RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17866
(127 letters)
>gnl|CDD|184256 PRK13700, PRK13700, conjugal transfer protein TraD; Provisional.
Length = 732
Score = 33.4 bits (76), Expect = 0.020
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 13/84 (15%)
Query: 19 GAELKNGALVIYESVPSASPPYVCYVTLPGGSCFGSFQTLEVEVSRSQMALDWIAREQEN 78
G +++ LV Y + S P CYVTLPG +++L + AR +
Sbjct: 523 GKDMERQTLVSYSDIQSL-PDLTCYVTLPG------------PYPAVKLSLKYQARPKVA 569
Query: 79 PGALGRELDQAERELETARLAGRE 102
P + R+++ +A LA RE
Sbjct: 570 PEFIPRDINPEMENRLSAVLAARE 593
>gnl|CDD|162489 TIGR01690, ICE_RAQPRD, integrative conjugative element protein,
RAQPRD family. This model represents a small family of
proteins about 100 amino acids in length, including a
predicted signal sequence and a perfectly conserved
motif RAQPRD towards the C-terminus. Members are found
in the Pseudomonas putida TOL plasmid pWW0 and in
cryptic plasmid regions of Salmonella enterica subsp.
enterica serovar Typhi and Pseudomonas syringae DC3000.
The function is unknown [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 94
Score = 29.2 bits (66), Expect = 0.24
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 58 LEVEVSRSQMALDWIAREQENPGALGRELDQAERELETAR 97
L + + + AL A E+E A R+LD ER + A
Sbjct: 5 LALALLVAASALADQASEREQLAAAIRQLDALERSAQRAA 44
>gnl|CDD|220597 pfam10139, Virul_Fac, Putative bacterial virulence factor. Members
of this family of prokaryotic proteins include various
putative virulence factor effector proteins. Their exact
function is, as yet, unknown.
Length = 852
Score = 28.5 bits (64), Expect = 1.1
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 68 ALDWIAREQENPGALGRELDQAERELETARLAGREL 103
A+DW+ ++N L RE D +L +R R L
Sbjct: 1 AIDWVNETRQNAPRLDREADSLTVKLRRSRNRARRL 36
>gnl|CDD|226865 COG4458, SrfC, Uncharacterized protein conserved in bacteria,
putative virulence factor [Function unknown].
Length = 821
Score = 28.3 bits (63), Expect = 1.2
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 65 SQMALDWIAREQENPGALGRELDQAERELETARLAGREL 103
+Q A+DW+ + N L E D E+ L +R A R+L
Sbjct: 16 AQDAIDWVGNTRANAVRLDDEADSLEQHLRRSRNAARKL 54
>gnl|CDD|218199 pfam04665, Pox_A32, Poxvirus A32 protein. The A32 protein is
thought to be involved in viral DNA packaging.
Length = 241
Score = 27.3 bits (61), Expect = 1.8
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 18 RGAELKNGALVIYESVPSASPPYVCYVT 45
R AE K +I +SV +CY +
Sbjct: 186 RSAEKKRRVYIIEDSVFCEGEQRICYDS 213
>gnl|CDD|178584 PLN03007, PLN03007, UDP-glucosyltransferase family protein.
Length = 482
Score = 27.1 bits (60), Expect = 3.0
Identities = 22/90 (24%), Positives = 34/90 (37%), Gaps = 6/90 (6%)
Query: 35 SASPPYVCYVTLPGGSCFGSFQTLEVE--VSRSQMALDWIAREQENPGALGRELDQAERE 92
S P V Y++ + F + Q E+ + S W+ R+ EN G L + E
Sbjct: 281 SKKPDSVIYLSFGSVASFKNEQLFEIAAGLEGSGQNFIWVVRKNENQGEKEEWLPEGFEE 340
Query: 93 LETARLAGRELRFPKEKKDILMLAHTQING 122
R G+ L +L+L H G
Sbjct: 341 ----RTKGKGLIIRGWAPQVLILDHQATGG 366
>gnl|CDD|225224 COG2348, COG2348, Peptidoglycan interpeptide bridge formation
enzyme [Cell wall/membrane/envelope biogenesis].
Length = 418
Score = 27.0 bits (60), Expect = 3.0
Identities = 10/48 (20%), Positives = 20/48 (41%)
Query: 77 ENPGALGRELDQAERELETARLAGRELRFPKEKKDILMLAHTQINGGS 124
E L +EL + E+E + A +E ++ ++ L Q+
Sbjct: 246 EYLKKLNQELAKLAAEIERVQEALKESPKSEKAQNKLNRLQMQLEAFE 293
>gnl|CDD|236726 PRK10618, PRK10618, phosphotransfer intermediate protein in
two-component regulatory system with RcsBC; Provisional.
Length = 894
Score = 26.8 bits (60), Expect = 3.9
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 11/59 (18%)
Query: 59 EVEVSRSQMALD---WIAREQENPGALGRELDQAERELE---TARLA-----GRELRFP 106
E+ + RSQ+A ++ R+Q+ + ++L QA+RE E AR A G EL+ P
Sbjct: 406 EIRMFRSQLAPRTQLFLLRDQDREVLVNKKLQQAQREYEKNQQARKAFLQNIGDELKQP 464
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 26.7 bits (59), Expect = 5.0
Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 9/68 (13%)
Query: 55 FQTLEVEVSRSQMAL-DWIAREQENPGALGRELDQAERELETARLAGRELRFPKEKKDIL 113
+ LE E+ Q+ W + LD+AE EL R R+L K++ + L
Sbjct: 159 LKELEAEIREVQLKTRTWKDLVKA--------LDEAEEELANLRKELRQLEKEKQRLERL 210
Query: 114 MLAHTQIN 121
+
Sbjct: 211 RRLLPLLA 218
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P)-binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction.
Length = 436
Score = 26.2 bits (58), Expect = 5.3
Identities = 19/101 (18%), Positives = 31/101 (30%), Gaps = 2/101 (1%)
Query: 6 EALQEFWQ--MKQTRGAELKNGALVIYESVPSASPPYVCYVTLPGGSCFGSFQTLEVEVS 63
L E Q +K A +G ++ + + G G +TL E
Sbjct: 81 LQLLESLQRLLKAGLLAARASGRALLQVVTGLPGALGLDALDPAGAGLAGLLRTLAQEYP 140
Query: 64 RSQMALDWIAREQENPGALGRELDQAERELETARLAGRELR 104
L + + + AL REL A + R+
Sbjct: 141 GLTCRLIDLDAGEASAEALARELAAELAAPGAAEVRYRDGL 181
>gnl|CDD|206768 cd11363, RNase_PH_PNPase_1, Polyribonucleotide
nucleotidyltransferase, repeat 1. Polyribonucleotide
nucleotidyltransferase (PNPase) is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally, all members
of this family form hexameric rings. In the case of
PNPase the complex is a trimer, since each monomer
contains two tandem copies of the domain. PNPase is
involved in mRNA degradation in a 3'-5' direction and in
quality control of ribosomal RNA precursors. It is part
of the RNA degradosome complex and binds to the
scaffolding domain of the endoribonuclease RNase E.
Length = 229
Score = 25.9 bits (58), Expect = 6.7
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 84 RELDQAERELETARLAGRELR--FPK 107
RE +E+E+ T+RL R +R FPK
Sbjct: 76 REGRPSEKEILTSRLIDRPIRPLFPK 101
>gnl|CDD|150373 pfam09686, Plasmid_RAQPRD, Plasmid protein of unknown function
(Plasmid_RAQPRD). This entry identifies a family of
proteins, which are about 100 amino acids in length,
including a predicted signal sequence and a perfectly
conserved motif RAQPRD towards the C terminus. Members
are found in the Pseudomonas putida TOL plasmid pWW0
and in cryptic plasmid regions of Salmonella enterica
subsp. enterica serovar Typhi and Pseudomonas syringae
DC3000. The function of these proteins are unknown.
Length = 81
Score = 25.0 bits (55), Expect = 6.8
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 73 AREQENPGALGRELDQAERELETAR 97
A E+E A R+LD ER E A
Sbjct: 7 AAEREQLAAAIRQLDALERLAERAA 31
>gnl|CDD|226031 COG3500, COG3500, Phage protein D [General function prediction
only].
Length = 350
Score = 25.9 bits (57), Expect = 7.0
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 53 GSFQTLEVEVSRSQMALDWIAREQENPGALGRELDQAERELETARLAGRELRF 105
+ L VS +Q+A I + E+ L AER A++ L F
Sbjct: 129 AAEHGLTAAVSATQVAHPHIDQYYESDINFLLRL--AERYGAIAKVKEGRLIF 179
>gnl|CDD|180506 PRK06279, PRK06279, putative monovalent cation/H+ antiporter
subunit E; Reviewed.
Length = 100
Score = 25.0 bits (55), Expect = 7.5
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 6/35 (17%)
Query: 79 PGALGRELDQAERELETARLAGRELRFPKEKKDIL 113
PG L +LD ER L+ A ++ P+ + DI+
Sbjct: 61 PGTLTIDLDSEERILKVASIS------PRSRDDII 89
>gnl|CDD|233987 TIGR02733, desat_CrtD, C-3',4' desaturase CrtD. Members of this
family are slr1293, a carotenoid biosynthesis protein
which was shown to be the C-3',4' desaturase (CrtD) of
myxoxanthophyll biosynthesis in Synechocystis sp. strain
PCC 6803, and close homologs (presumed to be
functionally equivalent) from other cyanobacteria, where
myxoxanthophyll biosynthesis is either known or
expected. This enzyme can act on neurosporene and so
presumably catalyzes the first step that is committed to
myxoxanthophyll [Biosynthesis of cofactors, prosthetic
groups, and carriers, Other].
Length = 492
Score = 25.8 bits (57), Expect = 8.3
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 25 GALVIY-----ESVPSASPPYVCYVTLPGGSCFGS 54
GA V Y ++P PP++ +++ GS F S
Sbjct: 320 GAFVFYLGVKRAALPVDCPPHLQFLSDHQGSLFVS 354
>gnl|CDD|226732 COG4282, SMI1, Protein involved in beta-1,3-glucan synthesis
[Carbohydrate transport and metabolism].
Length = 191
Score = 25.6 bits (56), Expect = 8.5
Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 14/60 (23%)
Query: 71 WIAR------EQENPGALGRELDQAERELETARLAGRELRFPKEKKDILMLAHTQINGGS 124
W+A PGA ++ +AE +L P + ++ L + Q +G
Sbjct: 17 WVAEHHPDLLPFLRPGATCGDIQRAEADL--------GRTLPPDVRESLAIHDGQPDGSP 68
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
0.315 0.131 0.378
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,446,028
Number of extensions: 557731
Number of successful extensions: 587
Number of sequences better than 10.0: 1
Number of HSP's gapped: 584
Number of HSP's successfully gapped: 36
Length of query: 127
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 42
Effective length of database: 7,167,512
Effective search space: 301035504
Effective search space used: 301035504
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 (21.6 bits)
S2: 53 (24.2 bits)