RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2492
(162 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 = 87.6 bits (218), Expect = 4e-23
Identities = 36/110 (32%), Positives = 55/110 (50%), Gaps = 14/110 (12%)
Query: 52 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLV 111
+I E D++ R SGPGGQ V KT + V LTH+PTGIV+KC + RS +NR+ A E L
Sbjct: 9 EIPESDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNREKALERLK 68
Query: 112 AQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDALKKAWKEREDRRN 161
A++ + +++ + + R + KE+ N
Sbjct: 69 --------------AKLYEAELQKKREKTKPTRASQVRRGDRKEKIRTYN 104
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 70.0 bits (172), Expect = 3e-15
Identities = 36/114 (31%), Positives = 55/114 (48%), Gaps = 18/114 (15%)
Query: 38 RNLVSNIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSR 97
+ +DI I +I + D++ R SG GGQ V KT++ V LTH+PTGIV+ C R
Sbjct: 93 VEVFPELDISIEI-EIPDDDLRIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNER 151
Query: 98 SLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDALKK 151
S N+ AR++L ++ + + Q+K + ALKK
Sbjct: 152 SQHLNKALARKML-----------------KGKLYILAQEKRSQEKNRERALKK 188
>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 = 66.3 bits (162), Expect = 2e-13
Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 1/81 (1%)
Query: 51 PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELL 110
I+ D++ R SG GGQ V T++ V +TH+PTGIV++C RS +N+ A ++L
Sbjct: 216 VDINPADLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVL 275
Query: 111 VAQ-WDVQVNGEDSLNAQIRR 130
A+ ++ + + + A R+
Sbjct: 276 RARLYEAEQEKQQAAQASTRK 296
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 64.1 bits (157), Expect = 1e-12
Identities = 30/70 (42%), Positives = 45/70 (64%), Gaps = 5/70 (7%)
Query: 43 NIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSEN 102
I+I +I+ KD++ R SG GGQ V KT++ V +THIPTGIV++C RS +N
Sbjct: 227 TIEI-----EINPKDLRIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQN 281
Query: 103 RKTARELLVA 112
+ +A ++L A
Sbjct: 282 KASAMKMLKA 291
>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 = 64.0 bits (156), Expect = 1e-12
Identities = 27/61 (44%), Positives = 41/61 (67%)
Query: 53 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 112
I +D++ R SG GGQ V KT++ V +THIPTGIV++C RS +N+ +A ++L A
Sbjct: 232 IKPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKA 291
Query: 113 Q 113
+
Sbjct: 292 K 292
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 62.4 bits (153), Expect = 4e-12
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 51 PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELL 110
+I+ KD++ R SG GGQ V T++ V +TH+PTGIV++C RS +N+ A ++L
Sbjct: 216 VEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVL 275
Query: 111 VAQ-WDVQVNGEDSLNAQIRR 130
A+ +D + + A R+
Sbjct: 276 RARLYDAERQKAQAEEAATRK 296
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 62.2 bits (152), Expect = 5e-12
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 51 PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELL 110
+I+ KD++ R SG GGQ V T++ V +TH+PTGIV++C RS +N+ A ++L
Sbjct: 218 IEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVL 277
Query: 111 VAQ-WDVQVNGEDSLNAQIRR 130
A+ +D + + A R+
Sbjct: 278 RARLYDAERQKAQAEEASERK 298
>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 = 59.0 bits (143), Expect = 2e-11
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 47 YSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTA 106
+S + E +I+ +R SGPGGQ V KT + V TH+ +GI +K RS N++ A
Sbjct: 97 FSASEEATEDEIRFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLA 156
Query: 107 RELL---VAQWDVQ 117
LL +A +
Sbjct: 157 TLLLAVRLADLQQE 170
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 58.5 bits (142), Expect = 3e-11
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 55 EKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELL---V 111
+I+ +R SGPGGQ V KT++ V TH+ +GI +K RS N++ AR L+ +
Sbjct: 106 SDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKL 165
Query: 112 AQWDVQVNGE 121
Q + +
Sbjct: 166 EQQQQEQSAA 175
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 59.1 bits (143), Expect = 6e-11
Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 53 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 112
++E D++ R SG GGQ V T++ V +THIPTGIV++C Q RS +NR A +L A
Sbjct: 196 VNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRA 255
Query: 113 Q 113
+
Sbjct: 256 R 256
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 57.9 bits (140), Expect = 1e-10
Identities = 30/71 (42%), Positives = 42/71 (59%), Gaps = 7/71 (9%)
Query: 43 NIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSEN 102
+I+I S KID R G GGQ V KT + V +THIPTGIV++C RS N
Sbjct: 190 DIEIRSEDLKIDT-------YRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSN 242
Query: 103 RKTARELLVAQ 113
++TA ++L ++
Sbjct: 243 KETAMKMLKSK 253
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 57.0 bits (137), Expect = 3e-10
Identities = 29/71 (40%), Positives = 40/71 (56%), Gaps = 5/71 (7%)
Query: 43 NIDIYSTIPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSEN 102
NI+I I+ D++ R SG GGQ V KT + V +THIPT V+ C RS +N
Sbjct: 168 NIEI-----DINPADLRTDVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQN 222
Query: 103 RKTARELLVAQ 113
R A ++L A+
Sbjct: 223 RDNAMKMLAAK 233
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 49.0 bits (118), Expect = 4e-08
Identities = 37/123 (30%), Positives = 56/123 (45%), Gaps = 32/123 (26%)
Query: 53 IDEKDIQERFVRGSGPGGQAVAKTNNCVVL------THIP---------------TG--- 88
I E +++ RF+R SGPGGQ V K + V L + +P T
Sbjct: 10 IPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGV 69
Query: 89 IVIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDA 148
IVIK + RS NR+ A E LVA ++L +R + T+ K+R+L++
Sbjct: 70 IVIKAQEFRSQERNREDALERLVALI------REALKPPKKRR--ATKPTRGSKERRLES 121
Query: 149 LKK 151
K+
Sbjct: 122 KKQ 124
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 46.3 bits (109), Expect = 1e-06
Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 5/89 (5%)
Query: 52 KIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLV 111
++ +D++ R SG GGQ V T++ V +TH PT V+ C RS +NR+ A ++L
Sbjct: 193 EVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLK 252
Query: 112 AQWDVQVNGEDSLNAQIRRIDEKRRATQE 140
A+ + L Q +DE R +E
Sbjct: 253 AKL-----YQKKLEEQQAELDEIRGEQKE 276
>gnl|CDD|226844 COG4420, COG4420, Predicted membrane protein [Function unknown].
Length = 191
Score = 32.8 bits (75), Expect = 0.047
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 99 LSENRKTARELLVAQWDVQVN--GEDSLNAQIRRIDEKRRATQEQKKRKLDALKKAWKER 156
+S+NR+ R+ L A+ D QVN E + A ++DE R + LD L++ E
Sbjct: 109 MSQNRQAERDRLRAELDYQVNLKAEQEVAALHEKLDELRLDLGYVRDE-LDDLRELLAEI 167
Query: 157 ED 158
E
Sbjct: 168 EP 169
>gnl|CDD|173789 cd04059, Peptidases_S8_Protein_convertases_Kexins_Furin-like,
Peptidase S8 family domain in Protein convertases.
Protein convertases, whose members include furins and
kexins, are members of the peptidase S8 or Subtilase
clan of proteases. They have an Asp/His/Ser catalytic
triad that is not homologous to trypsin. Kexins are
involved in the activation of peptide hormones, growth
factors, and viral proteins. Furin cleaves cell surface
vasoactive peptides and proteins involved in
cardiovascular tissue remodeling in the TGN, at cell
surface, or in endosomes but rarely in the ER. Furin
also plays a key role in blood pressure regulation
though the activation of transforming growth factor
(TGF)-beta. High specificity is seen for cleavage after
dibasic (Lys-Arg or Arg-Arg) or multiple basic residues
in protein convertases. There is also strong sequence
conservation.
Length = 297
Score = 32.5 bits (75), Expect = 0.064
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 14 NLAGIRLLESQVTITRELRNDGYHRNLVSNIDIYS 48
L GIR+L+ VT E + G + + IDIYS
Sbjct: 112 KLGGIRMLDGDVTDVVEAESLGLNPDY---IDIYS 143
>gnl|CDD|143452 cd07134, ALDH_AlkH-like, Pseudomonas putida Aldehyde dehydrogenase
AlkH-like. Aldehyde dehydrogenase AlkH (locus name
P12693, EC=1.2.1.3) of the alkBFGHJKL operon that allows
Pseudomonas putida to metabolize alkanes and the
aldehyde dehydrogenase AldX of Bacillus subtilis (locus
P46329, EC=1.2.1.3), and similar sequences, are present
in this CD.
Length = 433
Score = 31.4 bits (72), Expect = 0.19
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 125 NAQIRRIDEKRRATQEQKKRKLDALKKAWKEREDR 159
AQ R +T ++ KL LKKA R +
Sbjct: 5 AAQQAHALALRASTAAERIAKLKRLKKAILARREE 39
>gnl|CDD|187774 cd09643, Csn1, CRISPR/Cas system-associated protein Cas9. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; Very large protein
containing McrA/HNH-nuclease related domain and a
RuvC-like nuclease domain; signature gene for type II.
Length = 799
Score = 30.1 bits (68), Expect = 0.57
Identities = 24/139 (17%), Positives = 45/139 (32%), Gaps = 15/139 (10%)
Query: 15 LAGIRLLESQVTITRELRNDGY-HRNLVSNIDIYSTIPKIDEKDIQERFVRGSGPGGQAV 73
L GIR L Q E + + N N D +P I + +++ V
Sbjct: 439 LRGIRPLMEQGKRYDEAILELGGNHNQKINSDELKFLPIIKKAQVKDEI------LNPVV 492
Query: 74 AKT--------NNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLN 125
+ N V P IVI+ + ++ K ++ D +L
Sbjct: 493 KRALLQARKVVNELVKKYGPPDKIVIEMARENGTNKGTKNRKKRQKKNEDNIKEAASALE 552
Query: 126 AQIRRIDEKRRATQEQKKR 144
+++ + ++ K R
Sbjct: 553 QKLKELPLDIKSKNILKLR 571
>gnl|CDD|220248 pfam09455, Cas_DxTHG, CRISPR-associated (Cas) DxTHG family. CRISPR
is a term for Clustered Regularly Interspaced Short
Palidromic Repeats. A number of protein families appear
only in association with these repeats and are
designated Cas (CRISPR associated) proteins. The family
describes Cas proteins of about 400 residues that
include the motif [VIL]-D-x-[ST]-H-[GS]. The CRISPR and
associated proteins are thought to be involved in the
evolution of host resistance. The exact molecular
function of this family is currently unknown.
Length = 370
Score = 28.2 bits (63), Expect = 2.0
Identities = 12/56 (21%), Positives = 23/56 (41%)
Query: 106 ARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDALKKAWKEREDRRN 161
ARE L++ ++ ++ + + R E+ E + + L W D RN
Sbjct: 307 AREWLISVLCLRYGLDNIKDRKEREKAEEALKLLELRLKNEKELADKWSCLSDERN 362
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 28.1 bits (63), Expect = 2.5
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 127 QIRRIDEKRRATQEQKKRKLDALKKAWKEREDRR 160
Q RR DEKR+A QE K ++ E+E+R
Sbjct: 680 QRRRNDEKRQAQQEAKALNVEEQSVQETEQEERV 713
>gnl|CDD|219581 pfam07795, DUF1635, Protein of unknown function (DUF1635). The
members of this family include sequences that are parts
of hypothetical proteins expressed by plant species. The
region in question is about 170 amino acids long.
Length = 214
Score = 26.8 bits (59), Expect = 4.6
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 133 EKRRATQEQKKRKLDALKKAWKEREDRR 160
E+ R EQ + LD LKK KER++
Sbjct: 26 EELRKHDEQVIQLLDLLKKTIKERDEAL 53
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 27.3 bits (61), Expect = 4.7
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 113 QWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDALKKAWKER 156
QWD QV D L R +D+K + E K L LK A K +
Sbjct: 957 QWD-QV--PDHLKITFRVVDDKNKKLAEGK--DLQELKDALKGK 995
>gnl|CDD|218207 pfam04676, CwfJ_C_2, Protein similar to CwfJ C-terminus 2. This
region is found in the N terminus of Schizosaccharomyces
pombe protein CwfJ. CwfJ is part of the Cdc5p complex
involved in mRNA splicing.
Length = 97
Score = 26.1 bits (58), Expect = 4.9
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 124 LNAQIRRIDEKRRATQEQKKRKLDALKKAWKE 155
LN R K + ++E+++ ++A KKA+K
Sbjct: 62 LNLPKRVDWRKCKQSKEEERADVEAFKKAFKP 93
>gnl|CDD|220464 pfam09903, DUF2130, Uncharacterized protein conserved in bacteria
(DUF2130). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 267
Score = 26.5 bits (59), Expect = 6.7
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 7/70 (10%)
Query: 90 VIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDAL 149
IK + + EN K + N E I + Q+ +++ A+
Sbjct: 169 AIKSLEYKQEQENVKDKNIDIY-------NFEKEFRQFKEAIVKNFELAQKDLDKEIKAI 221
Query: 150 KKAWKEREDR 159
KAWK+ E +
Sbjct: 222 DKAWKKLEKQ 231
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 26.6 bits (59), Expect = 7.9
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 99 LSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDALKKAWKER 156
L ++ + R +A+W V E L+ Q+ ++ A + Q K +L LKK +
Sbjct: 708 LKDDFRELRTERLAKWQVV---EGELDNQLAQLSAAIEAARTQAKARLKELKKQYDRE 762
>gnl|CDD|221466 pfam12220, U1snRNP70_N, U1 small nuclear ribonucleoprotein of 70kDa
MW N terminal. This domain is found in eukaryotes. This
domain is about 90 amino acids in length. This domain is
found associated with pfam00076. This domain is part of
U1 snRNP, which is the pre-mRNA binding protein of the
penta-snRNP spliceosome complex. It extends over a
distance of 180 A from its RNA binding domain, wraps
around the core domain of U1 snRNP consisting of the
seven Sm proteins and finally contacts U1-C, which is
crucial for 5'-splice-site recognition.
Length = 94
Score = 25.3 bits (56), Expect = 9.2
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 130 RIDEKRRATQEQKKRKLDALKKAWKERED 158
+ + ++R +E+ ++KL+ K W ED
Sbjct: 65 KREREKREKKEKLEKKLEEELKEWDPNED 93
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
0.318 0.133 0.381
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,194,473
Number of extensions: 734891
Number of successful extensions: 1206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1176
Number of HSP's successfully gapped: 85
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
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 (21.7 bits)
S2: 55 (24.9 bits)