RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14432
(189 letters)
>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 = 109 bits (273), Expect = 2e-31
Identities = 40/114 (35%), Positives = 71/114 (62%), Gaps = 9/114 (7%)
Query: 62 KAPDGLKFNGVIPVVIPRFSYITEELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWL 121
+ + IP + L I+Y RSSGPGGQ+VN V++K ++RF + +A+W+
Sbjct: 6 SGEHAKQASSYIP---------LDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWI 56
Query: 122 NEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAKPA 175
E V++++ +KN++NK G L++ S+ +R Q NLA+ + +R+MI +A+ P+
Sbjct: 57 EEPVRQKIALTHKNKINKAGELVLTSESSRYQFRNLAECLQKIRDMIAEASGPS 110
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 109 bits (273), Expect = 2e-31
Identities = 35/93 (37%), Positives = 59/93 (63%), Gaps = 1/93 (1%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNKNRLNKDGYLI 144
E+++T R+ G GGQ+VN VS+ + +RF +NA+ L K++L+ LN +R+ DG ++
Sbjct: 13 AEIELTAIRAQGAGGQNVNKVSSAMHLRFDINAS-SLPPFYKERLLALNDSRITSDGVIV 71
Query: 145 IKSDRTRSQQLNLADAMTTLRNMIWKAAKPAPQ 177
+K+ + R+Q+ N ADA+ L +I AAK
Sbjct: 72 LKAQQYRTQEQNRADALLRLSELIVNAAKLEHH 104
>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 = 109 bits (273), Expect = 5e-31
Identities = 37/103 (35%), Positives = 56/103 (54%), Gaps = 6/103 (5%)
Query: 75 VVIPRFSYITEELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAANWLNEDVKKQLIELNK 134
V IP EL+IT R+ G GGQHVN ST + +RF + A+ L E K++L+ +
Sbjct: 8 VAIPD-----GELEITAIRAQGAGGQHVNKTSTAIHLRFDIRAS-SLPEYYKERLLAASH 61
Query: 135 NRLNKDGYLIIKSDRTRSQQLNLADAMTTLRNMIWKAAKPAPQ 177
+ ++ DG ++IK+ RSQ+LN A+ L MI +
Sbjct: 62 HLISSDGVIVIKAQEYRSQELNREAALARLVAMIKELTTEKKA 104
>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 = 47.5 bits (112), Expect = 7e-07
Identities = 26/181 (14%), Positives = 63/181 (34%), Gaps = 29/181 (16%)
Query: 7 FHKLISNQRNVVKRFYKSSISLDKLYPNSSMLLKTPTPDQVKAPDGLKFNGVIPVKAPDG 66
F L+S Q +V++F + + ++ Y L +P + + P + ++ D
Sbjct: 68 FWTLLSKQEEMVQKFVEEVLRIN--YK----FLMSPIKTEQRQPSM---MTRMYIEQRDR 118
Query: 67 LKFNGVIPVV---IPRFSYITEELDITYSRSSGPG---------GQHVNSVSTKVDIRFK 114
L +N + R + G+ ++ + + +
Sbjct: 119 L-YNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQ 177
Query: 115 VNAAN---WLN---EDVKKQLIELNKNRLNK-DGYLIIKSDRTRSQQLNLADAMTTLRNM 167
WLN + + ++E+ + L + D +SD + + +L + LR +
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237
Query: 168 I 168
+
Sbjct: 238 L 238
Score = 26.7 bits (58), Expect = 6.3
Identities = 28/168 (16%), Positives = 58/168 (34%), Gaps = 39/168 (23%)
Query: 17 VVKRFYKSSISLDKLYPNSSMLLKTPTP----------DQVKAPDGLKFNGVIPVKAPDG 66
V K+ +S+IS+ +Y + LK D P + +IP D
Sbjct: 417 VEKQPKESTISIPSIY----LELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL-DQ 471
Query: 67 LKFN---------------GVIPVVIPRFSYITEELDITYSRSSGPGGQHVNSV-STKVD 110
++ + +V F ++ +++ R S+ +T
Sbjct: 472 YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI-----RHDSTAWNASGSILNTLQQ 526
Query: 111 IRF-KVNAANWLNEDVKKQLIELNKNRLNKDGYLIIKSDRTRSQQLNL 157
++F K + N+ ++L+ + L K +I S T ++ L
Sbjct: 527 LKFYKPYICD--NDPKYERLVNAILDFLPKIEENLICSKYTDLLRIAL 572
Score = 26.4 bits (57), Expect = 7.9
Identities = 10/62 (16%), Positives = 17/62 (27%), Gaps = 14/62 (22%)
Query: 109 VDIRFKVNAANW-----------LNEDVKKQLIELNKNRLNK---DGYLIIKSDRTRSQQ 154
I + + W +N+ K L+E YL +K
Sbjct: 385 AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA 444
Query: 155 LN 156
L+
Sbjct: 445 LH 446
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 38.5 bits (90), Expect = 2e-04
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
EL+ + + GPGGQ N S V +
Sbjct: 46 SELEEQFVKGHGPGGQATNKTSNCVVL 72
>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 = 39.9 bits (94), Expect = 2e-04
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
++L + +SG GGQ+VN V+T V I
Sbjct: 233 KDLRVDIYHASGAGGQNVNKVATAVRI 259
>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 = 39.1 bits (92), Expect = 3e-04
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 85 EELDI-TYSRSSGPGGQHVNSVSTKVDI 111
EEL I R+SGPGGQ VN+ + V +
Sbjct: 225 EELRIDVM-RASGPGGQGVNTTDSAVRV 251
>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 = 37.6 bits (86), Expect = 6e-04
Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 17/46 (36%)
Query: 14 QRNVVKRFYKSSISLDKLYPNSSMLLKTPTPDQVKAPDGLKFNGVI 59
++ +K+ ++S+ KLY D AP L +
Sbjct: 18 EKQALKKL-QASL---KLY----------ADDS--AP-ALAIKATM 46
Score = 25.7 bits (55), Expect = 9.0
Identities = 5/31 (16%), Positives = 9/31 (29%), Gaps = 8/31 (25%)
Query: 46 QVKAPDGLKFNGVIPVKAPD---GLKFNGVI 73
+K K + + A D L +
Sbjct: 21 ALK-----KLQASLKLYADDSAPALAIKATM 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 = 38.4 bits (90), Expect = 8e-04
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
+L I R+SG GGQHVN + V I
Sbjct: 237 ADLRIDVYRASGAGGQHVNRTESAVRI 263
>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 = 38.3 bits (90), Expect = 8e-04
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
+E+ I R+SGPGGQ VN+ + V +
Sbjct: 215 DEIRIDVMRASGPGGQGVNTTDSAVRV 241
>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 = 37.9 bits (89), Expect = 0.001
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 85 EELDITYSRSSGPGGQHVNSVSTKVDI 111
+L I RSSG GGQHVN+ + + I
Sbjct: 220 ADLRIDTFRSSGAGGQHVNTTDSAIRI 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 = 37.2 bits (87), Expect = 0.002
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 11/37 (29%)
Query: 85 EELDI----------TYSRSSGPGGQHVNSVSTKVDI 111
EE DI T+ R+SG GGQ+VN + V I
Sbjct: 187 EEKDIEIRPEDLKIETF-RASGHGGQYVNKTESAVRI 222
>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 = 29.6 bits (66), Expect = 0.72
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 8/58 (13%)
Query: 10 LISNQRNVVKRFYKSSISLDKLYP---NSSMLLKTP--TPDQ---VKAPDGLKFNGVI 59
LI + ++++ +K++ N L+ P TPD+ + P GVI
Sbjct: 187 LIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVI 244
Score = 28.5 bits (63), Expect = 1.9
Identities = 20/132 (15%), Positives = 37/132 (28%), Gaps = 45/132 (34%)
Query: 11 ISNQRNVVKRFYKSSISLDKLYPN--SSMLLKTPTPDQVKAPDG-----LKFNGVIPVKA 63
+ + ++K + + I + + +S L + +G F G
Sbjct: 116 LVKTKELIKNYITARIMAKRPFDKKSNSALFR-------AVGEGNAQLVAIFGG------ 162
Query: 64 PDGLKFNGVIPVVIPRFSYITEEL-DI--TYS-------RSSGPGGQHVNSVSTKVDIRF 113
G Y EEL D+ TY + S + + + F
Sbjct: 163 ------QGNTD------DYF-EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVF 209
Query: 114 K--VNAANWLNE 123
+N WL
Sbjct: 210 TQGLNILEWLEN 221
>3axy_A Protein heading DATE 3A; phosphatidylethanolamine-binding protein,
14-3-3 protein, BZ protein, floral induction; HET: SEP;
2.40A {Oryza sativa japonica group} PDB: 1wkp_A
Length = 170
Score = 27.2 bits (60), Expect = 2.7
Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 1/44 (2%)
Query: 65 DGLKFNGVIPVVIPRFSYITEELDITYSRSSGPGGQHVNSVSTK 108
D L V+ V+ F + L +TY + G +
Sbjct: 9 DPLVVGRVVGDVLDAFVR-STNLKVTYGSKTVSNGLELKPSMVT 51
>1wko_A Terminal flower 1 protein; CIS-peptide, PEBP, signaling protein;
1.80A {Arabidopsis thaliana} PDB: 1qou_A
Length = 180
Score = 26.8 bits (59), Expect = 3.5
Identities = 9/55 (16%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 65 DGLKFNGVIPVVIPRFSYITEELDITYSRSSGPGGQHVNSVSTKVDIRFKVNAAN 119
+ L V+ V+ F+ T +++++Y++ G + S R +++ +
Sbjct: 13 EPLIMGRVVGDVLDFFT-PTTKMNVSYNKKQVSNGHELFPSSVSSKPRVEIHGGD 66
>3udf_A Penicillin-binding protein 1A; transglycosylase, transpeptidase;
HET: MES; 1.70A {Acinetobacter baumannii} PDB: 3udi_A*
3udx_A* 3ue0_A* 3ue1_A*
Length = 731
Score = 26.1 bits (58), Expect = 7.7
Identities = 8/67 (11%), Positives = 24/67 (35%), Gaps = 17/67 (25%)
Query: 82 YITEELDITYSRSSGPGGQHVNSVSTKVDIRFKVNA----ANWLNEDVKKQLIELNKNRL 137
YI++ ++ +V+ +++ + E V+ +L++ +
Sbjct: 207 YISQA-------------EYQKAVAEPINLNMPNRDLNNIHPYAGEMVRSELVKHFGEQA 253
Query: 138 NKDGYLI 144
GY +
Sbjct: 254 IDSGYKV 260
>3d3y_A Uncharacterized protein; APC29635, conserved protein, enterococcus
faecalis V583, STR genomics, PSI-2, protein structure
initiative; 1.95A {Enterococcus faecalis}
Length = 425
Score = 26.1 bits (58), Expect = 9.4
Identities = 11/46 (23%), Positives = 20/46 (43%)
Query: 142 YLIIKSDRTRSQQLNLADAMTTLRNMIWKAAKPAPQISEDTIDRIR 187
+ I +D LA+A+ L+ +I+ A Q +T R +
Sbjct: 91 SMNIVNDHYLQDSQVLAEAVDFLKEIIFAPNIQAGQFEAETFQREK 136
>3sya_A G protein-activated inward rectifier potassium CH; ION channel,
potassium channel, inward rectification, sodium PIP2
binding, G protein binding; HET: PIO; 2.98A {Mus
musculus} PDB: 3syo_A 3syc_A 3syp_A 3syq_A*
Length = 340
Score = 25.9 bits (56), Expect = 9.6
Identities = 11/38 (28%), Positives = 14/38 (36%), Gaps = 1/38 (2%)
Query: 133 NKNRL-NKDGYLIIKSDRTRSQQLNLADAMTTLRNMIW 169
R KDG + R L D TTL ++ W
Sbjct: 5 KIQRYVRKDGKCNVHHGNVRETYRYLTDIFTTLVDLKW 42
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 0.134 0.380
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: 2,762,748
Number of extensions: 154385
Number of successful extensions: 230
Number of sequences better than 10.0: 1
Number of HSP's gapped: 226
Number of HSP's successfully gapped: 26
Length of query: 189
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 101
Effective length of database: 4,244,745
Effective search space: 428719245
Effective search space used: 428719245
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: 54 (24.7 bits)