RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10784
(69 letters)
>gnl|CDD|218235 pfam04734, Ceramidase_alk, Neutral/alkaline non-lysosomal
ceramidase. This family represents a group of
neutral/alkaline ceramidases found in both bacteria and
eukaryotes.
Length = 672
Score = 124 bits (313), Expect = 4e-35
Identities = 45/69 (65%), Positives = 51/69 (73%)
Query: 1 MDFLFDLNSLGFVPDTFNAMVRGIALSISRAHNNLQEGRLFVSKGELLDANINRSPTAYL 60
L+ + SLGF +F A+V GI LSI RAH +LQ GRL V KGELLDANINRSP+AYL
Sbjct: 104 HYLLYQITSLGFDKQSFQAIVDGIVLSIVRAHESLQPGRLSVGKGELLDANINRSPSAYL 163
Query: 61 QNPEEERMR 69
NPEEER R
Sbjct: 164 ANPEEERAR 172
>gnl|CDD|240437 PTZ00487, PTZ00487, ceramidase; Provisional.
Length = 715
Score = 79.2 bits (195), Expect = 2e-19
Identities = 29/64 (45%), Positives = 44/64 (68%)
Query: 4 LFDLNSLGFVPDTFNAMVRGIALSISRAHNNLQEGRLFVSKGELLDANINRSPTAYLQNP 63
L+ + +LGF F+ + GI +I +AH ++Q R++ + GEL ++NINRSPTAY NP
Sbjct: 145 LYGITTLGFYKKNFDTICEGIVQAIVKAHKSVQPARMYTNSGELWNSNINRSPTAYDNNP 204
Query: 64 EEER 67
EEE+
Sbjct: 205 EEEK 208
>gnl|CDD|187755 cd09294, SmpB, Small protein B (SmpB) is a component of the
trans-translation system in prokaryotes for releasing
stalled ribosome from damaged messenger RNAs. Small
protein B (SmpB) is a component of the
trans-translation system in prokaryotes for releasing
stalled ribosome from damaged messenger RNAs and
targeting incompletely synthesized protein fragments
for degradation. Trans-translation system is composed
of a ribonucleoprotein complex of tmRNA, a specialized
RNA with properties of both tRNA and mRNA, and SmpB.
SmpB is highly conserved and present in all bacterial
kingdoms and is also found in some chloroplasts and
mitochondria. This is suggesting Trans-translation
arose early in bacterial evolution and its mechanism is
a quality control for protein synthesis in spite of
challenges such as transcription errors, mRNA damage,
and translation frame shifting. SmpB deletion results
in phage development defects phenotype and absence of
tagged proteins translated from defective mRNAs.
Length = 116
Score = 31.9 bits (74), Expect = 0.007
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 13/67 (19%)
Query: 12 FVPDTFNAMVRGIAL------SISRAHN-NLQEGRLFVSKGE--LLDANINRSPTAYLQN 62
+ +TF A GI L S+ RA NL++ + + GE LL+A+I+ A N
Sbjct: 9 EIEETFEA---GIVLLGTEVKSL-RAGKVNLKDSYVRIKNGEAWLLNAHISPYEFANRFN 64
Query: 63 PEEERMR 69
+ +R R
Sbjct: 65 HDPKRPR 71
>gnl|CDD|223763 COG0691, SmpB, tmRNA-binding protein [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 29.5 bits (67), Expect = 0.068
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 19/70 (27%)
Query: 12 FVPDTFNAMVRGIAL------SISRAHNNLQEGRLFVSKGE--LLDANINRSPTAYLQ-- 61
F+ +TF A GI L S+ NL++ + KGE L++A+I + Y
Sbjct: 19 FIEETFEA---GIVLQGTEVKSLRAGKANLKDSYARIKKGEAWLINAHI----SPYEAGN 71
Query: 62 --NPEEERMR 69
N + R R
Sbjct: 72 RFNHDPRRTR 81
>gnl|CDD|178304 PLN02701, PLN02701, alpha-mannosidase.
Length = 1050
Score = 27.1 bits (60), Expect = 0.76
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 29 SRAHNNLQEGRLFVSK--GELLDANINRS-PTAYLQNPEEER 67
+R H +LQ+ ++F+S LL +S T PE+ R
Sbjct: 468 TRMHTSLQDLQIFMSAAVEVLLGIRHEKSDQTPSWFEPEQSR 509
>gnl|CDD|185292 PRK15394, PRK15394,
4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol
deformylase ArnD; Provisional.
Length = 296
Score = 26.0 bits (58), Expect = 1.3
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 9/47 (19%)
Query: 16 TFNAMVRGIALS------ISRAHNNLQEGRLFVSKGELLDANINRSP 56
T +A V GIA + + RA QEG F ELL ++ P
Sbjct: 231 TIHAEVEGIAYAHNFEDLLKRAA---QEGITFCPLSELLPDDLETLP 274
>gnl|CDD|213286 cd05919, BCL_like, Benzoate CoA ligase (BCL) and similar adenylate
forming enzymes. This family contains benzoate CoA
ligase (BCL) and related ligases that catalyze the
acylation of benzoate derivatives, 2-aminobenzoate and
4-hydroxybenzoate. Aromatic compounds represent the
second most abundant class of organic carbon compounds
after carbohydrates. Xenobiotic aromatic compounds are
also a major class of man-made pollutants. Some bacteria
use benzoate as the sole source of carbon and energy
through benzoate degradation. Benzoate degradation
starts with its activation to benzoyl-CoA by benzoate
CoA ligase. The reaction catalyzed by benzoate CoA
ligase proceeds via a two-step process; the first
ATP-dependent step forms an acyl-AMP intermediate, and
the second step forms the acyl-CoA ester with release of
the AMP.
Length = 436
Score = 25.8 bits (57), Expect = 1.8
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 13 VPDTFNAMVRGIALSISRAHNNLQEGRLFVSKGELLDANI 52
VP + A++ A S + ++ RL VS GE L A +
Sbjct: 189 VPALYRALLESGAGS-APLFRSV---RLCVSAGEALPAGL 224
>gnl|CDD|204358 pfam09965, DUF2199, Uncharacterized protein conserved in bacteria
(DUF2199). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 147
Score = 25.5 bits (56), Expect = 1.9
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 54 RSPTAYLQNPEEER 67
R+P Y PEEER
Sbjct: 19 RAPDPYFAVPEEER 32
>gnl|CDD|149159 pfam07925, RdRP_5, Reovirus RNA-dependent RNA polymerase lambda 3.
The sequences in this family are similar to the reoviral
minor core protein lambda 3, which functions as a
RNA-dependent RNA polymerase within the protein capsid.
It is organised into 3 domains. N- and C-terminal domains
create a 'cage' that encloses a conserved central
catalytic domain within a hollow centre; this catalytic
domain is arranged to form 'fingers', 'palm' and 'thumb'
subdomains. Unlike other RNA polymerases, like HIV
reverse transcriptase and T7 RNA polymerase, lambda 3
protein binds template and substrate with only localised
rearrangements, and catalytic activity can occur with
little structural change. However, the structure of the
catalytic complex is similar to that of other polymerase
catalytic complexes with known structure.
Length = 1271
Score = 24.9 bits (54), Expect = 4.3
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 4 LFDLNSLGFVPDTFNAMVRGIALSISRAH 32
L L LG P+ A + GI +S S AH
Sbjct: 1136 LLRLRILGADPEALTAQLLGIGMSDSEAH 1164
>gnl|CDD|224581 COG1667, COG1667, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 254
Score = 24.4 bits (53), Expect = 4.9
Identities = 9/44 (20%), Positives = 17/44 (38%)
Query: 15 DTFNAMVRGIALSISRAHNNLQEGRLFVSKGELLDANINRSPTA 58
+ ++ G R NL E +FV G+++ A +
Sbjct: 24 EIVLSLSTGYVRITIRIGENLNEAFIFVEGGKIVGAYHIDVRSL 67
>gnl|CDD|177190 MTH00132, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 227
Score = 24.4 bits (54), Expect = 5.8
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 1 MDFLFDLNSLGFVPDTF 17
M FL LN LG +P TF
Sbjct: 77 MLFLITLNMLGLLPYTF 93
>gnl|CDD|184865 PRK14863, PRK14863, bifunctional regulator KidO; Provisional.
Length = 292
Score = 24.1 bits (52), Expect = 8.3
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 7 LNSLGFVP-DTFNAMVRGIALSISRAHNNLQEGR 39
LN L F+P D A ++G + +SR + EGR
Sbjct: 195 LNGLLFLPPDRVPAQLKGASGRLSRVRRMIAEGR 228
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 23.9 bits (52), Expect = 9.1
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 11/36 (30%)
Query: 14 PDTFNAMVRGIALSISRAHNNLQEGRLFVSKGELLD 49
PD FN + L I L +GRL SKG +D
Sbjct: 625 PDIFNLL-----LQI------LDDGRLTDSKGRTID 649
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 23.8 bits (52), Expect = 9.8
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 10/30 (33%)
Query: 1 MDFLFDLNSLGFVPDTFNAMVRGIAL-SIS 29
++ LF + +LGF RG AL SI+
Sbjct: 84 LEDLFRIRTLGF---------RGEALASIA 104
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
0.321 0.137 0.387
Gapped
Lambda K H
0.267 0.0667 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,600,911
Number of extensions: 262096
Number of successful extensions: 193
Number of sequences better than 10.0: 1
Number of HSP's gapped: 193
Number of HSP's successfully gapped: 17
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.3 bits)