RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2492
(162 letters)
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 91.3 bits (227), Expect = 9e-25
Identities = 39/73 (53%), Positives = 56/73 (76%)
Query: 51 PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELL 110
++E +++E+FV+G GPGGQA KT+NCVVL H+P+GIV+KCHQ+RS+ +NRK AR++L
Sbjct: 41 LPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIARKVL 100
Query: 111 VAQWDVQVNGEDS 123
+ DV N S
Sbjct: 101 QEKVDVFYNSGPS 113
>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 = 65.4 bits (160), Expect = 2e-13
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 43 NIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSEN 102
+IDI +I+ D++ R SG GGQ V +T + V +THIPTGIV +C RS +N
Sbjct: 229 DIDI-----EINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKN 283
Query: 103 RKTARELLVAQ 113
+ A + + A+
Sbjct: 284 KDQAMKQMKAK 294
>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 = 64.9 bits (159), Expect = 4e-13
Identities = 27/82 (32%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 50 IPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTAREL 109
+P ++ D++ R SG GGQ V T++ + +TH+PTGIV++C RS +N+ A +
Sbjct: 214 LPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSV 273
Query: 110 LVAQ-WDVQVNGEDSLNAQIRR 130
L A+ ++ A RR
Sbjct: 274 LGARIHAAEMAKRQQAEASTRR 295
>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 = 63.8 bits (156), Expect = 7e-13
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 52 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLV 111
+ID KD++ SG GGQ V K V + H+PT I ++ + R+ +NR A +++
Sbjct: 229 EIDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIR 288
Query: 112 AQ-WDVQVNGEDSLNAQIRR 130
A+ D R+
Sbjct: 289 ARVADHFAQIAQDEQDAERK 308
>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 = 63.3 bits (155), Expect = 9e-13
Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 52 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLV 111
++ +I+ +R SGPGGQ V T++ V + H+PTGI++ C SRS +NR+ A +L
Sbjct: 211 ALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALMILR 270
Query: 112 AQ-WDVQVNGEDSLNAQIRR 130
++ +++ E + R
Sbjct: 271 SRLLEMKRAEEAERLRKTRL 290
>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 = 63.0 bits (154), Expect = 1e-12
Identities = 30/80 (37%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 52 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLV 111
+I +D++ R SG GGQ V KT + V +TH+PTGIV+ C RS +N++TA +L
Sbjct: 192 EIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILR 251
Query: 112 AQ-WDVQVNGEDSLNAQIRR 130
A+ + +Q ++ +Q R+
Sbjct: 252 ARLYQLQKEQKEREISQKRK 271
>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 = 63.0 bits (154), Expect = 1e-12
Identities = 22/70 (31%), Positives = 42/70 (60%), Gaps = 5/70 (7%)
Query: 43 NIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSEN 102
+++ + ++++ +R SGPGGQ V T++ V + H+PTGI + C +RS +N
Sbjct: 217 EVEV-----VLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKN 271
Query: 103 RKTARELLVA 112
++ A ++L A
Sbjct: 272 KELALKILKA 281
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 53.4 bits (128), Expect = 3e-10
Identities = 18/85 (21%), Positives = 29/85 (34%), Gaps = 24/85 (28%)
Query: 52 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTG----------------------- 88
+ + +I+ +R G GGQ V K ++ + L
Sbjct: 9 HLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDG 68
Query: 89 -IVIKCHQSRSLSENRKTARELLVA 112
IV+K Q R+ +NR A L
Sbjct: 69 VIVLKAQQYRTQEQNRADALLRLSE 93
>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 = 52.1 bits (125), Expect = 2e-09
Identities = 32/137 (23%), Positives = 46/137 (33%), Gaps = 45/137 (32%)
Query: 44 IDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLT-------------------- 83
I I + I + +++ +R G GGQ V KT+ + L
Sbjct: 2 IVISRHV-AIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAAS 60
Query: 84 ----HIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQ 139
IVIK + RS NR+ A LVA + T
Sbjct: 61 HHLISSDGVIVIKAQEYRSQELNREAALARLVA--------------------MIKELTT 100
Query: 140 EQKKRKLDALKKAWKER 156
E+K R+ +A KER
Sbjct: 101 EKKARRPTRPTRASKER 117
>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 = 48.6 bits (115), Expect = 2e-08
Identities = 15/85 (17%), Positives = 23/85 (27%), Gaps = 25/85 (29%)
Query: 53 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTG------------------------ 88
I + + R SGPGGQ V K N+ +
Sbjct: 17 IPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAG 76
Query: 89 -IVIKCHQSRSLSENRKTARELLVA 112
+V+ SR N + +
Sbjct: 77 ELVLTSESSRYQFRNLAECLQKIRD 101
>1gl4_A Nidogen-1, entactin; immunoglobulin-like domain, extracellular
matrix; HET: EPE; 2.0A {Mus musculus} SCOP: d.22.1.2
g.3.11.5 PDB: 1h4u_A
Length = 285
Score = 30.5 bits (68), Expect = 0.21
Identities = 8/87 (9%), Positives = 24/87 (27%), Gaps = 8/87 (9%)
Query: 22 ESQVTITRELRNDGYHRNLVSNIDIYSTIPKIDE------KDIQERFVRGSGPGGQAVAK 75
++ + ++ H +L + ++ +P+I + E + +
Sbjct: 146 PGKLVLKQQFSGIDEHGHLTISTELEGRVPQIPYGASVHIEPYTELYHY--SSSVITSSS 203
Query: 76 TNNCVVLTHIPTGIVIKCHQSRSLSEN 102
T V+ G +
Sbjct: 204 TREYTVMEPDQDGAAPSHTHIYQWRQT 230
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.4 bits (65), Expect = 0.46
Identities = 8/35 (22%), Positives = 18/35 (51%)
Query: 127 QIRRIDEKRRATQEQKKRKLDALKKAWKEREDRRN 161
Q +R+ E A++ ++ + KK +E R++
Sbjct: 94 QRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQS 128
>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 = 28.7 bits (63), Expect = 0.94
Identities = 20/162 (12%), Positives = 44/162 (27%), Gaps = 31/162 (19%)
Query: 6 VMWPMRDRNLAGIRLLESQVTITRELRNDG-----YHRNLVSNIDIYSTIPKIDEKDIQE 60
+M P++ + + L ND Y+ VS + Y + + +
Sbjct: 94 LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN---VSRLQPYLKLRQALLELRPA 150
Query: 61 RFVRGSGPGGQAVAKT-------NNCVVLTHIPTGI----VIKCHQSRSLSENRKTAREL 109
+ V G G KT + V + I + C+ + +
Sbjct: 151 KNVLIDGVLG--SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN----------SPETV 198
Query: 110 LVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDALKK 151
L + + + ++ + + LK
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS 240
Score = 25.6 bits (55), Expect = 9.7
Identities = 6/46 (13%), Positives = 18/46 (39%), Gaps = 3/46 (6%)
Query: 35 GYHRNLVSNIDIYSTIPKI--DEKDIQERFVRGSGPGGQAVAKTNN 78
G+H + + + + + D + ++++ +R A N
Sbjct: 478 GHHLKNIEHPERMTLFRMVFLDFRFLEQK-IRHDSTAWNASGSILN 522
>3mzf_A D-alanyl-D-alanine carboxypeptidase DACA; beta-lactam antibiotic,
penicillin-binding protein, DD- carboxypeptidase,
hydrolase; HET: IM2; 1.50A {Escherichia coli} PDB:
1nzu_A 1nzo_A* 3beb_A* 3bec_A* 3mzd_A* 3mze_A* 1z6f_A*
1nj4_A 1hd8_A 1sdn_A 4drt_A
Length = 363
Score = 27.2 bits (61), Expect = 2.3
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 6/43 (13%)
Query: 39 NLVSNIDIYSTIPKIDEKDIQERFVRGSGP------GGQAVAK 75
+L + D+Y TIP+ KD++ +V S Q V
Sbjct: 289 SLGVDKDVYLTIPRGRMKDLKASYVLNSSELHAPLQKNQVVGT 331
>3a3j_A PBP5; penicillin binding protein 5, DACA, hydrolase; 2.15A
{Haemophilus influenzae}
Length = 344
Score = 26.8 bits (60), Expect = 3.7
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 6/43 (13%)
Query: 39 NLVSNIDIYSTIPKIDEKDIQERFVRGSGP------GGQAVAK 75
L + +D + TIPK + +++ R+ GQ + K
Sbjct: 279 KLGAFMDHFITIPKGKQSEVKARYELADKNLQAPLAKGQVIGK 321
>2qzu_A Putative sulfatase YIDJ; Q64XZ4_bacfr, arylsulfatase, BFR123, NESG,
structural genomics, PSI-2, protein structure
initiative; 1.70A {Bacteroides fragilis}
Length = 491
Score = 26.5 bits (59), Expect = 4.5
Identities = 6/35 (17%), Positives = 15/35 (42%)
Query: 3 IKIVMWPMRDRNLAGIRLLESQVTITRELRNDGYH 37
K+ + G+ L ++ + L++ GY+
Sbjct: 92 SKVTGNCNSETAPYGVELSQNARCWSDVLKDQGYN 126
>2vqr_A Putative sulfatase; phosphonate monoester hydrolase, hydrolase,
plasmid, formylglycine, phosphodiesterase; 1.42A
{Rhizobium leguminosarum BV} PDB: 2w8s_A
Length = 543
Score = 26.6 bits (59), Expect = 4.9
Identities = 5/21 (23%), Positives = 10/21 (47%)
Query: 17 GIRLLESQVTITRELRNDGYH 37
+ L + + + + LR GY
Sbjct: 108 TVPLDQRHLNLGKALRGVGYD 128
>3sp1_A Cysteinyl-tRNA synthetase; structural genomics, seattle structural
genomics center for infectious disease, ssgcid, LYME
disease; HET: AMP; 2.55A {Borrelia burgdorferi}
Length = 501
Score = 26.4 bits (59), Expect = 5.2
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 26 TITRELRNDGYHRNLVSNI-DIYSTIPKIDEKD 57
+ + LR GY N NI DI +D+ +
Sbjct: 69 LLIKTLRFLGYKVNYAMNITDIGHLTGDLDDGE 101
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
0.318 0.133 0.381
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,447,898
Number of extensions: 137108
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 403
Number of HSP's successfully gapped: 29
Length of query: 162
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 76
Effective length of database: 4,300,587
Effective search space: 326844612
Effective search space used: 326844612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.9 bits)