RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029341
(195 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 = 89.2 bits (222), Expect = 3e-23
Identities = 32/59 (54%), Positives = 43/59 (72%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLLA 128
+ +D ++S GPGGQ+ 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 = 85.3 bits (212), Expect = 8e-20
Identities = 32/72 (44%), Positives = 48/72 (66%), Gaps = 5/72 (6%)
Query: 60 LELTDDELFRECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASA 119
+E+ +L +D Y+S G GGQH NK +SAVR+ H+PTG++ Q +RSQH+N+ASA
Sbjct: 230 IEINPKDL----RIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASA 285
Query: 120 LSRLRT-LLALK 130
+ L+ L L+
Sbjct: 286 MKMLKAKLYELE 297
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 84.4 bits (210), Expect = 1e-19
Identities = 27/62 (43%), Positives = 42/62 (67%), Gaps = 1/62 (1%)
Query: 72 EMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRT-LLALK 130
+D ++S G GGQH N +SAVR+ H+PTG++ + ++RSQHKN+A A+ LR L +
Sbjct: 224 RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAE 283
Query: 131 VR 132
+
Sbjct: 284 RQ 285
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 81.5 bits (202), Expect = 2e-18
Identities = 27/57 (47%), Positives = 40/57 (70%)
Query: 72 EMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLLA 128
+D ++S G GGQH N +SAVR+ H+PTG++ + ++RSQHKN+A A+ LR L
Sbjct: 226 RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLY 282
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 79.1 bits (195), Expect = 9e-18
Identities = 35/78 (44%), Positives = 53/78 (67%), Gaps = 5/78 (6%)
Query: 61 ELTDDELFR----ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNR 116
ELTDD+ + ++D Y++ G GGQH NK ESAVR+ H+PTG++ Q +RSQH N+
Sbjct: 184 ELTDDQDIEIRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNK 243
Query: 117 ASALSRLRT-LLALKVRS 133
+A+ L++ L+ LK R+
Sbjct: 244 ETAMKMLKSKLVELKERA 261
>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 = 79.0 bits (195), Expect = 1e-17
Identities = 29/54 (53%), Positives = 39/54 (72%)
Query: 74 DAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLL 127
D Y++ G 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 = 78.0 bits (192), Expect = 2e-17
Identities = 31/58 (53%), Positives = 41/58 (70%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLL 127
+ +D Y+S G GGQH N +SAVR+ H+PTG++ Q ++RSQHKNRA A S LR L
Sbjct: 200 DVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARL 257
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 75.3 bits (186), Expect = 6e-17
Identities = 30/65 (46%), Positives = 43/65 (66%), Gaps = 4/65 (6%)
Query: 60 LELTDDELFRECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASA 119
+E+ DD+L +D Y++ G GGQH NK +SAVRL H+PTG++ +RSQH N+A A
Sbjct: 105 IEIPDDDL----RIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALA 160
Query: 120 LSRLR 124
L+
Sbjct: 161 RKMLK 165
>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 = 77.0 bits (190), Expect = 7e-17
Identities = 26/58 (44%), Positives = 40/58 (68%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLL 127
+ +D ++S G 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 = 64.4 bits (157), Expect = 5e-13
Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 61 ELTDDELFRECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASAL 120
E T+DE+ E +S GPGGQH NK ESAVR H+ +G+ + +RSQH N+ L
Sbjct: 102 EATEDEIRFE----TLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANK--RL 155
Query: 121 SRLRTLLALKVRSS 134
+ L + L
Sbjct: 156 ATLLLAVRLADLQQ 169
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 65.1 bits (158), Expect = 7e-13
Identities = 26/50 (52%), Positives = 33/50 (66%)
Query: 74 DAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRL 123
D Y+S G 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 = 62.0 bits (151), Expect = 3e-12
Identities = 23/60 (38%), Positives = 33/60 (55%)
Query: 69 RECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLLA 128
E + +S GPGGQH 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 = 55.9 bits (134), Expect = 1e-09
Identities = 25/61 (40%), Positives = 36/61 (59%)
Query: 70 ECEMDAYKSPGPGGQHRNKRESAVRLKHVPTGVIAQAAEDRSQHKNRASALSRLRTLLAL 129
+ ++D Y++ G GGQH N +SAVR+ H PT + +RSQ KNR A+ L+ L
Sbjct: 198 DLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLKAKLYQ 257
Query: 130 K 130
K
Sbjct: 258 K 258
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 44.4 bits (106), Expect = 3e-06
Identities = 30/93 (32%), Positives = 42/93 (45%), Gaps = 28/93 (30%)
Query: 60 LELTDDELFRECEMDAYKSPGPGGQHRNKRESAVRLK------HVPT------------- 100
L + ++EL E ++ GPGGQ+ NK +AV L+ +P
Sbjct: 8 LVIPENEL----EWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHR 63
Query: 101 ----GVIA-QAAEDRSQHKNRASALSRLRTLLA 128
GVI +A E RSQ +NR AL RL L+
Sbjct: 64 ITKDGVIVIKAQEFRSQERNREDALERLVALIR 96
>gnl|CDD|240596 cd12935, LEM_like, LEM-like domain of lamina-associated
polypeptide 2 (LAP2) and similar proteins. LAP2, also
termed thymopoietin (TP), or thymopoietin-related
peptide (TPRP), is composed of isoform alpha and
isoforms beta/gamma and may be involved in chromatin
organization and postmitotic reassembly. Some of the
LAP2 isoforms are inner nuclear membrane proteins that
can bind to nuclear lamins and chromatin, while others
are nonmembrane nuclear polypeptides. All LAP2 isoforms
contain an N-terminal lamina-associated
polypeptide-Emerin-MAN1 (LEM)-domain that is connected
to a highly divergent LEM-like domain by an
unstructured linker. Both LEM and LEM-like domains
share the same structural fold, mainly composed of two
large parallel alpha helices. However, their
biochemical nature of the solvent-accessible residues
is completely different, which indicates the two
domains may target different protein surfaces. The LEM
domain is responsible for the interaction with the
nonspecific DNA binding protein
barrier-to-autointegration factor (BAF), and the
LEM-like domain is involved in chromosome binding. The
family also includes the yeast helix-extension-helix
domain-containing proteins, Heh1p (formerly called
Src1p) and Heh2p, and their uncharacterized homologs
found mainly in fungi and several in bacteria. Heh1p
and Heh2p are inner nuclear membrane proteins that
might interact with nuclear pore complexes (NPCs).
Heh1p is involved in mitosis. It functions at the
interface between subtelomeric gene expression and
transcription export (TREX)-dependent messenger RNA
export through NPCs. The function of Heh2p remains
ill-defined. Both Heh1p and Heh2p contain a LEM-like
domain (also termed HeH domain), but lack a LEM domain.
Length = 36
Score = 25.4 bits (57), Expect = 2.7
Identities = 7/30 (23%), Positives = 12/30 (40%), Gaps = 4/30 (13%)
Query: 9 LRIPQLRR----KNINFPSYKHRGNYQPLF 34
L + +LR + +PS + LF
Sbjct: 4 LTVAELRSILTEHGVEYPSNAKKAELVKLF 33
>gnl|CDD|216221 pfam00971, EIAV_GP90, EIAV coat protein, gp90. Equine infectious
anaemia (EIAV). EIAV belongs to the family Retroviridae.
EIAV gp90 is hypervariable in the carboxyl-end region
and more stable in the amino-end region. This
variability is a pathogenicity factor that allows the
evasion of the host's immune response.
Length = 385
Score = 27.7 bits (61), Expect = 4.6
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 13 QLRRKNINFPSYKHRGNYQ-PLFLSCNYSTNDNCSSSS 49
+ R IN Y G YQ P+F +CN++ +C++ S
Sbjct: 266 NVNRLEINRKDYT--GIYQVPIFYTCNFTNITSCNNES 301
>gnl|CDD|214346 CHL00045, ccsA, cytochrome c biogenesis protein.
Length = 319
Score = 27.1 bits (61), Expect = 7.0
Identities = 12/45 (26%), Positives = 20/45 (44%)
Query: 15 RRKNINFPSYKHRGNYQPLFLSCNYSTNDNCSSSSSSSSSSSRNY 59
RKNI+ K+ + S N+ + ++S SS+NY
Sbjct: 166 FRKNIDIFGKKNNLLNKSFSFSEIQYLNEKNNVLKNTSFFSSKNY 210
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
0.314 0.128 0.361
Gapped
Lambda K H
0.267 0.0592 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,497,106
Number of extensions: 828892
Number of successful extensions: 677
Number of sequences better than 10.0: 1
Number of HSP's gapped: 664
Number of HSP's successfully gapped: 29
Length of query: 195
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 103
Effective length of database: 6,857,034
Effective search space: 706274502
Effective search space used: 706274502
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: 56 (25.7 bits)