RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5912
(122 letters)
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 33.5 bits (76), Expect = 0.009
Identities = 8/58 (13%), Positives = 12/58 (20%), Gaps = 16/58 (27%)
Query: 18 SSPPPSSTRASNTSTTAVTSTPAAPRSTSPGSRC--CDTGRP-IFTDPISGQTICS-C 71
+ + T C C P I G +C+ C
Sbjct: 3 TRESIDKRAGRRGPNLNIVLT------------CPECKVYPPKIVERFSEGDVVCALC 48
>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 = 32.6 bits (74), Expect = 0.024
Identities = 8/43 (18%), Positives = 13/43 (30%)
Query: 5 PESTVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSP 47
+T A + P + +PP + P P P
Sbjct: 14 AAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPKNPTPPRP 56
Score = 28.4 bits (63), Expect = 0.69
Identities = 7/42 (16%), Positives = 14/42 (33%)
Query: 10 APSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPGSRC 51
A +SP + ++ A+ T A + P +
Sbjct: 3 AAPTSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKK 44
>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 = 31.2 bits (70), Expect = 0.064
Identities = 31/116 (26%), Positives = 45/116 (38%), Gaps = 8/116 (6%)
Query: 7 STVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPGSRCCDTGRPIFTDPISGQ 66
S +PS SPTS S P+S S TS + ++P+ ++ S + P T P
Sbjct: 1592 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP--TSPSYSP 1649
Query: 67 TICSCQYDLLNYQRLAAGGGPGLPLSMYSAP-YPEGMAAYFPALGADQAPFYSSAS 121
T S Y + P P ++P Y +Y P +P YS S
Sbjct: 1650 TSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT-----SPNYSPTS 1700
Score = 30.4 bits (68), Expect = 0.14
Identities = 13/45 (28%), Positives = 18/45 (40%)
Query: 6 ESTVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPGSR 50
S +P+ SPTS S P+S S S + + SR
Sbjct: 1689 YSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR 1733
Score = 30.1 bits (67), Expect = 0.16
Identities = 31/116 (26%), Positives = 44/116 (37%), Gaps = 8/116 (6%)
Query: 7 STVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPGSRCCDTGRPIFTDPISGQ 66
S +PS SPTS S P+S S TS + ++P+ ++ S + P T P
Sbjct: 1599 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP--TSPSYSP 1656
Query: 67 TICSCQYDLLNYQRLAAGGGPGLPL-SMYSAPYPEGMAAYFPALGADQAPFYSSAS 121
T + +Y + P P S S Y Y P +P YS S
Sbjct: 1657 TSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPT-----SPSYSPTS 1707
Score = 27.0 bits (59), Expect = 2.0
Identities = 30/119 (25%), Positives = 39/119 (32%), Gaps = 22/119 (18%)
Query: 5 PESTVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPGSRCCDTGRPIFTDPIS 64
A +PTS SS S TS T ++PA SP S P ++ P S
Sbjct: 1520 TSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAY----SPTSPSYSPTSPSYS-PTS 1574
Query: 65 GQTICSCQYDLLNYQRLAAGGGPGLP-LSMYSAPYPEGMAAYFPALGADQAPFYSSASY 122
+Y + P P S S Y +Y P +P YS S
Sbjct: 1575 P-----------SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT-----SPSYSPTSP 1617
Score = 25.8 bits (56), Expect = 4.7
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 5 PESTVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPGS 49
S +PS SPTS S P+S S TS ++P+ ++ S
Sbjct: 1632 SYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYS 1676
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 30.8 bits (69), Expect = 0.083
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 7 STVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPG 48
S +PS SPTS S P+S S TS + ++P + TSP
Sbjct: 1649 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSPS 1689
Score = 28.5 bits (63), Expect = 0.61
Identities = 33/123 (26%), Positives = 47/123 (38%), Gaps = 8/123 (6%)
Query: 7 STVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPA---APRSTSPGSRCCDTGRPIFTDPI 63
S +PS SPTS S P+S S TS + ++P+ S SP S P ++
Sbjct: 1621 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1680
Query: 64 SGQTICSCQYDLL--NYQRLAAGGGPGLPL-SMYSAPYPEGMAAYFPALGAD--QAPFYS 118
+ S Y +Y + P P S S Y +Y P + +P YS
Sbjct: 1681 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1740
Query: 119 SAS 121
S
Sbjct: 1741 PTS 1743
Score = 27.3 bits (60), Expect = 1.4
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 7 STVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPG 48
S +PS SPTS S +S S TS + ++P + TSP
Sbjct: 1593 SPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSP-SYSPTSPS 1633
Score = 26.2 bits (57), Expect = 3.6
Identities = 14/44 (31%), Positives = 17/44 (38%), Gaps = 5/44 (11%)
Query: 10 APSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRS-----TSPG 48
+P SS S +S S +S TS P S TSP
Sbjct: 1541 SPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPS 1584
Score = 25.4 bits (55), Expect = 6.5
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 7 STVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPG 48
S +PS SPTS S P+S S TS + ++P+ TSP
Sbjct: 1579 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYS-PTSPS 1619
Score = 25.4 bits (55), Expect = 7.0
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 5 PESTVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRS--TSPGS 49
S ++P TS S PSS S + +S +P S SP S
Sbjct: 1543 FSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSPTS 1589
>2vp8_A Dihydropteroate synthase 2; RV1207 transferase, folate
biosynthesis, antibiotic resistance; 2.64A
{Mycobacterium tuberculosis}
Length = 318
Score = 27.6 bits (62), Expect = 1.0
Identities = 9/40 (22%), Positives = 18/40 (45%)
Query: 18 SSPPPSSTRASNTSTTAVTSTPAAPRSTSPGSRCCDTGRP 57
S+PP S+ R++ + ++ PA ++ R R
Sbjct: 3 STPPASAGRSTPPALAGHSTPPALAGHSTLCGRPVAGDRA 42
>3hhs_B Propo-P1, phenoloxidase subunit 1; alpha helix, beta strand,
melanin biosynthesis, metal-bindin monooxygenase,
oxidoreductase, secreted; 1.97A {Manduca sexta}
Length = 684
Score = 26.5 bits (58), Expect = 2.5
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 73 YDLLNYQRLAAGGGPGLPLSMYSAPYPEGMAAYFPAL 109
Y++ +R+ G P S +SAP EG YFP L
Sbjct: 245 YNV---ERMCNGLPQVKPFSDFSAPIEEG---YFPKL 275
>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 = 25.7 bits (55), Expect = 3.9
Identities = 5/17 (29%), Positives = 10/17 (58%), Gaps = 3/17 (17%)
Query: 2 LKIPESTV---APSSSP 15
LK ++++ A S+P
Sbjct: 22 LKKLQASLKLYADDSAP 38
>2coy_A Dynactin-1; microtubule binding, cytoskeleton associated protein,
P150- glued, DAP-150, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: b.34.10.1
Length = 112
Score = 25.2 bits (55), Expect = 4.1
Identities = 12/45 (26%), Positives = 17/45 (37%)
Query: 13 SSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPGSRCCDTGRP 57
SS +S S T + + S A+ R GSR G+
Sbjct: 2 SSGSSGMAQSKRHVYSRTPSGSRMSAEASARPLRVGSRVEVIGKG 46
>1gai_A Glucoamylase-471; hydrolase, glycosidase, polysaccharide
degradation, glycoPro; HET: MAN NAG BMA GAC; 1.70A
{Aspergillus awamori} SCOP: a.102.1.1 PDB: 1gah_A*
3gly_A* 1dog_A* 1glm_A* 1agm_A* 3eqa_A*
Length = 472
Score = 25.5 bits (55), Expect = 5.8
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 6 ESTVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAA-PRSTSPG 48
S V PS TS+S P + A++ S T + T + P + G
Sbjct: 429 NSVVPPSWGETSASSVPGTCAATSASGTYSSVTVTSWPSIVATG 472
>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting,
protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP:
a.4.5.54 a.4.5.54
Length = 566
Score = 25.4 bits (54), Expect = 7.2
Identities = 8/49 (16%), Positives = 18/49 (36%)
Query: 5 PESTVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPGSRCCD 53
+ + SS S++ P++ + + PA + P C+
Sbjct: 150 ADYELTKSSINCSNAIDPNANPQNQFGVNSENICPACTFANHPQIGNCE 198
>3r8n_N 30S ribosomal protein S14; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 1p6g_N 1p87_N 2aw7_N 2avy_N
2i2u_N 2i2p_N* 2qan_N* 2qb9_N* 2qbb_N* 2qbd_N 2qbf_N
2qbh_N* 2qbj_N* 2qou_N* 2qow_N* 2qoy_N* 2qp0_N* 2vho_N
2vhp_N 2ykr_N ...
Length = 100
Score = 24.5 bits (54), Expect = 7.2
Identities = 10/19 (52%), Positives = 12/19 (63%), Gaps = 3/19 (15%)
Query: 42 PRSTSPG---SRCCDTGRP 57
PR +SP +RC TGRP
Sbjct: 51 PRDSSPSRQRNRCRQTGRP 69
>3gdb_A Endo-D, putative uncharacterized protein SPR0440;
alpha-beta-barrels, cell WALL, peptidoglycan-anchor,
secreted, hydrolase; HET: PGE; 1.87A {Streptococcus
pneumoniae} PDB: 2xqx_A
Length = 937
Score = 25.3 bits (54), Expect = 7.3
Identities = 4/40 (10%), Positives = 11/40 (27%)
Query: 3 KIPESTVAPSSSPTSSSPPPSSTRASNTSTTAVTSTPAAP 42
+PE++ A + + S ++
Sbjct: 25 AVPENSGANTELVSGESEHSTNEADKQNEGEHARENKLEK 64
>2ig8_A Hypothetical protein PA3499; structural genomics, PSI-2, Pro
structure initiative; 1.90A {Pseudomonas aeruginosa}
Length = 144
Score = 24.6 bits (54), Expect = 7.6
Identities = 6/38 (15%), Positives = 12/38 (31%), Gaps = 3/38 (7%)
Query: 30 TSTTAVTSTPAAPRSTSPGSRCCDTGRPIFTDPISGQT 67
T+ + + + S G + +SG T
Sbjct: 2 TAVRRIRAAALPDLPDASWSNALLVGEELV---MSGMT 36
>2q9o_A Laccase-1; multicopper oxidase, 2-OXOH oxidoreductase; HET: OHI NAG
MAN GOL; 1.30A {Melanocarpus albomyces} SCOP: b.6.1.3
b.6.1.3 b.6.1.3 PDB: 3fu7_A* 3fu8_A* 3fu7_B* 1gw0_A*
2ih9_A* 2ih8_A* 3fu9_A* 3qpk_A* 3dkh_A* 3pps_A*
Length = 559
Score = 25.0 bits (55), Expect = 8.9
Identities = 8/39 (20%), Positives = 13/39 (33%)
Query: 10 APSSSPTSSSPPPSSTRASNTSTTAVTSTPAAPRSTSPG 48
AP PT PP + +T + P ++
Sbjct: 315 APGGLPTDEGTPPVDHQCLDTLDVRPVVPRSVPVNSFVK 353
>1imv_A PEDF, pigment epithelium-derived factor; serpin, angiogenesis,
signaling protein; HET: NAG; 2.85A {Homo sapiens} SCOP:
e.1.1.1
Length = 398
Score = 24.9 bits (55), Expect = 9.1
Identities = 10/29 (34%), Positives = 11/29 (37%)
Query: 11 PSSSPTSSSPPPSSTRASNTSTTAVTSTP 39
P+S P SP P ST A P
Sbjct: 2 PASPPEEGSPDPDSTGALVEEEDPFFKVP 30
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
0.310 0.125 0.378
Gapped
Lambda K H
0.267 0.0507 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,752,718
Number of extensions: 89291
Number of successful extensions: 287
Number of sequences better than 10.0: 1
Number of HSP's gapped: 244
Number of HSP's successfully gapped: 60
Length of query: 122
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 40
Effective length of database: 4,412,271
Effective search space: 176490840
Effective search space used: 176490840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 51 (23.9 bits)