RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16255
(156 letters)
>gnl|CDD|205867 pfam13691, Lactamase_B_4, Family description. This is family of
tRNase Z enzymes, that are closely related structurally
to the Lactamase_B family members. tRNase Z is the
endonuclease that is involved in tRNA 3'-end maturation
through removal of the 3'-trailer sequences from tRNA
precursors. The fission yeast Schizosaccharomyces pombe
contains two candidate tRNase Zs encoded by two
essential genes. The first is targeted to the nucleus
and has an SV40 nuclear localisation signal at its
N-terminus, consisting of four consecutive arginine and
lysine residues between residues 208 and 211 (KKRK)
that is critical for the NLS function. The second is
targeted to the mitochondria, with an N-terminal
mitochondrial targeting signal within the first 38
residues.
Length = 63
Score = 75.7 bits (187), Expect = 3e-19
Identities = 29/63 (46%), Positives = 39/63 (61%), Gaps = 3/63 (4%)
Query: 35 QVLGSGARGAPK-SLYLFTDQSRYLF-NCGEGTQRLAHEHKMKLAKLDSVFITQPV-WEN 91
QV+ + P L L D RYLF N GEGTQR +E K++L+KL+ +F+T V W N
Sbjct: 1 QVVTTPTADTPGPLLLLHFDSKRYLFGNVGEGTQRALNERKVRLSKLEDIFLTGKVSWSN 60
Query: 92 LGG 94
+GG
Sbjct: 61 IGG 63
>gnl|CDD|224155 COG1234, ElaC, Metal-dependent hydrolases of the beta-lactamase
superfamily III [General function prediction only].
Length = 292
Score = 56.3 bits (136), Expect = 4e-10
Identities = 28/94 (29%), Positives = 49/94 (52%), Gaps = 8/94 (8%)
Query: 32 VNLQVLGSGA------RGAPKSLYLFTDQSRYLFNCGEGTQRLAHEHKMKLAKLDSVFIT 85
+ + LG+G R S+ L + ++LF+CGEGTQ + K+D++FIT
Sbjct: 2 MEITFLGTGGAVPTKDRNVS-SILLRLEGEKFLFDCGEGTQHQLLRAGLPPRKIDAIFIT 60
Query: 86 QPVWENLGGLLGLALTIQDVGVPE-INLHGPEGL 118
+++ GL GL ++ G E + ++GP G+
Sbjct: 61 HLHGDHIAGLPGLLVSRSFRGRREPLKIYGPPGI 94
>gnl|CDD|233963 TIGR02651, RNase_Z, ribonuclease Z. Processing of the 3-prime end
of tRNA precursors may be the result of endonuclease or
exonuclease activity, and differs in different species.
Member of this family are ribonuclease Z, a tRNA 3-prime
endonuclease that processes tRNAs to prepare for
addition of CCA. In species where all tRNA sequences
already have the CCA tail, such as E. coli, the need for
such an enzyme is unclear. Protein similar to the E.
coli enzyme, matched by TIGR02649, are designated
ribonuclease BN [Transcription, RNA processing].
Length = 299
Score = 55.3 bits (134), Expect = 7e-10
Identities = 29/93 (31%), Positives = 46/93 (49%), Gaps = 8/93 (8%)
Query: 33 NLQVLGSGARGAPK------SLYLFTDQSRYLFNCGEGTQRLAHEHKMKLAKLDSVFITQ 86
+ LG+G G P S+ L + +LF+CGEGTQR + K+D +FIT
Sbjct: 1 EITFLGTGG-GVPTKERNLPSIALKLNGELWLFDCGEGTQRQMLRSGISPMKIDRIFITH 59
Query: 87 PVWENLGGLLGLALTI-QDVGVPEINLHGPEGL 118
+++ GL GL T+ + ++GP G+
Sbjct: 60 LHGDHILGLPGLLSTMSFQGRKEPLTIYGPPGI 92
>gnl|CDD|234602 PRK00055, PRK00055, ribonuclease Z; Reviewed.
Length = 270
Score = 47.9 bits (115), Expect = 3e-07
Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 16/97 (16%)
Query: 33 NLQVLGSGA-----RGAPKSLYLFTDQSRYLFNCGEGTQRLAHEHKMKLAKLDSVFITQP 87
L LG+G+ S+ L +LF+CGEGTQR + +K K+D +FIT
Sbjct: 3 ELTFLGTGSGVPTPTRNVSSILLRLGGELFLFDCGEGTQRQLLKTGIKPRKIDKIFIT-- 60
Query: 88 VWENL-----GGLLGLALTIQDVGVPE-INLHGPEGL 118
+L GL GL T G E + ++GP+G+
Sbjct: 61 ---HLHGDHIFGLPGLLSTRSLSGRTEPLTIYGPKGI 94
>gnl|CDD|131697 TIGR02649, true_RNase_BN, ribonuclease BN. Members of this protein
family are ribonuclease BN of Escherichia coli K-12 and
closely related proteins believed to be equivalent in
function. Note that E. coli appears to lack RNase Z per
se, and this protein of E. coli appears orthologous to
(but not functionally equivalent to) RNase Z of Bacillus
subtilis and various other species. Meanwhile, the yihY
gene product of E. coli previously was incorrectly
identified as RNase BN [Transcription, RNA processing].
Length = 303
Score = 41.9 bits (98), Expect = 4e-05
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 52 TDQSRYLFNCGEGTQRLAHEHKMKLAKLDSVFITQPVWENLGGLLGLALTIQDVGVPE-I 110
T +LF+CGEGTQ KLD +FI+ ++L GL GL + G+ + +
Sbjct: 28 TQSGLWLFDCGEGTQHQLLHTAFNPGKLDKIFISHLHGDHLFGLPGLLCSRSMSGIIQPL 87
Query: 111 NLHGPEGL 118
++GP+G+
Sbjct: 88 TIYGPQGI 95
>gnl|CDD|177109 MTH00034, CYTB, cytochrome b; Validated.
Length = 379
Score = 29.3 bits (66), Expect = 0.89
Identities = 14/31 (45%), Positives = 16/31 (51%), Gaps = 6/31 (19%)
Query: 79 LDSVFITQP------VWENLGGLLGLALTIQ 103
L+S I P +W N G LLGL L IQ
Sbjct: 14 LNSSLIDLPSPSNLSIWWNFGSLLGLCLIIQ 44
>gnl|CDD|223697 COG0624, ArgE, Acetylornithine deacetylase/Succinyl-diaminopimelate
desuccinylase and related deacylases [Amino acid
transport and metabolism].
Length = 409
Score = 28.6 bits (64), Expect = 1.2
Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 3/71 (4%)
Query: 62 GEGTQRLAHEHKMKLAKL-DSVFITQPVWENLGGLLGLALTIQDVGVPEINLHGPEGLVS 120
G G + E + L D + +P E+ GG + + + E+ + G G S
Sbjct: 154 GAGGKAYLEEGEEALGIRPDYEIVGEPTLESEGGDII-VVGHKGSLWLEVTVKGKAGHAS 212
Query: 121 -ENMGLASNSI 130
L N I
Sbjct: 213 TTPPDLGRNPI 223
>gnl|CDD|203947 pfam08446, PAS_2, PAS fold. The PAS fold corresponds to the
structural domain that has previously been defined as
PAS and PAC motifs. The PAS fold appears in archaea,
eubacteria and eukarya.
Length = 107
Score = 26.8 bits (60), Expect = 2.6
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 90 ENLGGLLGLALTIQDVGVPEINLHGPEGLVSENMGLASNSISPSDPALIQART 142
EN +LGL Q +G L P + LA+ +S +P + +RT
Sbjct: 33 ENAAEMLGLVPQ-QLLGTDLRTLLTPSSAAALEKALAAGDLSLLNPITVHSRT 84
>gnl|CDD|164924 PHA02523, 43B, DNA polymerase subunit B; Provisional.
Length = 391
Score = 27.8 bits (61), Expect = 2.7
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 124 GLASNSISPSD---PALIQARTLMKIPLRPRLPLD 155
LA N I+ +D P + + +M +PLR R P +
Sbjct: 296 VLAYNRIAKTDTAIPMISEGEKVMVLPLRDRNPFN 330
>gnl|CDD|177203 MTH00145, CYTB, cytochrome b; Provisional.
Length = 379
Score = 27.2 bits (61), Expect = 4.2
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 88 VWENLGGLLGLALTIQ 103
+W N G LLGL L IQ
Sbjct: 30 IWWNFGSLLGLCLGIQ 45
>gnl|CDD|179371 PRK02113, PRK02113, putative hydrolase; Provisional.
Length = 252
Score = 27.1 bits (60), Expect = 4.5
Identities = 14/50 (28%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 47 SLYLFTDQSRYLFNCG-EGTQRLAHEHKMKLAKLDSVFITQPVWENLGGL 95
S + T+ +R L +CG + +++ + K+D+V IT ++++GGL
Sbjct: 37 SALVETEGARILIDCGPDFREQMLR---LPFGKIDAVLITHEHYDHVGGL 83
>gnl|CDD|177102 MTH00016, CYTB, cytochrome b; Validated.
Length = 378
Score = 26.6 bits (59), Expect = 6.8
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 88 VWENLGGLLGLALTIQ 103
+W N G LLGL L IQ
Sbjct: 30 IWWNFGSLLGLCLVIQ 45
>gnl|CDD|221727 pfam12706, Lactamase_B_2, Beta-lactamase superfamily domain.
This family is part of the beta-lactamase superfamily
and is related to pfam00753.
Length = 197
Score = 26.3 bits (58), Expect = 7.0
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 56 RYLFNCGEGT----QRLAHEHKMKLAKLDSVFIT 85
R L + G GT Q+ + L ++D+V ++
Sbjct: 2 RILIDPGPGTRDLRQQPLAAPAL-LPRIDAVLLS 34
>gnl|CDD|234946 PRK01355, PRK01355, azoreductase; Reviewed.
Length = 199
Score = 26.2 bits (58), Expect = 7.6
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 33 NLQVLGSGARGAPKSLYLFTDQSRYLFNCGEGT 65
+L+V +GAP Y + + YL EGT
Sbjct: 126 HLKVQILTTQGAPLGWYPWGSHTNYL----EGT 154
>gnl|CDD|214440 MTH00156, CYTB, cytochrome b; Provisional.
Length = 356
Score = 26.3 bits (59), Expect = 8.5
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 89 WENLGGLLGLALTIQ 103
W N G LLGL L IQ
Sbjct: 20 WWNFGSLLGLCLMIQ 34
>gnl|CDD|164767 MTH00224, CYTB, cytochrome b; Provisional.
Length = 379
Score = 26.0 bits (57), Expect = 8.6
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 88 VWENLGGLLGLALTIQ 103
+W N G LLGL L IQ
Sbjct: 30 IWWNYGSLLGLCLVIQ 45
>gnl|CDD|214425 MTH00119, CYTB, cytochrome b; Provisional.
Length = 380
Score = 26.0 bits (58), Expect = 9.8
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 8/40 (20%)
Query: 70 HEHKMKLAKLDSVFITQPV------WENLGGLLGLALTIQ 103
+K+ +++ I P W N G LLGL L Q
Sbjct: 8 SHPLLKI--INNSLIDLPTPSNISAWWNFGSLLGLCLITQ 45
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 0.136 0.393
Gapped
Lambda K H
0.267 0.0793 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,671,747
Number of extensions: 675655
Number of successful extensions: 471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 470
Number of HSP's successfully gapped: 27
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
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 (24.8 bits)