RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14514
(91 letters)
>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M
domain, RNA-binding, signal sequence-binding,
helix-turn-helix, protein targeting; 3.20A {Thermus
aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB:
2iy3_A
Length = 425
Score = 25.9 bits (58), Expect = 2.0
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 51 NDFLAQLDMLRKGG 64
DFL Q+ L++ G
Sbjct: 323 EDFLKQMQNLKRLG 336
>2xvm_A Tellurite resistance protein TEHB; antibiotic resistance,
transferase; HET: SAH; 1.48A {Escherichia coli} PDB:
2xva_A* 4dq0_A* 2i6g_A*
Length = 199
Score = 25.5 bits (56), Expect = 2.2
Identities = 8/41 (19%), Positives = 19/41 (46%), Gaps = 10/41 (24%)
Query: 23 SVWDSDYYTGQVGSYPYSGFYQDLSANHNDFLAQLDMLRKG 63
+ D +Y+T Y +L+ H++ L + +++ G
Sbjct: 4 VIRDENYFTD-----KY-----ELTRTHSEVLEAVKVVKPG 34
>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition
particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A
{Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A
Length = 433
Score = 25.6 bits (57), Expect = 2.4
Identities = 7/14 (50%), Positives = 8/14 (57%)
Query: 51 NDFLAQLDMLRKGG 64
D AQ+ LRK G
Sbjct: 331 RDVYAQIIALRKMG 344
>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA
binding protein, hydrolase, gtpas; HET: GCP; 3.94A
{Escherichia coli} PDB: 2j28_9
Length = 433
Score = 25.6 bits (57), Expect = 2.5
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 51 NDFLAQLDMLRKGG 64
NDFL QL ++ G
Sbjct: 332 NDFLEQLRQMKNMG 345
>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal
recognition particle, SRP-GTPase, protein targeting,
cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus
furiosus}
Length = 443
Score = 25.2 bits (56), Expect = 3.3
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 51 NDFLAQLDMLRKGG 64
D AQL+ +RK G
Sbjct: 331 KDMYAQLEAMRKMG 344
>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding,
signal recognition particle, GTP-binding, RNA-binding;
2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B
Length = 432
Score = 25.2 bits (56), Expect = 3.3
Identities = 4/14 (28%), Positives = 8/14 (57%)
Query: 51 NDFLAQLDMLRKGG 64
N+ + QL+ + G
Sbjct: 328 NELMTQLEAIENMG 341
>1ffy_A Isoleucyl-tRNA synthetase; protein-RNA complex, metal IONS, editing
tRNA synthetase, double-sieve, ligase/RNA, mupiroci;
HET: MRC; 2.20A {Staphylococcus aureus} SCOP: a.27.1.1
b.51.1.1 c.26.1.1 PDB: 1qu2_A* 1qu3_A*
Length = 917
Score = 25.2 bits (56), Expect = 3.9
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 9 KGIYEENLPVFEGSSVWDSD 28
KG++ E FEG ++
Sbjct: 352 KGVFTEEGGQFEGMFYDKAN 371
>2jqe_A SRP54, signal recognition 54 kDa protein; AF54, structure,
solution, signaling protein; NMR {Archaeoglobus
fulgidus}
Length = 119
Score = 24.4 bits (54), Expect = 4.3
Identities = 4/15 (26%), Positives = 7/15 (46%), Gaps = 1/15 (6%)
Query: 51 NDFLAQLDMLRK-GG 64
D Q++ + K G
Sbjct: 13 KDIYKQIEAMNKMGP 27
>1rw7_A YDR533CP; alpha-beta sandwich, DJ-1/THIJ/PFPI superfamily, unknown
function; 1.80A {Saccharomyces cerevisiae} SCOP:
c.23.16.2 PDB: 1qvv_A* 1qvz_A 1qvw_A
Length = 243
Score = 25.0 bits (54), Expect = 4.5
Identities = 8/35 (22%), Positives = 13/35 (37%), Gaps = 3/35 (8%)
Query: 2 FLVQTVLK---GIYEENLPVFEGSSVWDSDYYTGQ 33
V+ V K Y + ++ S+ D TG
Sbjct: 185 ATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGV 219
>1hq1_A Signal recognition particle protein; protein-RNA complex, double
helix, tetraloop, internal loop, SRP,
ribonucleoprotein; HET: CCC; 1.52A {Escherichia coli}
SCOP: a.36.1.1 PDB: 3lqx_A* 2pxb_A 2pxd_A 2pxe_A 2pxf_A
2pxk_A 2pxl_A 2pxp_A 2pxq_A 2pxt_A 2pxu_A 2pxv_A
Length = 105
Score = 24.4 bits (54), Expect = 4.8
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 7/25 (28%)
Query: 41 GFYQDLSANHNDFLAQLDMLRK-GG 64
GF DL NDFL QL ++ GG
Sbjct: 1 GF--DL----NDFLEQLRQMKNMGG 19
>3n7t_A Macrophage binding protein; seattle structural genomics center for
infectious disease, S macrophage, pathogenic fungus,
coccidioidomycosis; 2.10A {Coccidioides immitis}
Length = 247
Score = 24.6 bits (53), Expect = 5.3
Identities = 4/35 (11%), Positives = 9/35 (25%), Gaps = 3/35 (8%)
Query: 2 FLVQTVLK---GIYEENLPVFEGSSVWDSDYYTGQ 33
+ + + Y ++ D TG
Sbjct: 191 HTIADMAQTANAEYVPPEDPWDDFCKVDGRIVTGA 225
>3eps_A Isocitrate dehydrogenase kinase/phosphatase; ATP-binding,
glyoxylate bypass, nucleotide-binding, protein
phosphatase; HET: AMP ATP; 2.80A {Escherichia coli O157}
PDB: 3lcb_A* 3lc6_A*
Length = 578
Score = 24.8 bits (54), Expect = 5.4
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 58 DMLRKGGWITRATRVVFIDF 77
DML K +TR RVVF D+
Sbjct: 457 DMLFKNFGVTRHGRVVFYDY 476
>1xf1_A C5A peptidase, SCP; hydrolase; HET: CIT; 1.90A {Streptococcus
pyogenes} PDB: 3eif_A*
Length = 926
Score = 24.6 bits (53), Expect = 5.7
Identities = 10/34 (29%), Positives = 13/34 (38%)
Query: 15 NLPVFEGSSVWDSDYYTGQVGSYPYSGFYQDLSA 48
N EG + D ++ S PY GF D
Sbjct: 577 NGYFLEGFVRFKQDPTKEELMSIPYIGFRGDFGN 610
>2y3u_A Collagenase, collagenase G; hydrolase, gluzincin, metalloprotease;
HET: P6G FLC; 2.55A {Clostridium histolyticum} PDB:
2y50_A* 2y6i_A*
Length = 785
Score = 24.5 bits (52), Expect = 6.1
Identities = 5/51 (9%), Positives = 9/51 (17%), Gaps = 2/51 (3%)
Query: 17 PVFEGSSVWDSDYYTGQVGSYPYSGFYQDLSANH--NDFLAQLDMLRKGGW 65
+ +S Y Y Y F+ +
Sbjct: 492 HRYSLKKTLNSGYDDSDWMFYNYGFAVAHYLYEKDMPTFIKMNKAILNTDV 542
>1pp9_B Ubiquinol-cytochrome C reductase complex core Pro mitochondrial;
cytochrome BC1, membrane protein, heme protein, rieske
iron protein, cytochrome B, complex III; HET: BHG HEM
HEC SMA UQ CDL PEE; 2.10A {Bos taurus} SCOP: d.185.1.1
d.185.1.1 PDB: 1bgy_B* 1be3_B* 1l0n_B* 1ntk_B* 1ntm_B*
1ntz_B* 1nu1_B* 1l0l_B* 1ppj_B* 1sqq_B* 1sqv_B* 1sqx_B*
2a06_B* 2fyu_B* 2ybb_B* 1sqb_B* 1sqp_B* 1qcr_B* 2bcc_B*
3bcc_B* ...
Length = 439
Score = 24.1 bits (53), Expect = 7.7
Identities = 2/16 (12%), Positives = 7/16 (43%)
Query: 19 FEGSSVWDSDYYTGQV 34
E +++ ++ V
Sbjct: 259 AESAAIGSAEANAFSV 274
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
0.325 0.140 0.440
Gapped
Lambda K H
0.267 0.0596 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,422,843
Number of extensions: 70796
Number of successful extensions: 242
Number of sequences better than 10.0: 1
Number of HSP's gapped: 242
Number of HSP's successfully gapped: 19
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: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.7 bits)