RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 029341
(195 letters)
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 85.5 bits (212), Expect = 5e-22
Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 60 LELTDDELFRECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASA 119
L L + EL E K GPGGQ NK + V LKHVP+G++ + + RS +NR A
Sbjct: 41 LPLNESEL----EEQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIA 96
Query: 120 LSRLRTLL 127
L+ +
Sbjct: 97 RKVLQEKV 104
>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 = 87.3 bits (217), Expect = 9e-21
Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRT-LLA 128
E +D ++ GPGGQ N +SAVR+ H+PTG+ RSQ KN+ AL L+ L
Sbjct: 226 ELRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYE 285
Query: 129 LKVR 132
L+ +
Sbjct: 286 LERK 289
>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 = 85.8 bits (213), Expect = 3e-20
Identities = 27/58 (46%), Positives = 41/58 (70%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLL 127
+ +D Y++ G GGQH N+ ESAVR+ H+PTG++ Q DRSQHKN+ A+ +++ L
Sbjct: 238 DLRIDVYRASGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKL 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 = 85.7 bits (213), Expect = 3e-20
Identities = 22/58 (37%), Positives = 36/58 (62%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLL 127
+ +D Y + G GGQ+ NK +AVR+ H+PT + + E+R+Q KNR A+ +R +
Sbjct: 234 DLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIRARV 291
>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 = 84.9 bits (211), Expect = 5e-20
Identities = 27/58 (46%), Positives = 37/58 (63%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLL 127
E +D ++ GPGGQ N +SAVR+ H+PTG++ + RSQ KNR AL LR+ L
Sbjct: 216 EIRIDVMRASGPGGQGVNTTDSAVRVVHLPTGIMVTCQDSRSQIKNREKALMILRSRL 273
>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 = 84.9 bits (211), Expect = 6e-20
Identities = 26/58 (44%), Positives = 41/58 (70%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLL 127
+ +D ++S G GGQH N +SA+R+ H+PTG++ + ++RSQHKN+A ALS L +
Sbjct: 221 DLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARI 278
>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 = 83.8 bits (208), Expect = 1e-19
Identities = 24/55 (43%), Positives = 39/55 (70%)
Query: 73 MDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLL 127
++ +++ G GGQ+ NK ESAVR+ H+PTG++ +RSQ++N+ +AL LR L
Sbjct: 200 IETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARL 254
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 61.5 bits (149), Expect = 6e-13
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 24/83 (28%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTG------------------------VIAQ 105
E E+ A ++ G GGQ+ NK SA+ L+ ++ +
Sbjct: 14 EIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITSDGVIVLK 73
Query: 106 AAEDRSQHKNRASALSRLRTLLA 128
A + R+Q +NRA AL RL L+
Sbjct: 74 AQQYRTQEQNRADALLRLSELIV 96
>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 = 61.7 bits (150), Expect = 1e-12
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 24/83 (28%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLK------------------------HVPTGVIAQ 105
E E+ A ++ G GGQH NK +A+ L+ ++ +
Sbjct: 14 ELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIK 73
Query: 106 AAEDRSQHKNRASALSRLRTLLA 128
A E RSQ NR +AL+RL ++
Sbjct: 74 AQEYRSQELNREAALARLVAMIK 96
>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 = 54.0 bits (129), Expect = 4e-10
Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 25/84 (29%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTG-------------------------VIA 104
+ +S GPGGQ+ NK S ++ ++
Sbjct: 21 RLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALTHKNKINKAGELVL 80
Query: 105 QAAEDRSQHKNRASALSRLRTLLA 128
+ R Q +N A L ++R ++A
Sbjct: 81 TSESSRYQFRNLAECLQKIRDMIA 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 = 36.4 bits (83), Expect = 0.004
Identities = 22/143 (15%), Positives = 42/143 (29%), Gaps = 41/143 (28%)
Query: 33 LFLSCNYSTNDNCSSSSSSSSSSSRNYLELTDDE---LFREC-EMDAYKSPGPGGQHRNK 88
L + D S+++++ S + + LT DE L + + P
Sbjct: 269 LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP--------- 319
Query: 89 RESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRS--SVNLDAYSP---- 142
RE L P ++ AE + + K+ + +L+ P
Sbjct: 320 REV---LTTNPR-RLSIIAESIRDGLAT---WDNWKHVNCDKLTTIIESSLNVLEPAEYR 372
Query: 143 ---------------PPKLLQIL 150
P LL ++
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLI 395
Score = 28.3 bits (62), Expect = 1.9
Identities = 33/237 (13%), Positives = 62/237 (26%), Gaps = 66/237 (27%)
Query: 2 ALAAQFLLRIPQLRRKNI------------NFPSYKHRGNYQPLF------------LS- 36
L + N ++R + L LS
Sbjct: 335 ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL 394
Query: 37 --CNYSTND------NCSSSSSSSSSSSRNYLELTD--DELFRECEMDAYKSPGPGGQHR 86
+ +D S + + + EL + E + HR
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL-------HR 447
Query: 87 NKRESAVRLKHVPTGVIAQAAEDR------SQH---KNRASALSRLRTL------LALKV 131
+ + K + + D+ H ++ R + L K+
Sbjct: 448 SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKI 507
Query: 132 R-SSVNLDAYSPPPKLLQILPPKSTIRSSEVGAQIGPNNPKFALGMQALLDLIFAVE 187
R S +A LQ L + + I N+PK+ + A+LD + +E
Sbjct: 508 RHDSTAWNASGSILNTLQQL------KFYK--PYICDNDPKYERLVNAILDFLPKIE 556
>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 = 32.7 bits (74), Expect = 0.066
Identities = 24/121 (19%), Positives = 43/121 (35%), Gaps = 24/121 (19%)
Query: 83 GQHRNKRESA-VRLKHVPTGV-IAQAAEDRSQHKNRASALSRLRTLLALKVRSSVNLDAY 140
G+ R+ + A + + T V IA+ S + A + L + VR +AY
Sbjct: 261 GELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKA---ITVLFFIGVRC---YEAY 314
Query: 141 ---SPPPKLLQILPPKSTIRSSEVGAQIGPNNPKFA---LGMQALLDLIFAVEGSVSEAA 194
S PP +L+ S E G +P + L + + D + +
Sbjct: 315 PNTSLPPSILED--------SLENN--EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGK 364
Query: 195 K 195
+
Sbjct: 365 Q 365
>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 = 30.7 bits (68), Expect = 0.19
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 8/29 (27%)
Query: 130 KVRSSVNLDAYSP--PPKLLQILPPKSTI 156
K+++S+ L Y+ P L I K+T+
Sbjct: 24 KLQASLKL--YADDSAPA-LAI---KATM 46
>2giy_A Glycoprotein E; viral FC receptor, IG V domain, viral protein;
1.78A {Human herpesvirus 1} SCOP: b.1.1.1
Length = 191
Score = 30.1 bits (67), Expect = 0.35
Identities = 13/53 (24%), Positives = 23/53 (43%)
Query: 30 YQPLFLSCNYSTNDNCSSSSSSSSSSSRNYLELTDDELFRECEMDAYKSPGPG 82
Y P C + C++S+ +S + R+Y + C +A+ P PG
Sbjct: 71 YHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPG 123
>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 = 29.1 bits (65), Expect = 0.75
Identities = 7/21 (33%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 82 GGQHRNKRESAVRLKHVPTGV 102
G+ K++ VRL+H+ T
Sbjct: 134 SGKTW-KQDQRVRLQHIDTSG 153
>2gj7_F Glycoprotein E; FC receptor, low resolution, immune
system-virus-viral prote complex; HET: NAG BMA MAN GAL
FUC; 5.00A {Human herpesvirus 1} SCOP: b.1.1.1
Length = 401
Score = 29.3 bits (64), Expect = 0.93
Identities = 13/53 (24%), Positives = 23/53 (43%)
Query: 30 YQPLFLSCNYSTNDNCSSSSSSSSSSSRNYLELTDDELFRECEMDAYKSPGPG 82
Y P C + C++S+ +S + R+Y + C +A+ P PG
Sbjct: 262 YHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPG 314
>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 = 28.8 bits (64), Expect = 0.99
Identities = 4/15 (26%), Positives = 6/15 (40%)
Query: 88 KRESAVRLKHVPTGV 102
+L+H TG
Sbjct: 127 LESEQFKLRHAVTGS 141
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 27.8 bits (61), Expect = 1.9
Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 9/61 (14%)
Query: 127 LALKVRSSVNLDAYSPPPKLLQILPPKSTIRSSEVGAQIGPNNPKFALGMQALLDLIFAV 186
+A++V S + S +PP I S + KF L+ A
Sbjct: 118 MAIQVNYSSEVKENSVDSDDKAKVPPLIRIVSGLELSDTKQKGKKF---------LVIAY 168
Query: 187 E 187
E
Sbjct: 169 E 169
>3p01_A Two-component response regulator; PSI-2, midwest center for
structural genomics, protein struc initiative, MCSG,
signali protein; 2.65A {Nostoc SP}
Length = 184
Score = 27.2 bits (61), Expect = 2.4
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 102 VIAQAAEDRSQHKNRASALSR----LRTL--LALKVRSSVNLDA 139
V+ +AAE K R L R + L L ++S +L+A
Sbjct: 4 VVQRAAETYDLLKQRTEELRRANAQMSLLTVLVQVTQASNSLEA 47
>1uil_A Double-stranded RNA-binding motif; structural genomics, DSRM, riken
structural genomics/proteomics initiative, RSGI RNA
binding protein; NMR {Mus musculus} SCOP: d.50.1.1 PDB:
2rs7_A
Length = 113
Score = 25.8 bits (56), Expect = 6.0
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 5/70 (7%)
Query: 76 YKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLLALKVRSSV 135
Y GP E + +K + + A+ + ++ ALS +R L L V
Sbjct: 47 YTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYHLGV---- 102
Query: 136 NLDAYSPPPK 145
++AYS P
Sbjct: 103 -IEAYSSGPS 111
>2xoa_A Ryanodine receptor 1; metal transport, calcium channel, ION
channel, membrane PROT malignant hyperthermia, cardiac
arrhythmia; 2.50A {Oryctolagus cuniculus}
Length = 559
Score = 26.8 bits (58), Expect = 6.3
Identities = 9/70 (12%), Positives = 24/70 (34%), Gaps = 3/70 (4%)
Query: 33 LFLSCNYSTNDNCSSSSSSSSSSSRNYLELTDDELFRECEMDAYKSPGPGGQHRNKRESA 92
+L+ + + + ++ ++ ++L G G ES
Sbjct: 289 RYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKL---DTAPKRDVEGMGPPEIKYGESL 345
Query: 93 VRLKHVPTGV 102
++HV +G+
Sbjct: 346 CFVQHVASGL 355
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
0.314 0.128 0.361
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: 2,757,406
Number of extensions: 147076
Number of successful extensions: 224
Number of sequences better than 10.0: 1
Number of HSP's gapped: 221
Number of HSP's successfully gapped: 23
Length of query: 195
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 106
Effective length of database: 4,216,824
Effective search space: 446983344
Effective search space used: 446983344
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: 42 (22.0 bits)
S2: 55 (25.1 bits)