RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2490
(64 letters)
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 62.7 bits (153), Expect = 4e-15
Identities = 22/42 (52%), Positives = 33/42 (78%)
Query: 21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
DY + ++E +++E+FV+G GPGGQA KT+NCVVL H+P+
Sbjct: 36 DYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 77
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 50.3 bits (120), Expect = 3e-10
Identities = 12/45 (26%), Positives = 20/45 (44%)
Query: 20 LDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS 64
L S + + +I+ +R G GGQ V K ++ + L S
Sbjct: 2 LVISNNVHLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRFDINAS 46
>4dh9_Y YAEJ; ribosome, YAEJ, ribosome stalling, ribosome rescue, rescue
F alternative rescue factor, ARFB, release factor,
rescue of ribosomes; 3.20A {Escherichia coli} PDB:
2jy9_A
Length = 140
Score = 47.5 bits (113), Expect = 5e-09
Identities = 12/45 (26%), Positives = 21/45 (46%)
Query: 20 LDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS 64
+ S+ I + +++ +R G GGQ V KT+ + L S
Sbjct: 2 IVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRAS 46
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular
mimicry, translation; 1.81A {Escherichia coli} SCOP:
e.38.1.1 PDB: 1mi6_A 1ml5_Z*
Length = 365
Score = 47.7 bits (114), Expect = 2e-08
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
RRH S +S F ++D +I+ D++ R SG GGQ V +T + V +THIPT
Sbjct: 212 RRHTSFSS-AFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 268
>2b3t_B RF-1, peptide chain release factor 1; translation termination,
methylation, conformational changes; HET: SAH; 3.10A
{Escherichia coli} SCOP: e.38.1.1
Length = 360
Score = 47.2 bits (113), Expect = 2e-08
Identities = 14/38 (36%), Positives = 24/38 (63%)
Query: 25 VPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
+P ++ D++ R SG GGQ V T++ + +TH+PT
Sbjct: 214 LPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPT 251
>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation;
2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X
2x9r_Y* 2x9t_Y* 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y
Length = 365
Score = 46.5 bits (111), Expect = 4e-08
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
RRH S A + ++D + ++++ +R SGPGGQ V T++ V + H+PT
Sbjct: 200 RRHTSFAG-VEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPT 256
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide
release factor 1, ribosome, structural genomics, BSGC
structure funded by NIH; 2.65A {Thermotoga maritima}
SCOP: e.38.1.1 PDB: 2fvo_A
Length = 342
Score = 45.7 bits (109), Expect = 9e-08
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 27 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
+I +D++ R SG GGQ V KT + V +TH+PT
Sbjct: 192 EIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPT 227
>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor
1 (RF-1), structural joint center for structural
genomics, JCSG; 2.34A {Streptococcus mutans}
Length = 371
Score = 45.3 bits (108), Expect = 9e-08
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 27 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
+ID KD++ SG GGQ V K V + H+PT
Sbjct: 229 EIDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPT 264
>3d5a_X RF1, peptide chain release factor 1; ribosome, ribonucleoprotein,
ribosomal protein, RNA-binding, binding, metal-binding,
zinc-finger; 3.21A {Thermus thermophilus} PDB: 2b64_Y
3d5c_X 3mr8_V 3ms0_V
Length = 354
Score = 45.2 bits (108), Expect = 1e-07
Identities = 14/36 (38%), Positives = 23/36 (63%)
Query: 27 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPT 62
++ +I+ +R SGPGGQ V T++ V + H+PT
Sbjct: 211 ALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPT 246
>1j26_A Immature colon carcinoma transcript 1; peptide chain release
factors, RF-1, the GGQ motif, immature carcinoma
transcript 1; NMR {Mus musculus} SCOP: d.50.4.1
Length = 112
Score = 42.8 bits (100), Expect = 3e-07
Identities = 11/37 (29%), Positives = 16/37 (43%)
Query: 28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTDS 64
I + + R SGPGGQ V K N+ + +
Sbjct: 17 IPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASA 53
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 26.4 bits (57), Expect = 0.70
Identities = 12/57 (21%), Positives = 15/57 (26%), Gaps = 22/57 (38%)
Query: 6 RHLSLAS-----SLFRKYDLDYSKVPKIDEKDIQERF----VRGSGPGGQAVAKTNN 53
HL +LFR LD+ RF +R A N
Sbjct: 479 HHLKNIEHPERMTLFRMVFLDF-------------RFLEQKIRHDSTAWNASGSILN 522
>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 = 25.8 bits (56), Expect = 0.92
Identities = 6/18 (33%), Positives = 12/18 (66%)
Query: 20 LDYSKVPKIDEKDIQERF 37
L++ K+ KID ++Q+
Sbjct: 1869 LNFIKLQKIDIIELQKSL 1886
>2eq7_C 2-oxoglutarate dehydrogenase E2 component; protein-protein
complex, oxidoreductase; HET: FAD NAD; 1.80A {Thermus
thermophilus}
Length = 40
Score = 23.7 bits (52), Expect = 2.0
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 28 IDEKDIQERFVRGSGPGG 45
+ EK + V+G+G GG
Sbjct: 10 MQEKGVSPAEVQGTGLGG 27
>3dva_I Dihydrolipoyllysine-residue acetyltransferase component of pyruvate
dehydrogenase...; oxidoreductase, multienzyme complex;
HET: TPW; 2.35A {Bacillus stearothermophilus} PDB:
3dv0_I* 3duf_I* 1b5s_A 1lab_A 1lac_A 1w3d_A
Length = 428
Score = 23.7 bits (52), Expect = 5.4
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 30 EKDIQERFVRGSGPGGQ 46
EK + R V+G+G G+
Sbjct: 141 EKGVDIRLVQGTGKNGR 157
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 0.136 0.392
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 952,043
Number of extensions: 40569
Number of successful extensions: 136
Number of sequences better than 10.0: 1
Number of HSP's gapped: 136
Number of HSP's successfully gapped: 14
Length of query: 64
Length of database: 6,701,793
Length adjustment: 35
Effective length of query: 29
Effective length of database: 5,724,558
Effective search space: 166012182
Effective search space used: 166012182
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: 51 (23.6 bits)