RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15075
(389 letters)
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 33.0 bits (75), Expect = 0.35
Identities = 17/61 (27%), Positives = 20/61 (32%), Gaps = 5/61 (8%)
Query: 252 AAAPTVPVRSRGMPRKMTDTTPLKGIPSRVPSGG-----FRSPTLSSSLSRPIMSIPRNP 306
A P P R T P P P+ G R S S SR + P +P
Sbjct: 2745 PAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDP 2804
Query: 307 A 307
A
Sbjct: 2805 A 2805
>gnl|CDD|200601 cd10979, CE4_PuuE_like, Putative catalytic domain of
uncharacterized prokaryotic polysaccharide deacetylases
similar to bacterial PuuE allantoinases. The family
includes a group of uncharacterized prokaryotic
polysaccharide deacetylases (DCAs) that show high
sequence similarity to the catalytic domain of bacterial
PuuE (purine utilization E) allantoinases. PuuE
allantoinase specifically catalyzes the hydrolysis of
(S)-allantoin into allantoic acid. It functions as a
homotetramer. Its monomer is composed of a 7-stranded
barrel with detectable sequence similarity to the
6-stranded barrel NodB homology domain of DCA-like
proteins in the CE4 superfamily, which removes N-linked
or O-linked acetyl groups from cell wall
polysaccharides. PuuE allantoinase appears to be
metal-independent and acts on a small substrate
molecule, which is distinct from the common feature of
DCAs which are normally metal ion dependent and
recognize multimeric substrates.
Length = 281
Score = 31.1 bits (71), Expect = 0.95
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 10/66 (15%)
Query: 81 PATMSLNTEIGDQDPYLIEAV----------GFNGGGTHEDLSRHHWKVELEEILEVATV 130
P T++LN + D+ P LIEA+ G + H L + + E L+
Sbjct: 78 PPTVALNAAVADRYPELIEAIRERGWEFIAHGISNSTLHAGLDEAQEREVIAESLDRIEK 137
Query: 131 DTEQWV 136
T Q
Sbjct: 138 ATGQRP 143
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 30.8 bits (69), Expect = 1.2
Identities = 20/68 (29%), Positives = 26/68 (38%), Gaps = 12/68 (17%)
Query: 254 APTVPVRSRGMPR---KMTDTTPLKGIPSRVPSGGFRSPTLSSSLSRPIMSIPRNPAGRK 310
AP P RS PR +M + +P+ G P V S PTL P + A
Sbjct: 439 APPAPPRSGIPPRPAPRMPEASPVPGAPDSVASASDAPPTLGD---------PSDTAEHT 489
Query: 311 DGGIKLLD 318
G + D
Sbjct: 490 PSGPRTWD 497
>gnl|CDD|193524 cd05646, M20_AcylaseI_like, M20 Aminoacylase-I like subfamily.
Peptidase M20 family, Aminoacylase-I like (AcyI-like;
Acylase I; N-acyl-L-amino-acid amidohydrolase; EC
3.5.1.14) subfamily. Acylase I is involved in the
hydrolysis of N-acylated or N-acetylated amino acids
(except L-aspartate) and is considered as a potential
target of antimicrobial agents. Porcine AcyI is also
shown to deacetylate certain quorum-sensing
N-acylhomoserine lactones, while the rat enzyme has been
implicated in degradation of chemotactic peptides of
commensal bacteria. Prokaryotic arginine synthesis
usually involves the transfer of an acetyl group to
glutamate by ornithine acetyltransferase in order to
form ornithine. However, Escherichia coli
acetylornithine deacetylase (acetylornithinase, ArgE)
(EC 3.5.1.16) catalyzes the deacylation of
N2-acetyl-L-ornithine to yield ornithine and acetate.
Phylogenetic evidence suggests that the clustering of
the arg genes in one continuous sequence pattern arose
in an ancestor common to Enterobacteriaceae and
Vibrionaceae, where ornithine acetyltransferase was lost
and replaced by a deacylase.
Length = 391
Score = 29.9 bits (68), Expect = 2.4
Identities = 11/58 (18%), Positives = 27/58 (46%), Gaps = 12/58 (20%)
Query: 315 KLLDITEQPLGYAQAKKKKKQENPCPTYGNVVTIKLSESQEIHPLGDPVLVEHHFQMN 372
KL+ + E+ + + + + ++ + N T G+V ++ L +++ QMN
Sbjct: 210 KLMKVIEKFMEFREEQFQRLKSNGKLTIGDVTSVNL------------TMLKGGVQMN 255
>gnl|CDD|236303 PRK08579, PRK08579, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 625
Score = 29.7 bits (67), Expect = 2.8
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 45 RRNMDEWKVELEEILEVATVDTEQWVSMVAELMKTYPATMSLNTE 89
R + D++ EE LE+ + + + +L+KTYP S+ E
Sbjct: 351 RGDDDKFWELYEERLELVRITLDWFRERYVKLLKTYPEMYSMIKE 395
>gnl|CDD|217788 pfam03914, CBF, CBF/Mak21 family.
Length = 151
Score = 28.7 bits (65), Expect = 3.2
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 70 VSMVAELMKTYPATMSL---NTEIGDQDPYLIEA 100
+ ++ L+K +P SL G+ PY E
Sbjct: 86 LPLIRNLLKRHPNLKSLLHTEERGGEDGPYDPEE 119
>gnl|CDD|185751 cd09238, V_Alix_like_1, Protein-interacting V-domain of an
uncharacterized family of the V_Alix_like superfamily.
This domain family is comprised of uncharacterized plant
proteins. It belongs to the V_Alix_like superfamily
which includes the V-shaped (V) domains of Bro1 and
Rim20 (also known as PalA) from Saccharomyces
cerevisiae, mammalian Alix (apoptosis-linked gene-2
interacting protein X), (His-Domain) type N23 protein
tyrosine phosphatase (HD-PTP, also known as PTPN23), and
related domains. Alix, also known as apoptosis-linked
gene-2 interacting protein 1 (AIP1), participates in
membrane remodeling processes during the budding of
enveloped viruses, vesicle budding inside late endosomal
multivesicular bodies (MVBs), and the abscission
reactions of mammalian cell division. It also functions
in apoptosis. HD-PTP functions in cell migration and
endosomal trafficking, Bro1 in endosomal trafficking,
and Rim20 in the response to the external pH via the
Rim101 pathway. Alix, HD-PTP, Bro1, and Rim20 all
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. The mammalian Alix
V-domain (belonging to a different family) contains a
binding site, partially conserved in the superfamily,
for the retroviral late assembly (L) domain YPXnL motif.
The Alix V-domain is also a dimerization domain. In
addition to this V-domain, members of the
V_Alix_Rim20_Bro1_like superfamily also have an
N-terminal Bro1-like domain, which binds components of
the ESCRT-III complex. The Bro1-like domains of Alix and
HD-PTP can also bind to human immunodeficiency virus
type 1 (HIV-1) nucleocapsid. Many members of the
V_Alix_like superfamily also have a proline-rich region
(PRR).
Length = 339
Score = 29.0 bits (65), Expect = 5.1
Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 10/82 (12%)
Query: 227 RKPKSAALRAELVQKSMDAASNMKKAAAPTVPVRSRGMPRKMTDTTPLKGIPSRVPSGGF 286
+P SA L L ++ N+++A +R R + D I P+
Sbjct: 121 TRPPSATLTKNLWERLNRFRVNLEQAGDSDESLRRR-----IEDAMDGMLILDDEPAAA- 174
Query: 287 RSPTLSSSLSRPIMSIPRNPAG 308
+PT L P++S + A
Sbjct: 175 AAPT----LRAPMLSTDEDDAS 192
>gnl|CDD|235899 PRK06975, PRK06975, bifunctional uroporphyrinogen-III
synthetase/uroporphyrin-III C-methyltransferase;
Reviewed.
Length = 656
Score = 28.5 bits (64), Expect = 8.0
Identities = 12/58 (20%), Positives = 18/58 (31%), Gaps = 1/58 (1%)
Query: 252 AAAPTVPVRSRGMPRKMTDTTPLKGIPSRVPSGGFRSPTLSSSLSRPIMSIPRNPAGR 309
A A P + P +MTDT K + P+ +P + P
Sbjct: 266 ADAAAQPATAAPAPSRMTDTNDSKS-VTSQPAAAAAAPAPPPNPPATPPEPPARRGRG 322
>gnl|CDD|152262 pfam11826, DUF3346, Protein of unknown function (DUF3346). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 231 to 659 amino acids in
length.
Length = 225
Score = 28.0 bits (62), Expect = 8.9
Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 110 EDLSRHHWKVELEEILEVATVDTEQWVSMVAELMKTYPATM---SLNTEIGEIVENKRIF 166
E L+R ++ + EIL+ T+ + + + + + + M LN ++ +E +R
Sbjct: 67 ELLTRDYFFLFPPEILKQHTLVFQLYSFFRSRMSRRHTDCMLLSELNQKLARNIEWRRFS 126
Query: 167 SDLINDLRKLVKRQGSE 183
DLI +L++L + + SE
Sbjct: 127 MDLIRELKRLSEGKVSE 143
>gnl|CDD|204170 pfam09226, Endonuc-HincII, Restriction endonuclease HincII.
Members of this family of prokaryotic restriction
endonucleases recognise the double-stranded sequence
5'-GTYRAC-3' and cleave after Y-3. They catalyze the
endonucleolytic cleavage of DNA to give specific
double-stranded fragments with terminal 5'-phosphates.
Length = 257
Score = 27.8 bits (61), Expect = 8.9
Identities = 23/97 (23%), Positives = 46/97 (47%), Gaps = 15/97 (15%)
Query: 50 EWKVELEEILEVATVDTEQWVSMVAELMKTYPATMSLNTEIGDQDPYLIEAVGFNGGGTH 109
+W++ E+++ V+T E + S +EL + A M + + D D GFN GT
Sbjct: 171 DWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQ------GFN--GTR 222
Query: 110 EDLSRHHWKVELEEILEVATVDTEQWVSMVAELMKTY 146
E+ ++ + K T ++ +SM+ + +K +
Sbjct: 223 EEWAKSYLK-------HFVTQAEQRAISMIDKFVKPF 252
>gnl|CDD|220459 pfam09892, DUF2119, Uncharacterized protein conserved in archaea
(DUF2119). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 193
Score = 27.7 bits (62), Expect = 9.0
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 41 FHIPRRNMDEWKVELEEILEVATVDTEQWVSMVAELMKTYP 81
IP DE + EILEV ++ + L K YP
Sbjct: 138 LEIPNWKSDESLEFVAEILEVG-KESRSREEFIEYLKKRYP 177
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
0.313 0.129 0.371
Gapped
Lambda K H
0.267 0.0590 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,337,537
Number of extensions: 1818992
Number of successful extensions: 1144
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1142
Number of HSP's successfully gapped: 19
Length of query: 389
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 290
Effective length of database: 6,546,556
Effective search space: 1898501240
Effective search space used: 1898501240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 60 (27.2 bits)