ K
Sbjct: 183 KIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLK 239
>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 = 38.2 bits (88), Expect = 0.007
Identities = 28/113 (24%), Positives = 42/113 (37%), Gaps = 9/113 (7%)
Query: 408 GVTPGGDKTAADLPVYSYKGVPLYIPRGRQSPSSTVQPTVESPSGQKSYYPGENSAPAGI 467
GVTP +++ K ++ P S S+ + G Y + A
Sbjct: 1469 GVTPYSNESGLVNADLDVKDELMFSP-LVDSGSNDAMAGGFTAYGGADYGEATSPFGAYG 1527
Query: 468 SSTESPGDIGVSGFTSPGPQPYSLPSGLGGTEGVSPHEEHVSLVFPSSPAPRP 520
+ SPG G +SPG P S P+ + SP S P+SP+ P
Sbjct: 1528 EAPTSPG----FGVSSPGFSPTS-PTYSPTSPAYSPTSPSYS---PTSPSYSP 1572
Score = 30.4 bits (68), Expect = 1.9
Identities = 55/267 (20%), Positives = 77/267 (28%), Gaps = 32/267 (11%)
Query: 259 DFLTNGKSLKQGVPLTDIPVMAFYTKHEL---DELKPFFKFFYMGDLEVTANSVAQPNRK 315
D + + +SL + +P I + + DL+V + P
Sbjct: 1442 DVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGL----VNADLDVKDELMFSPLVD 1497
Query: 316 SSMETAPAMPVPMQAGYNTGEGYKSVDGFKPDPVSGYPYANRLPSSHPQKHAFFLAPVPV 375
S A A G + GE + P S + P P + +P
Sbjct: 1498 SGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSP-GFGVSSPGFSPTSPTY--SPT-- 1552
Query: 376 ILPQPKPQEHHHDGPGQHNILNRSPSVQQESRGVTPGGDKTAADLPVYSYKGVPLYIPRG 435
P P + SPS S +P + P YS P Y P
Sbjct: 1553 -SPAYSPTSPSYSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYS-PTSPSYSP-- 1607
Query: 436 RQSPSSTVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVSGFTSPGPQPYSLPSGL 495
SPS + SP+ S + S SP S SP YS S
Sbjct: 1608 -TSPSYSPTSPSYSPTSPSY------SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP- 1659
Query: 496 GGTEGVSPHEEHVSLVFPSSPAPRPQP 522
SP S P+SP+ P
Sbjct: 1660 ----AYSPTSPSYS---PTSPSYSPTS 1679
Score = 28.9 bits (64), Expect = 5.6
Identities = 14/90 (15%), Positives = 22/90 (24%), Gaps = 11/90 (12%)
Query: 435 GRQSPSSTVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVSGFTSPGPQPYSLPSG 494
G +P S + +P S + G + + + P G
Sbjct: 1468 GGVTPYSNESG---LVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFG 1524
Query: 495 LGGTEGVSPHEEHVSLVFPSSPAPRPQPYS 524
G SP +P P S
Sbjct: 1525 AYGEAPTSP--------GFGVSSPGFSPTS 1546
>1deq_A Fibrinogen (alpha chain); coiled-coil, blood clotting; 3.50A {Bos
taurus} SCOP: i.9.1.1
Length = 390
Score = 32.5 bits (73), Expect = 0.31
Identities = 34/219 (15%), Positives = 55/219 (25%), Gaps = 10/219 (4%)
Query: 301 DLEVTANSVAQPNRKSSMETAPAMPVPMQAGYNTGEGYKSVDGFKPDPVSGYPYANRLPS 360
DLE N Q + ++ P+ + PV + +
Sbjct: 177 DLEDYKNQQKQLEQVIAINLLPSRDIQYLPILKMSTI--------TGPVPREFKSQLQEA 228
Query: 361 SHPQKHAFFLAPVPVILPQPKPQEHHHDGPGQHNILNRSPSVQQESRGVTPGGDKTAADL 420
K + ++L H +P ++ + G +
Sbjct: 229 PLEWKALLEMQQTKMVLETFGGDGHARGDSVSQG-TGLAPGSPRKPGTSSIGNVNPGSYG 287
Query: 421 PVYSYKGVPLYIPRGRQSPSSTVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVSG 480
P S P G + +P S P SA PG G
Sbjct: 288 PGSSGTWNPGRPEPGSAGTWNPGRPEPGSAGTWNPGRPEPGSAGTWNPGRPEPGSAGTWN 347
Query: 481 FTSPGP-QPYSLPSGLGGTEGVSPHEEHVSLVFPSSPAP 518
P P + +G G+ P + PSSP
Sbjct: 348 PGRPEPGSAGTWNTGSSGSSSFRPDSSGHGNIRPSSPDW 386
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 32.7 bits (74), Expect = 0.37
Identities = 27/135 (20%), Positives = 35/135 (25%), Gaps = 7/135 (5%)
Query: 389 GPGQHNILNRSPSVQQESRGVTPGGDKTAADLPVYSYKGVP-LYIPRGRQSPSSTVQPTV 447
G G +I + S G + +G Y P
Sbjct: 1443 GTGAFDIYLDQDMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDA 1502
Query: 448 E--SPSGQKSYYPGENSAPAGISSTESPGDIGVSGFTSPGPQPYSLPSGLGGTEGVSPHE 505
SP Q E G+ SP G SPG + G SP
Sbjct: 1503 AAFSPLVQGGSEGREGFGDYGLLGAASPY----KGVQSPGYTSPFSSAMSPGYGLTSPSY 1558
Query: 506 EHVSLVFPSSPAPRP 520
S + +SPA P
Sbjct: 1559 SPSSPGYSTSPAYMP 1573
Score = 28.9 bits (64), Expect = 6.3
Identities = 29/101 (28%), Positives = 38/101 (37%), Gaps = 6/101 (5%)
Query: 421 PVYSYKGVPLYIPRGRQSPSS-TVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVS 479
P YS SP+S + PT S S Y + + + S + SP S
Sbjct: 1653 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1712
Query: 480 GFTSPGPQPYSLPSGLGGTEGVSPHEEHVSLVFPSSPAPRP 520
TSP P S PS + SP S P+SP+ P
Sbjct: 1713 P-TSPSYSPTS-PSYSPTSPSYSPTSPSYS---PTSPSYSP 1748
Score = 28.5 bits (63), Expect = 6.5
Identities = 13/70 (18%), Positives = 18/70 (25%)
Query: 458 PGENSAPAGISSTESPGDIGVSGFTSPGPQPYSLPSGLGGTEGVSPHEEHVSLVFPSSPA 517
P E S SP S G + G SP++ S + S +
Sbjct: 1485 PYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFS 1544
Query: 518 PRPQPYSLPA 527
P
Sbjct: 1545 SAMSPGYGLT 1554
>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 = 31.5 bits (70), Expect = 0.38
Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 3/21 (14%)
Query: 451 SGQKSYYPGENSAPA-GISST 470
+ K Y +SAPA I +T
Sbjct: 27 ASLKLYAD--DSAPALAIKAT 45
Score = 28.8 bits (63), Expect = 2.7
Identities = 7/25 (28%), Positives = 12/25 (48%), Gaps = 5/25 (20%)
Query: 424 SYKGVPLYIPRGRQSPSSTVQPTVE 448
S K LY +P+ ++ T+E
Sbjct: 28 SLK---LYADD--SAPALAIKATME 47
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 31.7 bits (71), Expect = 0.79
Identities = 23/173 (13%), Positives = 36/173 (20%), Gaps = 19/173 (10%)
Query: 361 SHPQKHAFFLAPVPVILPQPKPQEHHHDGPGQHNILNRSPSVQQESRGVTPGGDKTAADL 420
SH +K + PQ + Q + + P + G++ G
Sbjct: 2 SHHKKRVY---------PQAQLQ-YGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQG 51
Query: 421 PVYSYKGVPLYIPRGRQSPSSTVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVSG 480
V S P Q Q T P P + P
Sbjct: 52 AVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPL--VDPNAYMQPQVPV------ 103
Query: 481 FTSPGPQPYSLPSGLGGTEGVSPHEEHVSLVFPSSPAPRPQPYSLPAGYGGVN 533
P G ++ + P LP +
Sbjct: 104 -QMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLT 155
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 31.2 bits (70), Expect = 1.0
Identities = 19/96 (19%), Positives = 35/96 (36%), Gaps = 5/96 (5%)
Query: 429 PLYIPRGRQSPSSTVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVSGFTSPGPQP 488
++ + S+ V ++ SP+G+ S + P+ SPG + T P
Sbjct: 6 HHHVDDDDKMFSTQVNSSLTSPTGRGSMAA-PSLHPSLGPGIGSPGQLHSPISTLSSPIN 64
Query: 489 YSLPSGLGGTEGVSPHEEHVSLVFPSSPAPRPQPYS 524
P + + PH S+ P++P S
Sbjct: 65 GMGPPFSVISSPMGPH----SMSVPTTPTLGFSTGS 96
>2yky_A Beta-transaminase; transferase; HET: PLP SFE; 1.69A {Mesorhizobium
SP} PDB: 2ykv_A* 2yku_A* 2ykx_A*
Length = 465
Score = 30.3 bits (69), Expect = 2.0
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 398 RSPSVQQESRGVTPGGDKTAADLPVYSYKGVPLYIPRGR 436
S + +R PGG + ++ PL I +G
Sbjct: 56 VSAGHHERARRSMPGG----NTRSILFHRPFPLVIAQGT 90
>2cy8_A D-phgat, D-phenylglycine aminotransferase; structural genomics,
NPPSFA, national PROJ protein structural and functional
analyses; 2.30A {Pseudomonas stutzeri}
Length = 453
Score = 29.9 bits (68), Expect = 2.4
Identities = 8/39 (20%), Positives = 13/39 (33%), Gaps = 4/39 (10%)
Query: 398 RSPSVQQESRGVTPGGDKTAADLPVYSYKGVPLYIPRGR 436
S Q +R V P G ++ L+I +
Sbjct: 13 GSVFWAQRARSVMPDG----VTADTRAFDPHGLFISDAQ 47
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 28.9 bits (64), Expect = 3.8
Identities = 9/69 (13%), Positives = 20/69 (28%), Gaps = 14/69 (20%)
Query: 286 ELDELKPFFKFFYMGDLEVTANSVAQPNRKSSM------ET----APAMPVPMQAGYNTG 335
+ ++ P + + LE++ Q +K + E P + +
Sbjct: 137 DKAKVPPLIRI--VSGLELS--DTKQKGKKFLVIAYEPFENIAIELPPNEILFSENNDMD 192
Query: 336 EGYKSVDGF 344
VD
Sbjct: 193 NNNDGVDEL 201
>2y2m_A PBP1B, penicillin-binding protein 1B; transferase, infection, cell
WALL, peptidoglycan, inhibitor; HET: E08; 1.62A
{Streptococcus pneumoniae} PDB: 2y2g_A* 2y2h_A* 2y2j_A*
2y2k_A* 2y2l_A* 2y2i_A* 2y2n_A* 2y2o_A* 2y2p_A* 2y2q_A*
2uwy_A* 2xd1_A* 2bg1_A 2xd5_A* 2uwx_A* 2fff_B
Length = 494
Score = 29.0 bits (65), Expect = 4.2
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 480 GFTSPGPQPYSLPSGLGGTEGVSPHE 505
G+ P SLP +GG V+ +
Sbjct: 246 GYEIPEYGIESLP--MGGGIEVTVAQ 269
>2jch_A Penicillin-binding protein 1B; peptidoglycan synthesis
multifunctional enzyme, cell WALL, peptidoglycan, gamma
lactam antibiotics; HET: PL7; 2.4A {Streptococcus
pneumoniae} PDB: 2jci_A* 2je5_A*
Length = 720
Score = 28.9 bits (65), Expect = 4.6
Identities = 8/26 (30%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 480 GFTSPGPQPYSLPSGLGGTEGVSPHE 505
G+ P SLP +GG V+ +
Sbjct: 472 GYEIPEYGIESLP--MGGGIEVTVAQ 495
>2dwc_A PH0318, 433AA long hypothetical phosphoribosylglycinamide
transferase; purine ribonucleotide biosynthesis; HET:
ADP; 1.70A {Pyrococcus horikoshii} PDB: 2czg_A*
Length = 433
Score = 28.8 bits (65), Expect = 5.0
Identities = 7/72 (9%), Positives = 19/72 (26%), Gaps = 20/72 (27%)
Query: 40 ELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQT----GMTP 95
E+ L + D ++ FP + ++
Sbjct: 210 EVTELAVRHFDENGEIVTTFPKP----------------VGHYQIDGDYHASWQPAEISE 253
Query: 96 SAKQSLVDMAPK 107
A++ + +A +
Sbjct: 254 KAEREVYRIAKR 265
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 28.6 bits (63), Expect = 5.9
Identities = 18/98 (18%), Positives = 32/98 (32%), Gaps = 6/98 (6%)
Query: 429 PLYIPRGRQSPSSTVQPTVESPSGQKSYYPGENSAPAGISSTESPGDIGVSGFTSPGPQP 488
+ IP + +++ P P P + +P D V+G +
Sbjct: 20 HMVIPSASVTSAASDFLAALHPPVT---VPDPAPPPPPAPAAGNPPD-TVTGDSVLQRIL 75
Query: 489 YSLPSGLGGTEGVSPHEEHVSLVFPSSPAPRPQPYSLP 526
P+G G T ++P + P +PA P
Sbjct: 76 RG-PTGPG-TTSLAPAVRYGRQPGPEAPASAPPAAGRA 111
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 28.1 bits (62), Expect = 6.4
Identities = 10/78 (12%), Positives = 17/78 (21%), Gaps = 5/78 (6%)
Query: 310 AQPNRKSSMETAPAMPVPMQAGYNTGEGYKSVDGFKPDPVSGYPYANRLPSSHPQKHAFF 369
Q + + G ++ + + P +R P
Sbjct: 157 MQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGG--- 213
Query: 370 LAPVPVILPQPKPQEHHH 387
P P HHH
Sbjct: 214 --PPPPFPAGQTHHHHHH 229
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
0.315 0.134 0.401
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,125,402
Number of extensions: 487687
Number of successful extensions: 894
Number of sequences better than 10.0: 1
Number of HSP's gapped: 859
Number of HSP's successfully gapped: 37
Length of query: 536
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 438
Effective length of database: 3,965,535
Effective search space: 1736904330
Effective search space used: 1736904330
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: 42 (22.0 bits)
S2: 60 (27.4 bits)