RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 038082
(149 letters)
>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain. This domain is found in peptide
chain release factors such as RF-1 and RF-2, and a
number of smaller proteins of unknown function. This
domain contains the peptidyl-tRNA hydrolase activity.
The domain contains a highly conserved motif GGQ, where
the glutamine is thought to coordinate the water that
mediates the hydrolysis.
Length = 114
Score = 93.8 bits (234), Expect = 1e-25
Identities = 33/59 (55%), Positives = 43/59 (72%)
Query: 18 ECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLA 76
+ +D ++SSGPGGQ+ NK ESAVRL H PTG++ + E+RSQHKNR AL RL+ L
Sbjct: 14 DLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNREKALERLKAKLY 72
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 86.9 bits (216), Expect = 4e-21
Identities = 33/72 (45%), Positives = 48/72 (66%), Gaps = 5/72 (6%)
Query: 8 LELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASA 67
+E+ +L +D Y+SSG GGQH NK +SAVR+ H PTG++ Q +RSQH+N+ASA
Sbjct: 230 IEINPKDL----RIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASA 285
Query: 68 LSRLRT-LLALK 78
+ L+ L L+
Sbjct: 286 MKMLKAKLYELE 297
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 86.7 bits (216), Expect = 5e-21
Identities = 28/62 (45%), Positives = 42/62 (67%), Gaps = 1/62 (1%)
Query: 20 EMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRT-LLALK 78
+D ++SSG GGQH N +SAVR+ H PTG++ + ++RSQHKN+A A+ LR L +
Sbjct: 224 RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAE 283
Query: 79 VR 80
+
Sbjct: 284 RQ 285
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 83.8 bits (208), Expect = 5e-20
Identities = 32/76 (42%), Positives = 48/76 (63%), Gaps = 3/76 (3%)
Query: 3 VLPNYLELTDDELFRECE--MDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQ 60
VLP +E ++ + +D ++SSG GGQH N +SAVR+ H PTG++ + ++RSQ
Sbjct: 208 VLPE-VEEVEEIEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQ 266
Query: 61 HKNRASALSRLRTLLA 76
HKN+A A+ LR L
Sbjct: 267 HKNKAKAMKVLRARLY 282
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 82.5 bits (204), Expect = 1e-19
Identities = 38/86 (44%), Positives = 56/86 (65%), Gaps = 8/86 (9%)
Query: 1 MNVLPNYLELTDDELFR----ECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAE 56
+ VLP ELTDD+ + ++D Y++ G GGQH NK ESAVR+ H PTG++ Q
Sbjct: 179 VEVLP---ELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQN 235
Query: 57 DRSQHKNRASALSRLRT-LLALKVRS 81
+RSQH N+ +A+ L++ L+ LK R+
Sbjct: 236 ERSQHSNKETAMKMLKSKLVELKERA 261
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 78.8 bits (195), Expect = 1e-18
Identities = 33/77 (42%), Positives = 46/77 (59%), Gaps = 9/77 (11%)
Query: 1 MNVLP-----NYLELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAA 55
+ V P +E+ DD+L +D Y++SG GGQH NK +SAVRL H PTG++
Sbjct: 93 VEVFPELDISIEIEIPDDDL----RIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQ 148
Query: 56 EDRSQHKNRASALSRLR 72
+RSQH N+A A L+
Sbjct: 149 NERSQHLNKALARKMLK 165
>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2. In many but not
all taxa, there is a conserved real translational
frameshift at a TGA codon. RF-2 helps terminate
translation at TGA codons and can therefore regulate its
own production by readthrough when RF-2 is insufficient.
There is a PFAM model called "RF-1" for the superfamily
of RF-1, RF-2, mitochondrial, RF-H, etc [Protein
synthesis, Translation factors].
Length = 364
Score = 79.4 bits (196), Expect = 2e-18
Identities = 30/54 (55%), Positives = 39/54 (72%)
Query: 22 DAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLL 75
D Y++SG GGQH NK +SAVR+ H PTG++ Q DRSQHKN+ SA+ L+ L
Sbjct: 240 DTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKL 293
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 79.5 bits (196), Expect = 2e-18
Identities = 32/58 (55%), Positives = 41/58 (70%)
Query: 18 ECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLL 75
+ +D Y+SSG GGQH N +SAVR+ H PTG++ Q ++RSQHKNRA A S LR L
Sbjct: 200 DVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARL 257
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 78.2 bits (193), Expect = 7e-18
Identities = 27/58 (46%), Positives = 40/58 (68%)
Query: 18 ECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLL 75
+ +D ++SSG GGQH N +SAVR+ H PTG++ + ++RSQHKN+ A+ LR L
Sbjct: 222 DLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARL 279
>gnl|CDD|213768 TIGR03072, release_prfH, putative peptide chain release factor H.
Members of this protein family are bacterial proteins
homologous to peptide chain release factors 1 (RF-1,
product of the prfA gene), and 2 (RF-2, product of the
prfB gene). The member from Escherichia coli K-12,
designated prfH, appears to be a pseudogene. This class
I release factor is always found as the downstream gene
of a two-gene operon [Protein synthesis, Translation
factors].
Length = 200
Score = 66.3 bits (162), Expect = 3e-14
Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 9 ELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASAL 68
E T+DE+ E +SSGPGGQH NK ESAVR H +G+ + +RSQH N+ L
Sbjct: 102 EATEDEIRFE----TLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANK--RL 155
Query: 69 SRLRTLLALKVRSS 82
+ L + L
Sbjct: 156 ATLLLAVRLADLQQ 169
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 66.2 bits (161), Expect = 9e-14
Identities = 27/50 (54%), Positives = 33/50 (66%)
Query: 22 DAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRL 71
D Y+SSG GGQH NK ESAVR+ H PT + RSQH+NR +A+ L
Sbjct: 181 DVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKML 230
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 63.5 bits (155), Expect = 4e-13
Identities = 24/60 (40%), Positives = 33/60 (55%)
Query: 17 RECEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQHKNRASALSRLRTLLA 76
E + +SSGPGGQH NK +SAVR H +G+ + +RSQH N+ A + L
Sbjct: 107 DEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLE 166
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 58.6 bits (141), Expect = 6e-11
Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 3 VLPNYLELTDDELFRE-CEMDAYKSSGPGGQHRNKRESAVRLKHAPTGVIAQAAEDRSQH 61
V+P + + + E+ E ++D Y++SG GGQH N +SAVR+ H PT + +RSQ
Sbjct: 182 VVPEFNDEVEIEVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQI 241
Query: 62 KNRASALSRLRTLLALK 78
KNR A+ L+ L K
Sbjct: 242 KNREHAMKMLKAKLYQK 258
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 48.6 bits (117), Expect = 4e-08
Identities = 31/93 (33%), Positives = 41/93 (44%), Gaps = 28/93 (30%)
Query: 8 LELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRL------------------KHA--- 46
L + ++EL E ++SGPGGQ+ NK +AV L A
Sbjct: 8 LVIPENEL----EWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHR 63
Query: 47 --PTGVIA-QAAEDRSQHKNRASALSRLRTLLA 76
GVI +A E RSQ +NR AL RL L+
Sbjct: 64 ITKDGVIVIKAQEFRSQERNREDALERLVALIR 96
>gnl|CDD|224781 COG1868, FliM, Flagellar motor switch protein [Cell motility and
secretion].
Length = 332
Score = 26.5 bits (59), Expect = 6.0
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 92 PQLHQILPPKSTIRSSEVGPQIGPNNPKFALVLPYSLLLP 131
PQ QI+ P + + +IG + F + +PYS+L P
Sbjct: 183 PQFAQIVSPNEIVVLITLEVEIGNLSGMFNICIPYSMLEP 222
>gnl|CDD|222863 PHA02540, 61, DNA primase; Provisional.
Length = 337
Score = 26.5 bits (59), Expect = 6.8
Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 1 MNVLPNYLELTDDELFRECEMDAYKSSGPGGQHRNKRESAVRLKHAP 47
N+L+ + +L+RE M+ +K G + + + +
Sbjct: 64 HRPFGNFLKDYEPDLYREYIMERFKE---RGTGKGRPVPKPKFEFKK 107
>gnl|CDD|111086 pfam02154, FliM, Flagellar motor switch protein FliM.
Length = 192
Score = 25.8 bits (57), Expect = 8.6
Identities = 13/52 (25%), Positives = 18/52 (34%)
Query: 82 SVNLDAYSPPPQLHQILPPKSTIRSSEVGPQIGPNNPKFALVLPYSLLLPFV 133
D PQ QI+ P + + +IG L LPY + P
Sbjct: 138 EPEYDRSEVNPQFAQIVSPNEIVVLVSLEIEIGERGGMMNLCLPYITIEPIR 189
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.315 0.132 0.375
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,385,582
Number of extensions: 638458
Number of successful extensions: 394
Number of sequences better than 10.0: 1
Number of HSP's gapped: 394
Number of HSP's successfully gapped: 22
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
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: 54 (24.6 bits)