RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4479
(135 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 = 88.4 bits (220), Expect = 8e-24
Identities = 37/113 (32%), Positives = 56/113 (49%), Gaps = 14/113 (12%)
Query: 19 DLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENR 78
LD +I E D++ R SGPGGQ V KT + V LTH+PTGIV+KC + RS +NR
Sbjct: 1 PLDEEVEIEIPESDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNR 60
Query: 79 KTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDALKKAWKER 131
+ A E L A++ + +++ + + R + KE+
Sbjct: 61 EKALERLK--------------AKLYEAELQKKREKTKPTRASQVRRGDRKEK 99
>gnl|CDD|224107 COG1186, PrfB, Protein chain release factor B [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 71.5 bits (176), Expect = 4e-16
Identities = 43/125 (34%), Positives = 61/125 (48%), Gaps = 18/125 (14%)
Query: 2 SIFRRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIP 61
S RRH S AS +LD S +I + D++ R SG GGQ V KT++ V LTH+P
Sbjct: 82 SNGRRHTSFASV-EVFPELDISIEIEIPDDDLRIDTYRASGAGGQHVNKTDSAVRLTHLP 140
Query: 62 TGIVIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKL 121
TGIV+ C RS N+ AR++L ++ + + Q+K +
Sbjct: 141 TGIVVLCQNERSQHLNKALARKML-----------------KGKLYILAQEKRSQEKNRE 183
Query: 122 DALKK 126
ALKK
Sbjct: 184 RALKK 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 = 65.9 bits (161), Expect = 1e-13
Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 1/81 (1%)
Query: 26 PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELL 85
I+ D++ R SG GGQ V T++ V +TH+PTGIV++C RS +N+ A ++L
Sbjct: 216 VDINPADLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVL 275
Query: 86 VAQ-WDVQVNGEDSLNAQIRR 105
A+ ++ + + + A R+
Sbjct: 276 RARLYEAEQEKQQAAQASTRK 296
>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 = 65.6 bits (160), Expect = 1e-13
Identities = 35/84 (41%), Positives = 53/84 (63%), Gaps = 1/84 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGI 64
RRH S AS +F ++D +I +D++ R SG GGQ V KT++ V +THIPTGI
Sbjct: 210 RRHTSFAS-VFVMPEVDDDIDIEIKPEDLRIDTYRASGAGGQHVNKTDSAVRITHIPTGI 268
Query: 65 VIKCHQSRSLSENRKTARELLVAQ 88
V++C RS +N+ +A ++L A+
Sbjct: 269 VVQCQNDRSQHKNKDSAMKVLKAK 292
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 64.5 bits (158), Expect = 3e-13
Identities = 35/83 (42%), Positives = 53/83 (63%), Gaps = 1/83 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGI 64
RRH S AS + ++D + +I+ KD++ R SG GGQ V KT++ V +THIPTGI
Sbjct: 210 RRHTSFAS-VEVYPEVDDTIEIEINPKDLRIDTYRSSGAGGQHVNKTDSAVRITHIPTGI 268
Query: 65 VIKCHQSRSLSENRKTARELLVA 87
V++C RS +N+ +A ++L A
Sbjct: 269 VVQCQNERSQHQNKASAMKMLKA 291
>gnl|CDD|234801 PRK00591, prfA, peptide chain release factor 1; Validated.
Length = 359
Score = 62.4 bits (153), Expect = 2e-12
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 26 PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELL 85
+I+ KD++ R SG GGQ V T++ V +TH+PTGIV++C RS +N+ A ++L
Sbjct: 216 VEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVL 275
Query: 86 VAQ-WDVQVNGEDSLNAQIRR 105
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 = 2e-12
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 26 PKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELL 85
+I+ KD++ R SG GGQ V T++ V +TH+PTGIV++C RS +N+ A ++L
Sbjct: 218 IEINPKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVL 277
Query: 86 VAQ-WDVQVNGEDSLNAQIRR 105
A+ +D + + A R+
Sbjct: 278 RARLYDAERQKAQAEEASERK 298
>gnl|CDD|235997 PRK07342, PRK07342, peptide chain release factor 2; Provisional.
Length = 339
Score = 61.8 bits (150), Expect = 3e-12
Identities = 36/84 (42%), Positives = 49/84 (58%), Gaps = 1/84 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGI 64
RRH S AS D +V ++E D++ R SG GGQ V T++ V +THIPTGI
Sbjct: 174 RRHTSFASIWVYPVIDDNIEV-DVNESDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGI 232
Query: 65 VIKCHQSRSLSENRKTARELLVAQ 88
V++C Q RS +NR A +L A+
Sbjct: 233 VVQCQQERSQHKNRAKAWSMLRAR 256
>gnl|CDD|136970 PRK08787, PRK08787, peptide chain release factor 2; Provisional.
Length = 313
Score = 60.4 bits (146), Expect = 8e-12
Identities = 33/84 (39%), Positives = 48/84 (57%), Gaps = 1/84 (1%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGI 64
RRH S +S+F ++D + I+ D++ R SG GGQ V KT + V +THIPT
Sbjct: 151 RRHTSF-TSVFVSPEVDDNIEIDINPADLRTDVYRSSGAGGQHVNKTESAVRITHIPTNT 209
Query: 65 VIKCHQSRSLSENRKTARELLVAQ 88
V+ C RS +NR A ++L A+
Sbjct: 210 VVACQTGRSQHQNRDNAMKMLAAK 233
>gnl|CDD|181271 PRK08179, prfH, peptide chain release factor-like protein;
Reviewed.
Length = 200
Score = 58.9 bits (143), Expect = 1e-11
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 22 YSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTA 81
+S + +I+ +R SGPGGQ V KT++ V TH+ +GI +K RS N++ A
Sbjct: 98 FSADEEEQSDEIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLA 157
Query: 82 RELL---VAQWDVQVNGE 96
R L+ + Q + +
Sbjct: 158 RLLIAWKLEQQQQEQSAA 175
>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 = 57.5 bits (139), Expect = 4e-11
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 22 YSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTA 81
+S + E +I+ +R SGPGGQ V KT + V TH+ +GI +K RS N++ A
Sbjct: 97 FSASEEATEDEIRFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLA 156
Query: 82 RELL---VAQWDVQ 92
LL +A +
Sbjct: 157 TLLLAVRLADLQQE 170
>gnl|CDD|235520 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
Length = 325
Score = 57.9 bits (140), Expect = 6e-11
Identities = 26/61 (42%), Positives = 39/61 (63%)
Query: 28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGIVIKCHQSRSLSENRKTARELLVA 87
I +D++ R G GGQ V KT + V +THIPTGIV++C RS N++TA ++L +
Sbjct: 193 IRSEDLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNKETAMKMLKS 252
Query: 88 Q 88
+
Sbjct: 253 K 253
>gnl|CDD|181730 PRK09256, PRK09256, hypothetical protein; Provisional.
Length = 138
Score = 49.0 bits (118), Expect = 2e-08
Identities = 37/123 (30%), Positives = 56/123 (45%), Gaps = 32/123 (26%)
Query: 28 IDEKDIQERFVRGSGPGGQAVAKTNNCVVL------THIP---------------TG--- 63
I E +++ RF+R SGPGGQ V K + V L + +P T
Sbjct: 10 IPENELEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGV 69
Query: 64 IVIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDA 123
IVIK + RS NR+ A E LVA ++L +R + T+ K+R+L++
Sbjct: 70 IVIKAQEFRSQERNREDALERLVALI------REALKPPKKRR--ATKPTRGSKERRLES 121
Query: 124 LKK 126
K+
Sbjct: 122 KKQ 124
>gnl|CDD|75726 PRK06746, PRK06746, peptide chain release factor 2; Provisional.
Length = 326
Score = 46.7 bits (110), Expect = 6e-07
Identities = 35/111 (31%), Positives = 54/111 (48%), Gaps = 6/111 (5%)
Query: 5 RRHLSLASSLFRKYDLDYSKVPKIDEKDIQERFVRGSGPGGQAVAKTNNCVVLTHIPTGI 64
RRH S S D ++ ++ +D++ R SG GGQ V T++ V +TH PT
Sbjct: 172 RRHTSFVSCEVVPEFNDEVEI-EVRTEDLKIDTYRASGAGGQHVNTTDSAVRITHTPTNT 230
Query: 65 VIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQE 115
V+ C RS +NR+ A ++L A+ + L Q +DE R +E
Sbjct: 231 VVTCQSERSQIKNREHAMKMLKAKL-----YQKKLEEQQAELDEIRGEQKE 276
>gnl|CDD|226844 COG4420, COG4420, Predicted membrane protein [Function unknown].
Length = 191
Score = 31.6 bits (72), Expect = 0.080
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 74 LSENRKTARELLVAQWDVQVN--GEDSLNAQIRRIDEKRRATQEQKKRKLDALKKAWKER 131
+S+NR+ R+ L A+ D QVN E + A ++DE R + LD L++ E
Sbjct: 109 MSQNRQAERDRLRAELDYQVNLKAEQEVAALHEKLDELRLDLGYVRDE-LDDLRELLAEI 167
Query: 132 E 132
E
Sbjct: 168 E 168
>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 = 29.9 bits (68), Expect = 0.42
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 100 NAQIRRIDEKRRATQEQKKRKLDALKKAWKERE 132
AQ R +T ++ KL LKKA R
Sbjct: 5 AAQQAHALALRASTAAERIAKLKRLKKAILARR 37
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 27.3 bits (61), Expect = 3.1
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 88 QWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDALKKAWKER 131
QWD QV D L R +D+K + E K L LK A K +
Sbjct: 957 QWD-QV--PDHLKITFRVVDDKNKKLAEGK--DLQELKDALKGK 995
>gnl|CDD|236812 PRK10992, PRK10992, iron-sulfur cluster repair di-iron protein;
Provisional.
Length = 220
Score = 26.5 bits (59), Expect = 4.9
Identities = 8/12 (66%), Positives = 12/12 (100%)
Query: 11 ASSLFRKYDLDY 22
A++LFR+YDLD+
Sbjct: 18 ATALFREYDLDF 29
>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 = 25.3 bits (56), Expect = 5.8
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 99 LNAQIRRIDEKRRATQEQKKRKLDALKKAWKE 130
LN R K + ++E+++ ++A KKA+K
Sbjct: 62 LNLPKRVDWRKCKQSKEEERADVEAFKKAFKP 93
>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 = 26.0 bits (57), Expect = 7.1
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 108 EKRRATQEQKKRKLDALKKAWKERE 132
E+ R EQ + LD LKK KER+
Sbjct: 26 EELRKHDEQVIQLLDLLKKTIKERD 50
>gnl|CDD|219327 pfam07195, FliD_C, Flagellar hook-associated protein 2 C-terminus.
The flagellar hook-associated protein 2 (HAP2 or FliD)
forms the distal end of the flagella, and plays a role
in mucin specific adhesion of the bacteria. This
alignment covers the C-terminal region of this family of
proteins.
Length = 230
Score = 25.7 bits (57), Expect = 7.1
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 96 EDSLNAQIRRIDEKRRATQEQKKRKLDALKK 126
EDSLN QI+R++++ + LK
Sbjct: 186 EDSLNKQIKRLNKQIEDLDRRLDTLEARLKA 216
>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 = 26.2 bits (58), Expect = 7.4
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 74 LSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDALKKAWKER 131
L ++ + R +A+W V E L+ Q+ ++ A + Q K +L LKK +
Sbjct: 708 LKDDFRELRTERLAKWQVV---EGELDNQLAQLSAAIEAARTQAKARLKELKKQYDRE 762
>gnl|CDD|177880 PLN02236, PLN02236, choline kinase.
Length = 344
Score = 25.8 bits (57), Expect = 7.9
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 3/20 (15%)
Query: 20 LDYSKVPKIDEKDIQERFVR 39
LDYSK P +E + RF+R
Sbjct: 257 LDYSKYPGEEE---RRRFIR 273
>gnl|CDD|237330 PRK13279, arnT, 4-amino-4-deoxy-L-arabinose transferase;
Provisional.
Length = 552
Score = 26.0 bits (58), Expect = 7.9
Identities = 11/30 (36%), Positives = 13/30 (43%)
Query: 9 SLASSLFRKYDLDYSKVPKIDEKDIQERFV 38
SL L R DL +P D+ Q R V
Sbjct: 517 SLVLRLDRDEDLPELALPPADKVYRQGRLV 546
>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 = 25.7 bits (57), Expect = 9.7
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 7/68 (10%)
Query: 65 VIKCHQSRSLSENRKTARELLVAQWDVQVNGEDSLNAQIRRIDEKRRATQEQKKRKLDAL 124
IK + + EN K + N E I + Q+ +++ A+
Sbjct: 169 AIKSLEYKQEQENVKDKNIDIY-------NFEKEFRQFKEAIVKNFELAQKDLDKEIKAI 221
Query: 125 KKAWKERE 132
KAWK+ E
Sbjct: 222 DKAWKKLE 229
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
0.317 0.132 0.374
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: 6,806,117
Number of extensions: 584696
Number of successful extensions: 1023
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1003
Number of HSP's successfully gapped: 86
Length of query: 135
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 48
Effective length of database: 7,078,804
Effective search space: 339782592
Effective search space used: 339782592
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: 53 (24.1 bits)