RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11162
(91 letters)
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 123
Score = 110 bits (277), Expect = 2e-33
Identities = 46/89 (51%), Positives = 59/89 (66%)
Query: 3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
K+ ELD+K PNAA+ T+ KEDHTL NM+ NQLL D VLFAGYK PHPL H FILR+Q
Sbjct: 16 PKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAGYKVPHPLNHNFILRVQ 75
Query: 63 TTAESTPHDALMNAITDLLAELSLFEERF 91
T + +P +++A L+ L + F
Sbjct: 76 TVEDCSPKQVIVDAAKSLITHLEEIKVNF 104
>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB:
1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K
1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K*
1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...
Length = 120
Score = 107 bits (269), Expect = 3e-32
Identities = 44/89 (49%), Positives = 54/89 (60%)
Query: 3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
K+ + DTK PNA + T KEDHTLGN+IR +LL D VLFA YK HP +F LRIQ
Sbjct: 17 SKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQ 76
Query: 63 TTAESTPHDALMNAITDLLAELSLFEERF 91
TT P DAL NA ++ +L + F
Sbjct: 77 TTEGYDPKDALKNACNSIINKLGALKTNF 105
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S
binding motif, platform for RNA polymer assembly,
transferase; 1.76A {Sulfolobus solfataricus} PDB:
2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L
Length = 92
Score = 101 bits (254), Expect = 2e-30
Identities = 31/84 (36%), Positives = 42/84 (50%)
Query: 8 ELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAES 67
+ N + EDHTLGN+I L + V FA Y QPHPL K I++I T
Sbjct: 4 RILKSESNYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVKILTDGSI 63
Query: 68 TPHDALMNAITDLLAELSLFEERF 91
TP DAL+ AI ++ S + +
Sbjct: 64 TPKDALLKAIENIRGMTSHYIDEI 87
>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural
genomics, protein structure initiative, MCSG; 1.60A
{Thermoplasma acidophilum} SCOP: d.74.3.2
Length = 115
Score = 96.9 bits (241), Expect = 5e-28
Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 1/84 (1%)
Query: 8 ELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAES 67
+ +K N+ + D+TL + ++LKD V A Y HP+ + ++
Sbjct: 14 RVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVK-SG 72
Query: 68 TPHDALMNAITDLLAELSLFEERF 91
P A+ A+ L +F
Sbjct: 73 KPQSAIKRAVRKLSKLYEDLGTQF 96
>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 = 34.3 bits (78), Expect = 0.002
Identities = 24/131 (18%), Positives = 37/131 (28%), Gaps = 54/131 (41%)
Query: 3 RKIIKELDTKVP---------------NA--AIFTVNK---EDHTLGNMIRNQLLKDPHV 42
KI KE++ A+ + K ED ++++ L
Sbjct: 1704 EKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFED------LKSKGLIPADA 1757
Query: 43 LFAGYKQPHPL-EH----------KF-----ILRI--QTTAESTPHDAL------MNAIT 78
FAG H L E+ ++ T + P D L M AI
Sbjct: 1758 TFAG----HSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAIN 1813
Query: 79 DLLAELSLFEE 89
S +E
Sbjct: 1814 PGRVAASFSQE 1824
>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 701
Score = 24.9 bits (54), Expect = 5.1
Identities = 7/31 (22%), Positives = 11/31 (35%)
Query: 38 KDPHVLFAGYKQPHPLEHKFILRIQTTAEST 68
K +F +K + K LR T+
Sbjct: 181 KILEDVFPEFKDLTAVSSKLTLRSHMTSGWF 211
>3dod_A Adenosylmethionine-8-amino-7-oxononanoate aminotr;
aminotransferase, biotin biosynthesis, pyridoxal
phosphate, adenosyl-L-methionine; HET: PLP; 1.90A
{Bacillus subtilis} PDB: 3drd_A 3du4_A*
Length = 448
Score = 24.5 bits (54), Expect = 5.9
Identities = 6/16 (37%), Positives = 7/16 (43%)
Query: 32 IRNQLLKDPHVLFAGY 47
I+ QL K H G
Sbjct: 69 IKKQLGKIAHSTLLGM 84
>2odr_D Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 685
Score = 24.6 bits (53), Expect = 6.5
Identities = 7/31 (22%), Positives = 11/31 (35%)
Query: 38 KDPHVLFAGYKQPHPLEHKFILRIQTTAEST 68
K +F +K + K LR T+
Sbjct: 181 KILEDVFPEFKDLTAVSSKLTLRSHMTSGWF 211
>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 665
Score = 24.6 bits (53), Expect = 7.3
Identities = 7/31 (22%), Positives = 11/31 (35%)
Query: 38 KDPHVLFAGYKQPHPLEHKFILRIQTTAEST 68
K +F +K + K LR T+
Sbjct: 181 KILEDVFPEFKDLTAVSSKLTLRSHMTSGWF 211
>1s0a_A Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; fold
type I, subclass II, homodimer; HET: LLP; 1.71A
{Escherichia coli} SCOP: c.67.1.4 PDB: 1qj5_A* 1mlz_A*
1qj3_A* 1mly_A* 1s06_A* 1s08_A* 1s09_A* 1s07_A* 1mgv_A*
1dty_A*
Length = 429
Score = 24.0 bits (53), Expect = 8.0
Identities = 5/15 (33%), Positives = 10/15 (66%)
Query: 32 IRNQLLKDPHVLFAG 46
+++Q+ HV+F G
Sbjct: 68 MKSQIDAMSHVMFGG 82
>2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class
II, ligase; 3.23A {Methanococcus maripaludis}
Length = 648
Score = 24.2 bits (52), Expect = 8.3
Identities = 7/31 (22%), Positives = 11/31 (35%)
Query: 38 KDPHVLFAGYKQPHPLEHKFILRIQTTAEST 68
K +F +K + K LR T+
Sbjct: 181 KILEDVFPEFKDLTAVSSKLTLRSHMTSGWF 211
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
0.322 0.137 0.390
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,345,645
Number of extensions: 67637
Number of successful extensions: 178
Number of sequences better than 10.0: 1
Number of HSP's gapped: 178
Number of HSP's successfully gapped: 15
Length of query: 91
Length of database: 6,701,793
Length adjustment: 58
Effective length of query: 33
Effective length of database: 5,082,375
Effective search space: 167718375
Effective search space used: 167718375
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 (21.9 bits)
S2: 51 (23.3 bits)