RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 043121
(169 letters)
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 72.4 bits (178), Expect = 2e-17
Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 17 LELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHA 74
L L + EL E K GPG Q NK + V LKHVP+G++ + RS +N
Sbjct: 41 LPLNESEL----EEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRK 94
>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 = 72.3 bits (178), Expect = 8e-16
Identities = 21/49 (42%), Positives = 27/49 (55%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHAS 75
E +D + SGPG Q N +SAVR+ H+PTG+ RSQ KN
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKEL 274
>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 = 71.9 bits (177), Expect = 1e-15
Identities = 24/53 (45%), Positives = 34/53 (64%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNL 79
+ +D Y+ SG G QH N+ ESAVR+ H+PTG++ DRSQHKN ++
Sbjct: 238 DLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQ 290
>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 = 71.5 bits (176), Expect = 2e-15
Identities = 19/48 (39%), Positives = 28/48 (58%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHA 74
+ +D Y SG G Q+ NK +AVR+ H+PT + E+R+Q KN
Sbjct: 234 DLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRD 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 = 71.0 bits (175), Expect = 3e-15
Identities = 22/48 (45%), Positives = 34/48 (70%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHA 74
+ +DT++ SG G QH N +SA+R+ H+PTG++ ++RSQHKN A
Sbjct: 221 DLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKA 268
>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 = 70.7 bits (174), Expect = 3e-15
Identities = 21/48 (43%), Positives = 29/48 (60%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHA 74
E +D + SGPG Q N +SAVR+ H+PTG++ + RSQ KN
Sbjct: 216 EIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNRE 263
>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 = 70.3 bits (173), Expect = 5e-15
Identities = 20/45 (44%), Positives = 32/45 (71%)
Query: 30 MDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHA 74
++T++ SG G Q+ NK ESAVR+ H+PTG++ +RSQ++N
Sbjct: 200 IETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQ 244
>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 = 44.4 bits (105), Expect = 2e-06
Identities = 16/72 (22%), Positives = 23/72 (31%), Gaps = 24/72 (33%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLK------------------------HVPTGVIAH 62
E E+ + G G QH NK +A+ L+ ++
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIK 73
Query: 63 AAEDRSQHKNHA 74
A E RSQ N
Sbjct: 74 AQEYRSQELNRE 85
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 43.4 bits (102), Expect = 2e-06
Identities = 15/72 (20%), Positives = 25/72 (34%), Gaps = 24/72 (33%)
Query: 27 ECEMDTYKLSGPGSQHRNKRESAVRLKHVPTG------------------------VIAH 62
E E+ + G G Q+ NK SA+ L+ ++
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVLK 73
Query: 63 AAEDRSQHKNHA 74
A + R+Q +N A
Sbjct: 74 AQQYRTQEQNRA 85
>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 = 38.2 bits (88), Expect = 2e-04
Identities = 13/75 (17%), Positives = 22/75 (29%), Gaps = 25/75 (33%)
Query: 25 LRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTG-------------------------V 59
L + + SGPG Q+ NK S ++ +
Sbjct: 19 LDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGEL 78
Query: 60 IAHAAEDRSQHKNHA 74
+ + R Q +N A
Sbjct: 79 VLTSESSRYQFRNLA 93
>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 = 30.6 bits (68), Expect = 0.30
Identities = 27/222 (12%), Positives = 60/222 (27%), Gaps = 78/222 (35%)
Query: 13 KKNYLELT---DD--------ELL------RECEMDTYKLSGPGSQHRNKRESAVRLKHV 55
+K + L+ L+ + + KL + +ES + + +
Sbjct: 372 RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI 431
Query: 56 PTGVIAHAAEDRSQHK--------------NHASSVNLDAYS-----------PPPQLLQ 90
+ + + H+ + LD Y P+ +
Sbjct: 432 YLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMT 491
Query: 91 ILPP-------------KSTITSSEVGP-------------QIGPNNPKFSLGMQALLDL 124
+ + + G I N+PK+ + A+LD
Sbjct: 492 LFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDF 551
Query: 125 IFAVEGSV--SEAAKLLWLSTGALSRLILSDDSHQIAVNELR 164
+ +E ++ S+ LL R+ L + I +
Sbjct: 552 LPKIEENLICSKYTDLL--------RIALMAEDEAIFEEAHK 585
Score = 29.4 bits (65), Expect = 0.72
Identities = 18/92 (19%), Positives = 30/92 (32%), Gaps = 19/92 (20%)
Query: 15 NYLELTDDELLRE-CEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHA---------- 63
YL+ +L RE + +LS R+ + KHV +
Sbjct: 309 KYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP 368
Query: 64 AEDRSQHKNHA---SSVNLDAYSPPPQLLQIL 92
AE R + S ++ P LL ++
Sbjct: 369 AEYRKMFDRLSVFPPSAHI-----PTILLSLI 395
>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 = 29.1 bits (64), Expect = 0.51
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 8/35 (22%)
Query: 66 DRSQHKNHASSVNLDAYSP--PPQLLQILPPKSTI 98
++ K +S+ L Y+ P L I K+T+
Sbjct: 18 EKQALKKLQASLKL--YADDSAPA-LAI---KATM 46
>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor;
structural GE DNA-binding protein, PSI-2, PROT structure
initiative; 2.30A {Agrobacterium tumefaciens str}
Length = 135
Score = 27.2 bits (60), Expect = 1.7
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 109 PNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150
P + G L+ LI A GS+S A + + +S L+
Sbjct: 19 PPGERLGHGKVELMQLI-AETGSISAAGRAMDMSYRRAWLLV 59
>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 = 27.6 bits (61), Expect = 1.8
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 45 KRESAVRLKHVPTGV 59
K++ VRL+H+ T
Sbjct: 139 KQDQRVRLQHIDTSG 153
>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 = 27.2 bits (60), Expect = 2.2
Identities = 4/15 (26%), Positives = 6/15 (40%)
Query: 45 KRESAVRLKHVPTGV 59
+L+H TG
Sbjct: 127 LESEQFKLRHAVTGS 141
>1b9m_A Protein (mode); DNA-binding, gene regulation, winged helix turn
helix, molybdate, OB fold, transcription; 1.75A
{Escherichia coli} SCOP: a.4.5.8 b.40.6.2 b.40.6.2 PDB:
1b9n_A 1o7l_A 1h9s_A 1h9r_A 1h9s_B
Length = 265
Score = 26.8 bits (59), Expect = 3.2
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 110 NNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLS 142
+LL I A+ GS+S+ AK +S
Sbjct: 16 QKLFADPRRISLLKHI-ALSGSISQGAKDAGIS 47
>2esn_A Probable transcriptional regulator; PA0477, APC5828,transcription,
PSI, protein struc initiative, MCSG; 2.10A {Pseudomonas
aeruginosa} SCOP: a.4.5.37 c.94.1.1
Length = 310
Score = 26.4 bits (59), Expect = 5.3
Identities = 11/35 (31%), Positives = 13/35 (37%), Gaps = 9/35 (25%)
Query: 119 QALLDLIFAVEGSVSEAAKLLWLST----GALSRL 149
AL +V AA L +S AL RL
Sbjct: 19 DALYR-----HRNVGTAASELAISASAFSHALGRL 48
>3hhg_A Transcriptional regulator, LYSR family; transcription factor,
structur genomics, oxford protein production facility,
OPPF; 3.20A {Neisseria meningitidis serogroup B}
Length = 306
Score = 26.0 bits (58), Expect = 7.6
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 127 AVE-GSVSEAAKLLWLSTGALSRLI 150
VE GS S AA+ L ++ A+SR++
Sbjct: 14 VVESGSFSRAAEQLAMANSAVSRIV 38
>2xoa_A Ryanodine receptor 1; metal transport, calcium channel, ION
channel, membrane PROT malignant hyperthermia, cardiac
arrhythmia; 2.50A {Oryctolagus cuniculus}
Length = 559
Score = 26.0 bits (56), Expect = 8.1
Identities = 8/45 (17%), Positives = 14/45 (31%)
Query: 28 CEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKN 72
+ G G ES ++HV +G+ A +
Sbjct: 324 DTAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALR 368
>3szp_A Transcriptional regulator, LYSR family; winged helix-turn helix,
DNA-binding, transcription factor; 2.20A {Vibrio
cholerae} PDB: 3t1b_B
Length = 291
Score = 25.6 bits (57), Expect = 8.4
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 3/29 (10%)
Query: 125 IFA--VE-GSVSEAAKLLWLSTGALSRLI 150
+F VE GS + +K + ++R I
Sbjct: 8 LFRLVVENGSYTSTSKKTMIPVATITRRI 36
>1uth_A LYSR-type regulatory protein; transcription regulation,
transcriptional regulator; 2.2A {Burkholderia SP} SCOP:
c.94.1.1 PDB: 1utb_A 1utb_B 1uth_B 2uyf_A 2uye_A
Length = 315
Score = 25.6 bits (57), Expect = 8.4
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 9/35 (25%)
Query: 119 QALLDLIFAVEGSVSEAAKLLWLS----TGALSRL 149
LL + SVS A + L L+ + +L RL
Sbjct: 23 NQLLL-----DRSVSTAGEKLGLTQPAVSNSLKRL 52
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
0.310 0.126 0.355
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: 2,346,122
Number of extensions: 126726
Number of successful extensions: 206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 203
Number of HSP's successfully gapped: 24
Length of query: 169
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 82
Effective length of database: 4,272,666
Effective search space: 350358612
Effective search space used: 350358612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (24.7 bits)