RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 045445
(128 letters)
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 61.6 bits (150), Expect = 1e-13
Identities = 16/32 (50%), Positives = 18/32 (56%)
Query: 33 RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
E E K GPGGQ NK + V LKHVP+
Sbjct: 46 SELEEQFVKGHGPGGQATNKTSNCVVLKHVPS 77
>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 = 63.4 bits (155), Expect = 3e-13
Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
E +D ++SGPGGQ N +SAVR+ H+PT
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPT 256
>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 = 62.3 bits (152), Expect = 9e-13
Identities = 25/54 (46%), Positives = 33/54 (61%), Gaps = 4/54 (7%)
Query: 15 TSSSSKKNYFELTDDEQF----RECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
TS SS Y E+ DD + +D Y++SG GGQH N+ ESAVR+ H+PT
Sbjct: 215 TSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPT 268
>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 = 60.3 bits (147), Expect = 5e-12
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
+ +D Y +SG GGQ+ NK +AVR+ H+PT
Sbjct: 234 DLRVDIYHASGAGGQNVNKVATAVRIIHLPT 264
>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 = 59.5 bits (145), Expect = 9e-12
Identities = 16/31 (51%), Positives = 24/31 (77%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
+ +DT++SSG GGQH N +SA+R+ H+PT
Sbjct: 221 DLRIDTFRSSGAGGQHVNTTDSAIRITHLPT 251
>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 = 59.5 bits (145), Expect = 9e-12
Identities = 16/31 (51%), Positives = 22/31 (70%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPT 64
E +D ++SGPGGQ N +SAVR+ H+PT
Sbjct: 216 EIRIDVMRASGPGGQGVNTTDSAVRVVHLPT 246
>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 = 59.1 bits (144), Expect = 1e-11
Identities = 16/28 (57%), Positives = 24/28 (85%)
Query: 37 MDTYKSSGPGGQHRNKRESAVRLKHVPT 64
++T+++SG GGQ+ NK ESAVR+ H+PT
Sbjct: 200 IETFRASGHGGQYVNKTESAVRITHLPT 227
>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 = 55.2 bits (133), Expect = 5e-11
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQIL 83
E E+ ++ G GGQH NK +A+ L+ ASS LP ++L
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASS------LPEYYKERLL 57
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 52.6 bits (126), Expect = 3e-10
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQIL 83
E E+ ++ G GGQ+ NK SA+ L+ ASS LPP ++L
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHLRFDINASS------LPPFYKERLL 57
>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 = 43.2 bits (101), Expect = 1e-06
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 5/50 (10%)
Query: 34 ECEMDTYKSSGPGGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQIL 83
+ +SSGPGGQ+ NK S ++ ++ ++ P +I
Sbjct: 21 RLSISYCRSSGPGGQNVNKVNSKAEVRFHLASAD-----WIEEPVRQKIA 65
>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 = 29.1 bits (64), Expect = 0.50
Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 9/66 (13%)
Query: 50 RNK----RESAVRLKHVPTASSVNLDAYLPPPQLLQILPPKFTIRCSEVGPQIRPNNPKF 105
R K SA H+ S + L P ++ +L R ++ ++ NP+
Sbjct: 273 RFKQVTDFLSAATTTHI---SLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR- 328
Query: 106 ALLDLI 111
L +I
Sbjct: 329 -RLSII 333
>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 = 26.1 bits (56), Expect = 3.4
Identities = 5/26 (19%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 48 QHRNKRESAVRLKHVP-TASSVNLDA 72
Q K +++++L + +A ++ + A
Sbjct: 20 QALKKLQASLKL-YADDSAPALAIKA 44
>3mal_A Stromal cell-derived factor 2-like protein; trefoil fold, MIR
motifs, unfolded protein response, putativ binding
protein, plant protein; 1.95A {Arabidopsis thaliana}
Length = 199
Score = 25.7 bits (56), Expect = 4.8
Identities = 7/19 (36%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 46 GGQHRNKRESAVRLKHVPT 64
G+ K++ VRL+H+ T
Sbjct: 134 SGKTW-KQDQRVRLQHIDT 151
>1t9f_A Protein 1D10; structural genomics, PSI, protein structure
initiative, southeast collaboratory for structural
genomics, secsg; 2.00A {Caenorhabditis elegans} SCOP:
b.42.6.1
Length = 187
Score = 24.9 bits (54), Expect = 7.2
Identities = 5/39 (12%), Positives = 10/39 (25%), Gaps = 10/39 (25%)
Query: 36 EMDTYKSSGPGGQHRN----------KRESAVRLKHVPT 64
E+ + S + +L+H T
Sbjct: 101 EVSAFGSEAESDTGDDWTVICNGDEWLESEQFKLRHAVT 139
>2f9i_A Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha;
zinc ribbon, crotonase superfamily, spiral domain; 1.98A
{Staphylococcus aureus}
Length = 327
Score = 25.0 bits (55), Expect = 8.9
Identities = 8/36 (22%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 46 GGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQ 81
GG H++ + A+ +K A +L++ L ++
Sbjct: 279 GGAHKDIEQQALAIKSAFVAQLDSLES-LSRDEIAN 313
>2f9y_A Acetyl-COA carboxylase, carboxyltransferase alpha; zinc ribbon,
crotonase superfamily, spiral domain, ligase; 3.20A
{Escherichia coli} SCOP: c.14.1.4
Length = 339
Score = 25.0 bits (55), Expect = 9.9
Identities = 13/36 (36%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 46 GGQHRNKRESAVRLKHVPTASSVNLDAYLPPPQLLQ 81
GG HRN A LK A +LD L L
Sbjct: 293 GGAHRNPEAMAASLKAQLLADLADLDV-LSTEDLKN 327
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
0.315 0.132 0.389
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: 1,829,627
Number of extensions: 94597
Number of successful extensions: 157
Number of sequences better than 10.0: 1
Number of HSP's gapped: 156
Number of HSP's successfully gapped: 18
Length of query: 128
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 45
Effective length of database: 4,384,350
Effective search space: 197295750
Effective search space used: 197295750
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 (21.6 bits)
S2: 51 (23.6 bits)