RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2248
(102 letters)
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.0 bits (59), Expect = 0.96
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 11/39 (28%)
Query: 52 DQLKEEREMLRKQNDNNHW--SQTVELA---AAQEKQME 85
D+L +E E +RK W Q L AA + +
Sbjct: 78 DRLTQEPESIRK------WREEQRKRLQELDAASKVMEQ 110
Score = 26.3 bits (57), Expect = 1.8
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 8/81 (9%)
Query: 9 SQQNENAEQITLLSEKINNLVSE---AERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQN 65
+ + E I E+ + E A +V + EKA+ L + + + E + K
Sbjct: 78 DRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAK--KDLEEWNQRQSEQVEKNK 135
Query: 66 DNNHWSQTVELAAAQEKQMEV 86
NN + + A Q+ ++
Sbjct: 136 INN---RIADKAFYQQPDADI 153
>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 = 26.9 bits (59), Expect = 1.0
Identities = 6/13 (46%), Positives = 9/13 (69%), Gaps = 2/13 (15%)
Query: 86 VCTVCGAFLIVGD 98
VC +CG L++ D
Sbjct: 44 VCALCG--LVLSD 54
>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 = 26.5 bits (57), Expect = 1.4
Identities = 8/14 (57%), Positives = 8/14 (57%), Gaps = 1/14 (7%)
Query: 42 EKAQGLMKLCDQLK 55
EK Q L KL LK
Sbjct: 18 EK-QALKKLQASLK 30
>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB,
proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR
binding; 6.93A {Bacillus subtilis}
Length = 758
Score = 26.4 bits (59), Expect = 1.9
Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 3/71 (4%)
Query: 5 RLSQSQQNENAEQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQ 64
RL N ++ L +K++ + E + EKA L +L+E+ E +K
Sbjct: 386 RLRSFTTPPNLKE---LEQKLDEVRKEKDAAVQSQEFEKAASLRDTEQRLREQVEDTKKS 442
Query: 65 NDNNHWSQTVE 75
+ E
Sbjct: 443 WKEKQGQENSE 453
>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport
protein; 2.50A {Saccharomyces cerevisiae}
Length = 814
Score = 26.2 bits (58), Expect = 2.4
Identities = 5/30 (16%), Positives = 12/30 (40%)
Query: 51 CDQLKEEREMLRKQNDNNHWSQTVELAAAQ 80
QL R++L ++ W + + +
Sbjct: 665 VGQLTLARDLLTDESAEMKWRALGDASLQR 694
>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB,
proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR
binding; 3.65A {Bacillus subtilis}
Length = 468
Score = 26.0 bits (58), Expect = 2.4
Identities = 12/60 (20%), Positives = 23/60 (38%)
Query: 16 EQITLLSEKINNLVSEAERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQNDNNHWSQTVE 75
+ L +K++ + E + EKA L +L+E+ E +K + E
Sbjct: 394 PNLKELEQKLDEVRKEKDAAVQSQEFEKAASLRDTEQRLREQVEDTKKSWKEKQGQENSE 453
>2ohf_A Protein OLA1, GTP-binding protein 9; ATPase, GTPase, P-loop,
OBG-like, hydrolase; HET: ACP; 2.70A {Homo sapiens}
Length = 396
Score = 25.1 bits (56), Expect = 4.6
Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 4/38 (10%)
Query: 57 EREMLRKQNDNNHWSQTV-ELAAAQEKQMEVCTVCGAF 93
E++ +RK N W + E + V GA
Sbjct: 233 EKDYIRK---KNKWLIKIKEWVDKYDPGALVIPFSGAL 267
>1ni3_A YCHF GTPase, YCHF GTP-binding protein; structural genomics,
GTP1OBG, PSI, protein structure initiative; 2.80A
{Schizosaccharomyces pombe} SCOP: c.37.1.8 d.15.10.2
Length = 392
Score = 24.8 bits (55), Expect = 6.3
Identities = 7/38 (18%), Positives = 14/38 (36%), Gaps = 4/38 (10%)
Query: 57 EREMLRKQNDNNHWSQTV-ELAAAQEKQMEVCTVCGAF 93
ER+ LR+ N + + + + + AF
Sbjct: 235 ERDFLRQ---KNKYLPKIKKWIDENSPGDTLIPMSVAF 269
>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix
bundle, rubre like, electron transport; 1.63A
{Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB:
1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A
1ryt_A
Length = 191
Score = 24.7 bits (53), Expect = 6.3
Identities = 9/60 (15%), Positives = 17/60 (28%), Gaps = 3/60 (5%)
Query: 32 AERVGMEGSVEKAQGLMKLCDQLKEEREMLRKQNDNNHWSQTVELAAAQEKQMEVCTVCG 91
A EG E A+ + + + D + + ++ C CG
Sbjct: 106 ARIAREEGYEEIARVFASIAVAEEFHEKRFL---DFARNIKEGRVFLREQATKWRCRNCG 162
>1a32_A Ribosomal protein S15; multiwavelength anomalous diffraction,
protein-RNA, ribosomal protein interactions, ribosome,
RNA-binding; 2.10A {Geobacillus stearothermophilus}
SCOP: a.16.1.2 PDB: 1qd7_H
Length = 88
Score = 24.0 bits (53), Expect = 6.5
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 17 QITLLSEKINNL 28
QI +L+E+INNL
Sbjct: 27 QIAILTEQINNL 38
>3r8n_O 30S ribosomal protein S15; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 1p6g_O 1p87_O 2ykr_O 3oar_O
3oaq_O 3ofb_O 3ofa_O 3ofp_O 3ofx_O 3ofy_O 3ofo_O 3r8o_O
3i1m_O 2qan_O* 2qb9_O* 2qbb_O* 2qbd_O 2qbf_O 2qbh_O*
2qbj_O* ...
Length = 88
Score = 23.7 bits (52), Expect = 7.9
Identities = 6/12 (50%), Positives = 10/12 (83%)
Query: 17 QITLLSEKINNL 28
Q+ LL+ +IN+L
Sbjct: 27 QVALLTAQINHL 38
>2vqe_O 30S ribosomal protein S15; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: i.1.1.1 PDB: 1eg0_F*
1gix_R* 1hnw_O* 1hnx_O* 1hnz_O* 1hr0_O 1ibk_O* 1ibl_O*
1ibm_O 1jgo_R* 1jgp_R* 1jgq_R* 1ml5_R* 1xmo_O* 1xmq_O*
1xnq_O* 1xnr_O* 1yl4_R 2b64_O* 2b9m_O* ...
Length = 89
Score = 23.7 bits (52), Expect = 8.8
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 17 QITLLSEKINNL 28
Q+ LL+ +IN L
Sbjct: 28 QVALLTLRINRL 39
>3ulw_A 30S ribosomal protein S15; structural genomics, IDP90515, CE
structural genomics of infectious diseases, csgid, rRNA
BIN translation; 2.36A {Campylobacter jejuni}
Length = 93
Score = 23.7 bits (52), Expect = 9.5
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 17 QITLLSEKINNL 28
Q+ LL+ +I L
Sbjct: 31 QVALLTARIAEL 42
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
0.309 0.124 0.332
Gapped
Lambda K H
0.267 0.0814 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,346,105
Number of extensions: 64086
Number of successful extensions: 185
Number of sequences better than 10.0: 1
Number of HSP's gapped: 185
Number of HSP's successfully gapped: 32
Length of query: 102
Length of database: 6,701,793
Length adjustment: 67
Effective length of query: 35
Effective length of database: 4,831,086
Effective search space: 169088010
Effective search space used: 169088010
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 51 (23.3 bits)