RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4479
(135 letters)
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 92.8 bits (231), Expect = 8e-26
Identities = 41/78 (52%), Positives = 59/78 (75%)
Query: 21 DYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKT 80
DY + ++E +++E+FV+G GPGGQA KT+NCVVL H+P+GIV+KCHQ+RS+ +NRK
Sbjct: 36 DYPALLPLNESELEEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKI 95
Query: 81 ARELLVAQWDVQVNGEDS 98
AR++L + DV N S
Sbjct: 96 ARKVLQEKVDVFYNSGPS 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 = 68.1 bits (167), Expect = 1e-14
Identities = 32/84 (38%), Positives = 48/84 (57%), Gaps = 1/84 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGI 64
RRH S +S F ++D +I+ D++ R SG GGQ V +T + V +THIPTGI
Sbjct: 212 RRHTSFSS-AFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGI 270
Query: 65 VIKCHQSRSLSENRKTARELLVAQ 88
V +C RS +N+ A + + A+
Sbjct: 271 VTQCQNDRSQHKNKDQAMKQMKAK 294
>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 = 65.3 bits (160), Expect = 9e-14
Identities = 28/83 (33%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGI 64
RRH S A + ++D + ++++ +R SGPGGQ V T++ V + H+PTGI
Sbjct: 200 RRHTSFAG-VEVIPEVDEEVEVVLKPEELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGI 258
Query: 65 VIKCHQSRSLSENRKTARELLVA 87
+ C +RS +N++ A ++L A
Sbjct: 259 TVTCQTTRSQIKNKELALKILKA 281
>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 = 1e-13
Identities = 27/82 (32%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 25 VPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTAREL 84
+P ++ D++ R SG GGQ V T++ + +TH+PTGIV++C RS +N+ A +
Sbjct: 214 LPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSV 273
Query: 85 LVAQ-WDVQVNGEDSLNAQIRR 105
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 = 64.1 bits (157), Expect = 2e-13
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 27 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLV 86
+ID KD++ SG GGQ V K V + H+PT I ++ + R+ +NR A +++
Sbjct: 229 EIDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIR 288
Query: 87 AQ-WDVQVNGEDSLNAQIRR 105
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 = 63.7 bits (156), Expect = 4e-13
Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 27 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLV 86
++ +I+ +R SGPGGQ V T++ V + H+PTGI++ C SRS +NR+ A +L
Sbjct: 211 ALNMDEIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALMILR 270
Query: 87 AQ-WDVQVNGEDSLNAQIRR 105
++ +++ 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 = 63.4 bits (155), Expect = 5e-13
Identities = 30/80 (37%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 27 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLV 86
+I +D++ R SG GGQ V KT + V +TH+PTGIV+ C RS +N++TA +L
Sbjct: 192 EIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILR 251
Query: 87 AQ-WDVQVNGEDSLNAQIRR 105
A+ + +Q ++ +Q R+
Sbjct: 252 ARLYQLQKEQKEREISQKRK 271
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 54.9 bits (132), Expect = 5e-11
Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 24/92 (26%)
Query: 20 LDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTG---------------- 63
L S + + +I+ +R G GGQ V K ++ + L
Sbjct: 2 LVISNNVHLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALND 61
Query: 64 --------IVIKCHQSRSLSENRKTARELLVA 87
IV+K Q R+ +NR A L
Sbjct: 62 SRITSDGVIVLKAQQYRTQEQNRADALLRLSE 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 = 52.8 bits (127), Expect = 5e-10
Identities = 31/136 (22%), Positives = 46/136 (33%), Gaps = 44/136 (32%)
Query: 20 LDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLT--------------------- 58
+ S+ I + +++ +R G GGQ V KT+ + L
Sbjct: 2 IVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASH 61
Query: 59 ---HIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQE 115
IVIK + RS NR+ A LVA + T E
Sbjct: 62 HLISSDGVIVIKAQEYRSQELNREAALARLVA--------------------MIKELTTE 101
Query: 116 QKKRKLDALKKAWKER 131
+K R+ +A KER
Sbjct: 102 KKARRPTRPTRASKER 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 = 48.2 bits (114), Expect = 2e-08
Identities = 15/85 (17%), Positives = 23/85 (27%), Gaps = 25/85 (29%)
Query: 28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTG------------------------ 63
I + + R SGPGGQ V K N+ +
Sbjct: 17 IPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAG 76
Query: 64 -IVIKCHQSRSLSENRKTARELLVA 87
+V+ SR N + +
Sbjct: 77 ELVLTSESSRYQFRNLAECLQKIRD 101
>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 = 0.72
Identities = 17/139 (12%), Positives = 39/139 (28%), Gaps = 31/139 (22%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDE------KDIQERFVRGSGPGGQAVAKT------- 51
R L + +F KY++ S++ + + + V G G KT
Sbjct: 116 RDRLYNDNQVFAKYNV--SRLQPYLKLRQALLELRPAKNVLIDGVLG--SGKTWVALDVC 171
Query: 52 NNCVVLTHIPTGI----VIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRID 107
+ V + I + C+ + +L + + + ++
Sbjct: 172 LSYKVQCKMDFKIFWLNLKNCN----------SPETVLEMLQKLLYQIDPNWTSRSDHSS 221
Query: 108 EKRRATQEQKKRKLDALKK 126
+ + LK
Sbjct: 222 NIKLRIHSIQAELRRLLKS 240
Score = 26.0 bits (56), Expect = 6.3
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
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.7 bits (58), Expect = 2.7
Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 86 VAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDALKKAWKER 131
+AQ D ++ E IR+ E++R ++ +++ W+E+
Sbjct: 74 IAQAD-RLTQEP---ESIRKWREEQRKRLQELDAASKVMEQEWREK 115
>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 = 26.2 bits (57), Expect = 4.7
Identities = 6/18 (33%), Positives = 12/18 (66%)
Query: 20 LDYSKVPKIDEKDIQERF 37
L++ K+ KID ++Q+
Sbjct: 1869 LNFIKLQKIDIIELQKSL 1886
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
0.317 0.132 0.374
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: 2,020,466
Number of extensions: 107074
Number of successful extensions: 359
Number of sequences better than 10.0: 1
Number of HSP's gapped: 352
Number of HSP's successfully gapped: 22
Length of query: 135
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 51
Effective length of database: 4,356,429
Effective search space: 222177879
Effective search space used: 222177879
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: 52 (24.5 bits)