RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5955
(134 letters)
>2vz8_A Fatty acid synthase; transferase, phosphopantetheine, multienzyme,
megasynthase, fatty acid synthesis; 3.2A {Sus scrofa}
PDB: 2vz9_A*
Length = 2512
Score = 91.5 bits (227), Expect = 1e-22
Identities = 40/96 (41%), Positives = 58/96 (60%), Gaps = 6/96 (6%)
Query: 3 CVKQEPGGLGARCVFITD----AKQPPFSPSSPTYAPLLAKDLLYNVYRAGTWGSMRHIL 58
C+++EPGG RCV +++ + P PSS +L DL+ NVYR G WG+ RH
Sbjct: 1459 CLRKEPGGHRIRCVLVSNLSSTSPAPEMHPSSSELQKVLQGDLVMNVYRDGAWGAFRHFP 1518
Query: 59 LDTTPDNATLQVEHAYINALTRGDLASLKWIEGPLS 94
L+ D Q EHA++N L+RGDL+S++W+ PL
Sbjct: 1519 LE--QDRPEKQTEHAFVNVLSRGDLSSIRWVCSPLH 1552
>3slk_A Polyketide synthase extender module 2; rossmann fold, NADPH,
oxidoreductase; HET: NDP; 3.00A {Saccharopolyspora
spinosa}
Length = 795
Score = 45.5 bits (108), Expect = 9e-07
Identities = 13/71 (18%), Positives = 21/71 (29%)
Query: 24 PPFSPSSPTYAPLLAKDLLYNVYRAGTWGSMRHILLDTTPDNATLQVEHAYINALTRGDL 83
P + P +LA R G + R L + + A G L
Sbjct: 162 PEPAQLLPALPGVLACGEPQLALRRGGAHAPRLAGLGSDDVLPVPDGTGWRLEATRPGSL 221
Query: 84 ASLKWIEGPLS 94
L ++ P +
Sbjct: 222 DGLALVDEPTA 232
Score = 28.2 bits (63), Expect = 0.87
Identities = 5/24 (20%), Positives = 9/24 (37%)
Query: 108 EHAYINALTRGDLASLKWIEGPLS 131
+ A G L L ++ P +
Sbjct: 209 TGWRLEATRPGSLDGLALVDEPTA 232
>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 = 0.001
Identities = 22/106 (20%), Positives = 40/106 (37%), Gaps = 34/106 (32%)
Query: 32 TYAPLLAKDLLYNVYRAGTWGSMRHILLDTTPDNATLQVEHAYINALTRG-DLASLKWIE 90
TY L+ DL+ L + E + T+G ++ L+W+E
Sbjct: 179 TYHVLV-GDLIK---------FSAETLSELIRTTL--DAEKVF----TQGLNI--LEWLE 220
Query: 91 GPLSF----YNITS-----VILLLQIEHAYINA-----LTRGDLAS 122
P + Y ++ +I ++Q+ H Y+ T G+L S
Sbjct: 221 NPSNTPDKDYLLSIPISCPLIGVIQLAH-YVVTAKLLGFTPGELRS 265
Score = 26.9 bits (59), Expect = 2.3
Identities = 20/95 (21%), Positives = 28/95 (29%), Gaps = 30/95 (31%)
Query: 4 VKQEPGGLGARCVFITDAKQPPFS----P-SSPTYAPLL-------------------AK 39
K G +R F ++ FS P +SP ++ LL AK
Sbjct: 396 AKAPSGLDQSRIPF--SERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAK 453
Query: 40 DLLYNVYRAGTWGSMRH----ILLDTTPDNATLQV 70
D+ VY +R I L V
Sbjct: 454 DIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPV 488
Score = 26.2 bits (57), Expect = 5.0
Identities = 27/180 (15%), Positives = 44/180 (24%), Gaps = 71/180 (39%)
Query: 19 TDAKQPPFSPSSPTYAPLLAKDLLY--NVYRAGTWGSMRHILL----------------- 59
T+ P++P A L+ K L Y ++ G +L
Sbjct: 45 TEGFAADDEPTTP--AELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIH 102
Query: 60 ---------DTTPDNATLQVEHAYINALTRGDLASLKWIEGPL----------------- 93
+ T T ++ YI A K L
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG 162
Query: 94 ------------SFYNI--TSVILLLQIEHAYINALTRGDLAS----------LKWIEGP 129
Y V L++ ++ L R L + L+W+E P
Sbjct: 163 QGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENP 222
>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 = 28.8 bits (63), Expect = 0.45
Identities = 10/34 (29%), Positives = 12/34 (35%), Gaps = 11/34 (32%)
Query: 5 KQEPGGLGARCVFITDAKQPPFSPSSPTYAPLLA 38
KQ L A K ++ S AP LA
Sbjct: 19 KQALKKLQASL------K--LYADDS---APALA 41
Score = 25.7 bits (55), Expect = 4.2
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 6/30 (20%)
Query: 85 SLKWIEGPLSFYNITSVILLLQIEHAYINA 114
+LK ++ L Y S L A I A
Sbjct: 21 ALKKLQASLKLYADDSAPAL-----A-IKA 44
>1iq0_A Arginyl-tRNA synthetase; riken structural genomics/proteomics
initiative, RSGI, structural genomics, ligase; 2.30A
{Thermus thermophilus} SCOP: a.27.1.1 c.26.1.1 d.67.2.1
Length = 592
Score = 26.9 bits (60), Expect = 2.6
Identities = 11/86 (12%), Positives = 23/86 (26%), Gaps = 11/86 (12%)
Query: 5 KQEPGGLGARCVFITDAKQPPFSPS--------SPTYAPLLAKDLLYNVYRAGTWGSMRH 56
+E GA + + P + TY AKD+ + ++ G +R
Sbjct: 265 PREGKYAGALVMDASPVIPGLEDPFFVLLRSNGTATYY---AKDIAFQFWKMGILEGLRF 321
Query: 57 ILLDTTPDNATLQVEHAYINALTRGD 82
+ + +
Sbjct: 322 RPYENPYYPGLRTSAPEGEAYTPKAE 347
>1p16_C Phosphorylated peptide from C-terminal of RNA polymerase II;
guanylyltransferase, transcription, capping, CTD, mRNA;
HET: SEP G GTP; 2.70A {Candida albicans}
Length = 26
Score = 24.2 bits (52), Expect = 3.3
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 24 PPFSPSSPTYAP 35
P +SP+SP+Y+P
Sbjct: 6 PSYSPTSPSYSP 17
>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein
biosynthesis, nucleotide-binding, phosphorylation, RNA-
binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces
cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A
Length = 986
Score = 26.5 bits (58), Expect = 3.8
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 82 DLASLKWIEGPLSFYNITSVI 102
D ++ W+ L+ ITS+
Sbjct: 580 DTVNVAWLVNYLNTCGITSIT 600
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 26.2 bits (57), Expect = 4.5
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 24 PPFSPSSPTYAP 35
P +SP+SP+Y+P
Sbjct: 1625 PSYSPTSPSYSP 1636
Score = 26.2 bits (57), Expect = 5.3
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 23 QPPFSPSSPTYAP 35
P +SP+SP+Y+P
Sbjct: 1631 SPSYSPTSPSYSP 1643
Score = 25.8 bits (56), Expect = 6.9
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 24 PPFSPSSPTYAP 35
P +SP+SP+Y+P
Sbjct: 1646 PSYSPTSPSYSP 1657
Score = 25.4 bits (55), Expect = 7.4
Identities = 7/12 (58%), Positives = 10/12 (83%)
Query: 24 PPFSPSSPTYAP 35
P + PSSP+Y+P
Sbjct: 1569 PAYMPSSPSYSP 1580
Score = 25.0 bits (54), Expect = 9.9
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 24 PPFSPSSPTYAP 35
P +SP+SP+Y+P
Sbjct: 1576 PSYSPTSPSYSP 1587
>2yew_B E1 envelope glycoprotein; alphavirus, molecular dynamics; 5.00A
{Barmah forest virus}
Length = 427
Score = 25.7 bits (56), Expect = 5.8
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 69 QVEHAYINALTRGDLASLKWIEGPLS 94
Q ++N + + K+I GP+S
Sbjct: 138 QTVDVFVNGDSPARIQQSKFILGPIS 163
Score = 25.4 bits (55), Expect = 7.8
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 109 HAYINALTRGDLASLKWIEGPLS 131
++N + + K+I GP+S
Sbjct: 141 DVFVNGDSPARIQQSKFILGPIS 163
>3j0f_E E1 envelope glycoprotein; alphavirus, virus assembly; 7.00A
{Sindbis virus} PDB: 1ld4_M 1z8y_I
Length = 439
Score = 25.8 bits (56), Expect = 5.8
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 69 QVEHAYINALTRGDLASLKWIEGPLS 94
Y+N +T G LK I GP+S
Sbjct: 142 SFLDVYVNGVTPGTSKDLKVIAGPIS 167
Score = 25.4 bits (55), Expect = 7.3
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 109 HAYINALTRGDLASLKWIEGPLS 131
Y+N +T G LK I GP+S
Sbjct: 145 DVYVNGVTPGTSKDLKVIAGPIS 167
>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 = 25.8 bits (56), Expect = 5.9
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 24 PPFSPSSPTYAP 35
P FSP+SPTY+P
Sbjct: 1540 PGFSPTSPTYSP 1551
Score = 25.8 bits (56), Expect = 7.0
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 20 DAKQPPFSPSSPTYAP 35
P +SP+SP+Y+P
Sbjct: 1613 SPTSPSYSPTSPSYSP 1628
Score = 25.4 bits (55), Expect = 8.3
Identities = 7/12 (58%), Positives = 10/12 (83%)
Query: 24 PPFSPSSPTYAP 35
P +SP+SP Y+P
Sbjct: 1701 PSYSPTSPGYSP 1712
>3muu_A Structural polyprotein; beta barrels, IG-like folds, viral protein;
HET: NAG BMA MAN; 3.29A {Sindbis virus} PDB: 3muw_A
3muw_U 1z8y_A 1z8y_B
Length = 750
Score = 25.8 bits (56), Expect = 6.1
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 69 QVEHAYINALTRGDLASLKWIEGPLS 94
Y+N +T G LK I GP+S
Sbjct: 502 SFLDVYVNGVTPGTSKDLKVIAGPIS 527
Score = 25.4 bits (55), Expect = 8.1
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 109 HAYINALTRGDLASLKWIEGPLS 131
Y+N +T G LK I GP+S
Sbjct: 505 DVYVNGVTPGTSKDLKVIAGPIS 527
>3n40_F E1 envelope glycoprotein; viral protein, immature heterodimer,
alphavirus, receptor BI membrane fusion; HET: NAG NDG;
2.17A {Chikungunya virus} PDB: 2xfb_A
Length = 393
Score = 25.3 bits (55), Expect = 6.9
Identities = 15/49 (30%), Positives = 18/49 (36%), Gaps = 3/49 (6%)
Query: 46 YRAGTWGSMRHILLDTTPDNATLQVEHAYINALTRGDLASLKWIEGPLS 94
YRA T S L N AY N + K+I GP+S
Sbjct: 124 YRAHT-ASASAKLRVLYQGNN--ITVTAYANGDHAVTVKDAKFIVGPMS 169
Score = 25.3 bits (55), Expect = 8.7
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 109 HAYINALTRGDLASLKWIEGPLS 131
AY N + K+I GP+S
Sbjct: 147 TAYANGDHAVTVKDAKFIVGPMS 169
>3n44_F E1 envelope glycoprotein; viral protein, immature heterodimer,
alphavirus, receptor BI membrane fusion; HET: NAG; 2.35A
{Chikungunya virus} PDB: 3n41_F* 3n42_F* 3n43_F* 2xfc_A
Length = 473
Score = 25.4 bits (55), Expect = 7.0
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 69 QVEHAYINALTRGDLASLKWIEGPLS 94
AY N + K+I GP+S
Sbjct: 164 ITVTAYANGDHAVTVKDAKFIVGPMS 189
Score = 25.4 bits (55), Expect = 8.2
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 109 HAYINALTRGDLASLKWIEGPLS 131
AY N + K+I GP+S
Sbjct: 167 TAYANGDHAVTVKDAKFIVGPMS 189
>3j0c_A E1 envelope glycoprotein; alphavirus, bioweapon; 4.80A {Venezuelan
equine encephalitis virus}
Length = 442
Score = 25.4 bits (55), Expect = 7.1
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 69 QVEHAYINALTRGDLASLKWIEGPLS 94
V Y+N T + +K GPLS
Sbjct: 142 IVTTVYVNGETPVNFNGVKITAGPLS 167
Score = 25.0 bits (54), Expect = 9.1
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 109 HAYINALTRGDLASLKWIEGPLS 131
Y+N T + +K GPLS
Sbjct: 145 TVYVNGETPVNFNGVKITAGPLS 167
>1i9w_A Fusion protein E1; envelope glycoprotein, membrane fusion, viral
protein; 3.00A {Semliki forest virus} SCOP: b.1.18.4
f.10.1.1 PDB: 2ala_A 1rer_A
Length = 390
Score = 25.3 bits (55), Expect = 7.1
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 46 YRAGTWGSMRHILLDTTPDNATLQVEHAYINALTRGDLASLKWIEGPLS 94
Y+A T S++ + + Q Y+N + ++I GPLS
Sbjct: 122 YKAHT-ASLKAKVRVMYGNVN--QTVDVYVNGDHAVTIGGTQFIFGPLS 167
Score = 25.3 bits (55), Expect = 8.9
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 109 HAYINALTRGDLASLKWIEGPLS 131
Y+N + ++I GPLS
Sbjct: 145 DVYVNGDHAVTIGGTQFIFGPLS 167
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
0.320 0.137 0.428
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,989,701
Number of extensions: 102339
Number of successful extensions: 257
Number of sequences better than 10.0: 1
Number of HSP's gapped: 254
Number of HSP's successfully gapped: 40
Length of query: 134
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 51
Effective length of database: 4,384,350
Effective search space: 223601850
Effective search space used: 223601850
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 (21.8 bits)
S2: 52 (23.9 bits)