RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9498
(240 letters)
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 52.8 bits (126), Expect = 4e-08
Identities = 50/195 (25%), Positives = 94/195 (48%), Gaps = 12/195 (6%)
Query: 30 TPSPTDRSTADTPSVP--SPTDLSTVVTPSLPNPTDLNIAKTPSVPSPTDRSTAETPSLP 87
+P+ S + +P+ P SPT S T +PT + + T SPT S + T
Sbjct: 1568 SPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSY 1627
Query: 88 NPTDLSTVVTPSLPNPTDLSTVETPNLPDRSTAETPSLPNPTDRSTVVTPSLPNPTDRST 147
+PT S +P+ P+ + S +P P S P+ P+ + S +P+ P+ + S
Sbjct: 1628 SPT--SPSYSPTSPSYSPTSPSYSPTSPSYS----PTSPSYSPTSPSYSPTSPSYSPTS- 1680
Query: 148 VETPNLPDRSTAETPSLPNPTDLSTVETPSVPSPTDRSTAETPSLPSPTDRSTAETPSLP 207
P+ S + +P+ P+ + S +P+ PS + S + +P+ PS + S + +P+ P
Sbjct: 1681 ---PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1737
Query: 208 NPTDLSTAETPSLPN 222
+ + S + +P+ P+
Sbjct: 1738 SYSPTSPSYSPTSPS 1752
Score = 37.7 bits (87), Expect = 0.003
Identities = 45/187 (24%), Positives = 73/187 (39%), Gaps = 13/187 (6%)
Query: 46 SPTDLSTVVTPSLPNPTDLNIAKTP--SVPSPTDRSTAETPSLPNPTDLSTVVTPSLPNP 103
SP L A +P V SP S + P S +PS P
Sbjct: 1506 SPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGY 1565
Query: 104 TDLSTVETPNLPDRSTAE---TPSLPNPTDRSTVVTPSLPNPTDRSTVETPNLPDRSTAE 160
+ S P+ P S +P+ P+ + S +P+ P+ + S +P P S
Sbjct: 1566 ST-SPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTS 1624
Query: 161 -----TPSLPNPTDLSTVETPSVPSPTDRSTAETPSLPSPTDRSTAETPSLPNPTDLSTA 215
T +PT S T SPT S + +P+ PS + S + +P+ P+ + S +
Sbjct: 1625 PSYSPTSPSYSPTSPSYSPTSPSYSPT--SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1682
Query: 216 ETPSLPN 222
+P+ P+
Sbjct: 1683 YSPTSPS 1689
Score = 36.2 bits (83), Expect = 0.009
Identities = 32/123 (26%), Positives = 58/123 (47%), Gaps = 8/123 (6%)
Query: 27 TTETPSPTDRSTADTPSVPSPTDLSTVVTPSLPNPTDLNIAKT-----PSVPSPTDRSTA 81
T+ + SPT S + T SPT S T +PT + + T P+ PS + S +
Sbjct: 1630 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1689
Query: 82 ETPSLPNPTDLSTVVTPSLPNPTDLSTVETPNLPDR---STAETPSLPNPTDRSTVVTPS 138
+P+ P+ + S +P+ P+ + S +P P S + +P+ P+ + S +P+
Sbjct: 1690 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1749
Query: 139 LPN 141
P+
Sbjct: 1750 SPS 1752
Score = 33.5 bits (76), Expect = 0.069
Identities = 43/194 (22%), Positives = 73/194 (37%), Gaps = 9/194 (4%)
Query: 41 TPSVPSPTDLSTVVTPSLPNPTDLNIAKTPSVPSPTDRSTAETPSLPNPTDLSTVVTPSL 100
+P + S +V D A +P V ++ S
Sbjct: 1479 PEGAGTPYERSPMVDSGFVGSPD-AAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSP 1537
Query: 101 PNPTDLSTVETPNLPDRSTAETPSLPNPTDRSTVVTPSLPNPTDRSTVETPNLPD---RS 157
+ S+ +P S + +PS P + S PS P+ + S +P P S
Sbjct: 1538 GYTSPFSSAMSPGYGLTSPSYSPSSPGYST-SPAYMPSSPSYSPTSPSYSPTSPSYSPTS 1596
Query: 158 TAETPSLPNPTDLSTVETPSVP--SPTDRSTAETPSLPSPTDRSTAETPSLPNPTDLSTA 215
+ +P+ P+ + S +P+ P SPT S + T SPT S + T +PT S +
Sbjct: 1597 PSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT--SPS 1654
Query: 216 ETPSLPNPPDRSTA 229
+P+ P+ S +
Sbjct: 1655 YSPTSPSYSPTSPS 1668
>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 = 43.2 bits (101), Expect = 5e-05
Identities = 48/196 (24%), Positives = 83/196 (42%), Gaps = 9/196 (4%)
Query: 32 SPTDRSTADTPSVPSPTDLSTVVTPSLPNPTDLNIAKTPSVPSPTDRSTAETPSLPNPTD 91
SPT + + T SPT S T +PT + + T SPT S + T +PT
Sbjct: 1543 SPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT- 1601
Query: 92 LSTVVTPSLPNPTDLSTVETPNLPD---RSTAETPSLPNPTDRSTVVTPSLPNPTDRSTV 148
S +P+ P+ + S +P P S + +P+ P+ + S +P+ P+ + S
Sbjct: 1602 -SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPA 1660
Query: 149 ETPNLPDRSTAETPSLPNPTDLSTVETPSVPSPTDRSTAETPSLPSPTDRSTAETPSLPN 208
+P P S P+ P+ + S +P+ PS + S +P+ PS + S +P P
Sbjct: 1661 YSPTSPSYS----PTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPA 1716
Query: 209 PTDLSTAETPSLPNPP 224
+ + +
Sbjct: 1717 YSPKQDEQKHNENENS 1732
Score = 40.8 bits (95), Expect = 3e-04
Identities = 47/205 (22%), Positives = 81/205 (39%), Gaps = 10/205 (4%)
Query: 32 SPTDRSTADTPSVPSPTDLSTVVTPSLPNPTDLNIAKTPSVPSPTDRSTAETPSLPNPTD 91
SP S ++ T +P + P+ P S +P+ P +
Sbjct: 1493 SPLVDSGSNDAMAGGFTAYGGADYGEATSPF-GAYGEAPTSPGFGVSSPGFSPTSPTYSP 1551
Query: 92 LSTVVTPSLPNPTDLSTVETPNLPDRSTAE---TPSLPNPTDRSTVVTPSLPNPTDRSTV 148
S +P+ P+ + S +P P S +P+ P+ + S +P+ P+ + S
Sbjct: 1552 TSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1611
Query: 149 ETPNLPDRSTAETPSLPNPTDLSTVETPSVP--SPTDRSTAETPSLPSPTDRSTAETPSL 206
+P P S P+ P+ + S +P+ P SPT S + T SPT + + T
Sbjct: 1612 YSPTSPSYS----PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPS 1667
Query: 207 PNPTDLSTAETPSLPNPPDRSTAET 231
+PT S + T +P S + T
Sbjct: 1668 YSPTSPSYSPTSPSYSPTSPSYSPT 1692
Score = 32.8 bits (74), Expect = 0.12
Identities = 37/146 (25%), Positives = 67/146 (45%), Gaps = 5/146 (3%)
Query: 21 NPLDRNTTETPSPTDRSTADTPSVPSPTDLSTVVTPSLP--NPTDLNIAKTPSVPSPTDR 78
+P T+ + SPT S + +P+ PS + S +P+ P +PT + + T SPT
Sbjct: 1588 SPSYSPTSPSYSPT--SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1645
Query: 79 STAETPSLPNPTDLSTVVTPSLPNPTDLS-TVETPNLPDRSTAETPSLPNPTDRSTVVTP 137
S + T +PT + T +PT S + +P+ S + +P+ PN + S +P
Sbjct: 1646 SYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSP 1705
Query: 138 SLPNPTDRSTVETPNLPDRSTAETPS 163
+ P + S +P ++ E +
Sbjct: 1706 TSPGYSPGSPAYSPKQDEQKHNENEN 1731
Score = 32.0 bits (72), Expect = 0.22
Identities = 37/140 (26%), Positives = 62/140 (44%), Gaps = 6/140 (4%)
Query: 18 SLPNPLDRNTTETPSPTDRSTADTPSVPSPTDLSTVVTPSLPNPTDLNIAKTPSVPSPTD 77
S +P T+ + SPT S + T SPT S T +PT + + T SPT
Sbjct: 1599 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT- 1657
Query: 78 RSTAETPSLPNPTDLSTVVTPSLPNPTDLSTVETPNLPDRSTAETPSLPNPTDRSTVVTP 137
S A +P+ P+ + S +P+ P+ + S +P P+ S P+ P+ + S +P
Sbjct: 1658 -SPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYS----PTSPSYSPTSPGYSP 1712
Query: 138 SLPNPTDRSTVETPNLPDRS 157
P + + + N + S
Sbjct: 1713 GSPAYSPKQDEQKHNENENS 1732
>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 = 31.6 bits (71), Expect = 0.30
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 14/55 (25%)
Query: 8 PTDLS--TVE-TLSLPNPL--------DRNTTETPSPTDRSTAD-TPSVPSPTDL 50
P LS ++E L +P ++ P PT+ AD P+ +P +L
Sbjct: 8 PLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPT--TPAEL 60
Score = 30.8 bits (69), Expect = 0.50
Identities = 21/93 (22%), Positives = 29/93 (31%), Gaps = 29/93 (31%)
Query: 167 PTDLS--TVETPSVPSPTDR-STAE------TPSLPSPTDRSTA-ETPSLPNPTDLSTAE 216
P LS ++E + PT A LP PT+ A + P+ + AE
Sbjct: 8 PLTLSHGSLEH-VLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPT-------TPAE 59
Query: 217 --------TPSLPNPPDRSTAE---TLSLQCFT 238
SL P + L L F
Sbjct: 60 LVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFE 92
Score = 27.3 bits (60), Expect = 6.1
Identities = 22/95 (23%), Positives = 31/95 (32%), Gaps = 38/95 (40%)
Query: 26 NTTETPSPTDRSTADTPSVPSP----TDLS--------TVVTPSLPNPTDLNIAKTPSVP 73
NT+ PS + S + VPSP ++L+ LP + I
Sbjct: 316 NTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI------- 368
Query: 74 SPTDRSTAETPSLPN-PTDLSTVVT-PSLPNPTDL 106
SL N +L VV+ P P L
Sbjct: 369 -----------SLVNGAKNL--VVSGP----PQSL 386
>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 = 30.5 bits (68), Expect = 0.47
Identities = 20/128 (15%), Positives = 38/128 (29%), Gaps = 2/128 (1%)
Query: 31 PSPTDRSTADTPSVPSPTDLSTVVTPSLPNPTDLNIAKTPSVPSPTDRSTAETPSL--PN 88
ST S+ SPT ++ PSL I + SP ++ + P
Sbjct: 11 DDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPPF 70
Query: 89 PTDLSTVVTPSLPNPTDLSTVETPNLPDRSTAETPSLPNPTDRSTVVTPSLPNPTDRSTV 148
S + S+ PT + + P S+ P + + + + +
Sbjct: 71 SVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSG 130
Query: 149 ETPNLPDR 156
+
Sbjct: 131 NMASFTKH 138
>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3
(6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...;
bifunctional enzyme, EDTA complex; HET: F6P EDT ADP;
2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B*
3qpu_A* 3qpv_A* 3qpw_A*
Length = 520
Score = 30.1 bits (67), Expect = 0.66
Identities = 25/125 (20%), Positives = 37/125 (29%), Gaps = 12/125 (9%)
Query: 116 DRSTAETPSLPNPTDRSTVVTPSLPNPTDRSTVETPNLPDRSTAETPSLPNPTDLSTVET 175
D+S E P L P +TP VE+ L S +
Sbjct: 401 DKSAEEMPYLKCPLHTVLKLTPV----AYGCRVESIYLNVESVCTHRERSE-------DA 449
Query: 176 PSVPSPTDRSTAETPSLPSPTDRSTAETPSLPNPTDLSTAETPSLPNPPDRSTAETLSLQ 235
P+P R + TP L SP S ++A PS P + +++
Sbjct: 450 KKGPNPLMRRNSVTP-LASPEPTKKPRINSFEEHVASTSAALPSCLPPEVPTQLPGQNMK 508
Query: 236 CFTKL 240
Sbjct: 509 GSRSS 513
>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 = 29.3 bits (65), Expect = 1.0
Identities = 13/100 (13%), Positives = 23/100 (23%)
Query: 111 TPNLPDRSTAETPSLPNPTDRSTVVTPSLPNPTDRSTVETPNLPDRSTAETPSLPNPTDL 170
+ +P S PS + S + P T P + ++ + L
Sbjct: 12 SGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDSVL 71
Query: 171 STVETPSVPSPTDRSTAETPSLPSPTDRSTAETPSLPNPT 210
+ T P + A P
Sbjct: 72 QRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRA 111
>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin,
armadillo repeat, nuclear receptor LIGA binding domain,
protein binding; HET: P6L; 2.76A {Homo sapiens}
Length = 352
Score = 28.8 bits (64), Expect = 1.8
Identities = 15/107 (14%), Positives = 23/107 (21%)
Query: 117 RSTAETPSLPNPTDRSTVVTPSLPNPTDRSTVETPNLPDRSTAETPSLPNPTDLSTVETP 176
+ PS + + + P DRS T +
Sbjct: 9 QVIQAMPSDLTISSAIQNIHSASKGLPLNHAALPPTDYDRSPFVTSPISMTMPPHGSLQG 68
Query: 177 SVPSPTDRSTAETPSLPSPTDRSTAETPSLPNPTDLSTAETPSLPNP 223
S A P P S T+ S+P+
Sbjct: 69 YQTYGHFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSSPASIPHL 115
>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane
fusion, viral P glycoprotein B, HSV-1, membrane; HET:
NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A*
3nwd_A*
Length = 703
Score = 28.0 bits (62), Expect = 3.6
Identities = 8/75 (10%), Positives = 16/75 (21%), Gaps = 2/75 (2%)
Query: 155 DRSTAETPSLPNPTDLSTVETPSVPSPTDRSTAETPSLPSPTDRSTAETPSLPNPTDLST 214
D + +P P + +P + P+ + P P P +
Sbjct: 1 DPAAPTSPGTPGVAAATQAANGGPATPAPPALGAAPT--GDPKPKKNKKPKNPTPPRPAG 58
Query: 215 AETPSLPNPPDRSTA 229
Sbjct: 59 DNATVAAGHATLREH 73
Score = 27.2 bits (60), Expect = 6.4
Identities = 11/81 (13%), Positives = 16/81 (19%), Gaps = 1/81 (1%)
Query: 151 PNLPDRSTAETPSLPNPTDLSTVETPSVPSPTDRSTAETPSLPSPTDRSTAETPSLPNPT 210
P P + TP+ P+ + P P
Sbjct: 2 PAAPTSPGTPGVAAATQAANGGPATPAPPALGA-APTGDPKPKKNKKPKNPTPPRPAGDN 60
Query: 211 DLSTAETPSLPNPPDRSTAET 231
A +L AE
Sbjct: 61 ATVAAGHATLREHLRDIKAEN 81
>2py8_A Hypothetical protein RBCX; all helical fold, chaperone; HET: PE4;
2.45A {Synechocystis SP} SCOP: a.280.1.1
Length = 147
Score = 27.0 bits (59), Expect = 4.1
Identities = 9/35 (25%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 197 DRSTAETPSLPN-PTDLSTAETPSLPNPPDRSTAE 230
+R T + N P++ S E+ + +PP + E
Sbjct: 107 ERLTRTVAEVDNFPSETSNGESNNNDSPPSAAALE 141
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
0.300 0.120 0.340
Gapped
Lambda K H
0.267 0.0412 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,219,651
Number of extensions: 171933
Number of successful extensions: 415
Number of sequences better than 10.0: 1
Number of HSP's gapped: 348
Number of HSP's successfully gapped: 105
Length of query: 240
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 149
Effective length of database: 4,160,982
Effective search space: 619986318
Effective search space used: 619986318
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.7 bits)
S2: 56 (26.2 bits)