RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14414
(76 letters)
>gnl|CDD|235050 PRK02546, PRK02546, NAD(P)H-quinone oxidoreductase subunit 4;
Provisional.
Length = 525
Score = 27.7 bits (62), Expect = 0.42
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 8 DFENPDLQKVSQVSWKPK 25
DF NP LQ V SW P+
Sbjct: 59 DFSNPGLQLVESYSWLPQ 76
>gnl|CDD|221959 pfam13177, DNA_pol3_delta2, DNA polymerase III, delta subunit. DNA
polymerase III, delta subunit (EC 2.7.7.7) is required
for, along with delta' subunit, the assembly of the
processivity factor beta(2) onto primed DNA in the DNA
polymerase III holoenzyme-catalyzed reaction. The delta
subunit is also known as HolA.
Length = 161
Score = 26.4 bits (59), Expect = 1.2
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 35 PLKGHQKVAILRNIEKMVAEA 55
P +G +KV I+ + EKM A
Sbjct: 97 PFEGKKKVYIIEDAEKMTESA 117
>gnl|CDD|199836 cd10278, PQQ_MDH, Large subunit of methanol dehydrogenase (moxF).
Methanol dehydrogenase is a key enzyme in the
utilization of C1 compounds as a source of energy and
carbon by bacteria. It catalyzes the oxidation of
methanol to formaldehyde, transfering two electrons per
methanol to cytochrome c(L) as the acceptor. Methanol
dehydrogenase belongs to a family of dehydrogenases with
pyrroloquinoline quinone (PQQ) as cofactor, which also
includes dehydrogenases specific to other alcohols and
membrane-bound glucose dehydrogenases. This alignment
model for the large subunit contains an 8-bladed
beta-propeller; the functional enzyme forms a
heterotetramer composed of two large and two small
subunits.
Length = 553
Score = 26.1 bits (58), Expect = 2.0
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 5/34 (14%)
Query: 16 KVSQVSWKPKTKPTGDIEYPL----KGHQKVAIL 45
K ++ WK K P+G I P+ G Q VA+L
Sbjct: 475 KTGKLLWKFKL-PSGIIGNPITYKHDGKQYVAVL 507
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 25.1 bits (56), Expect = 4.4
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 48 IEKMVAEALQNQEE 61
IE+MV +A N EE
Sbjct: 505 IERMVKDAEANAEE 518
>gnl|CDD|238312 cd00557, Translocase_SecB, Preprotein translocase subunit SecB.
SecB is a cytoplasmic component of the multisubunit
membrane-bound enzyme termed Sec protein translocase,
which is the main constituent of the General Secretory
(type II) Pathway involved in translocation of nascent
polypeptides across the cytoplasmic membrane. SecB has
been shown to function as export-specific molecular
chaperone that selectively binds preproteins, maintains
them in a translocation competent state and delivers
them to SecA, the membrane-bound ATPase, that drives
the translocation reaction. In solution, SecB exists as
homotetramer, which is organized as a dimer of dimers.
Length = 131
Score = 24.8 bits (54), Expect = 5.0
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 9 FENPDLQKVSQVSWKPKTKPTGDIE 33
FE P+ + Q WKP+ D E
Sbjct: 13 FEAPNAPHLFQKDWKPRLNLDLDTE 37
>gnl|CDD|99796 cd06199, SiR, Cytochrome p450- like alpha subunits of E. coli
sulfite reductase (SiR) multimerize with beta subunits
to catalyze the NADPH dependent reduction of sulfite to
sulfide. Beta subunits have an Fe4S4 cluster and a
siroheme, while the alpha subunits (cysJ gene) are of
the cytochrome p450 (CyPor) family having FAD and FMN
as prosthetic groups and utilizing NADPH. Cypor
(including cyt -450 reductase, nitric oxide synthase,
and methionine synthase reductase) are ferredoxin
reductase (FNR)-like proteins with an additional
N-terminal FMN domain and a connecting sub-domain
inserted within the flavin binding portion of the
FNR-like domain. The connecting domain orients the
N-terminal FMN domain with the C-terminal FNR domain.
Length = 360
Score = 24.9 bits (55), Expect = 5.1
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 36 LKGHQKVAILRNIEKMVAEALQNQEEVSHLMRALVLGRYT 75
L G + V+ + + EAL E++ L+ AL+
Sbjct: 57 LSGDEPVSTVGGGTLPLREALIKHYEITTLLLALLESYAA 96
>gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated.
Length = 313
Score = 24.6 bits (54), Expect = 5.4
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 35 PLKGHQKVAILRNIEKMVAEALQN 58
P +G +KV I+ N EKM +A QN
Sbjct: 89 PYEGDKKVIIIYNSEKMTEQA-QN 111
>gnl|CDD|187561 cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and
HSCARG (an NADPH sensor) like proteins, atypical (a)
SDRs. NmrA and HSCARG like proteins. NmrA is a negative
transcriptional regulator of various fungi, involved in
the post-translational modulation of the GATA-type
transcription factor AreA. NmrA lacks the canonical
GXXGXXG NAD-binding motif and has altered residues at
the catalytic triad, including a Met instead of the
critical Tyr residue. NmrA may bind nucleotides but
appears to lack any dehydrogenase activity. HSCARG has
been identified as a putative NADP-sensing molecule, and
redistributes and restructures in response to NADPH/NADP
ratios. Like NmrA, it lacks most of the active site
residues of the SDR family, but has an NAD(P)-binding
motif similar to the extended SDR family, GXXGXXG. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical SDRs
are distinct from classical SDRs. 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 15-hydroxyprostaglandin dehydrogenase numbering).
In addition to the Tyr and Lys, there is often an
upstream Ser and/or an Asn, 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. In
addition to the Rossmann fold core region typical of all
SDRs, extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids, 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 ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif.
Length = 242
Score = 24.5 bits (54), Expect = 5.7
Identities = 8/58 (13%), Positives = 17/58 (29%), Gaps = 4/58 (6%)
Query: 22 WKPKTKPTGDIEYPLKGHQKVAI----LRNIEKMVAEALQNQEEVSHLMRALVLGRYT 75
P+ G + L + + +I VA ++ + + L T
Sbjct: 153 PAPQKMEDGTLTLVLPLDPDTKLPMIDVADIGPAVAAIFKDPAKFNGKTIELAGDELT 210
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 24.5 bits (54), Expect = 5.8
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 45 LRNIEKMVAEALQNQEEVSHLMRAL 69
L + +++ EAL EE S +RA
Sbjct: 264 LSELAELLEEALYELEEASEELRAY 288
>gnl|CDD|233830 TIGR02350, prok_dnaK, chaperone protein DnaK. Members of this
family are the chaperone DnaK, of the DnaK-DnaJ-GrpE
chaperone system. All members of the seed alignment were
taken from completely sequenced bacterial or archaeal
genomes and (except for Mycoplasma sequence) found
clustered with other genes of this systems. This model
excludes DnaK homologs that are not DnaK itself, such as
the heat shock cognate protein HscA (TIGR01991).
However, it is not designed to distinguish among DnaK
paralogs in eukaryotes. Note that a number of dnaK genes
have shadow ORFs in the same reverse (relative to dnaK)
reading frame, a few of which have been assigned
glutamate dehydrogenase activity. The significance of
this observation is unclear; lengths of such shadow ORFs
are highly variable as if the presumptive protein
product is not conserved [Protein fate, Protein folding
and stabilization].
Length = 595
Score = 24.6 bits (54), Expect = 7.2
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 48 IEKMVAEALQNQEE 61
IE+MV EA N EE
Sbjct: 503 IERMVKEAEANAEE 516
>gnl|CDD|235798 PRK06416, PRK06416, dihydrolipoamide dehydrogenase; Reviewed.
Length = 462
Score = 24.3 bits (54), Expect = 7.6
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 6 KSDFENPDLQKVSQVSWKPKTKPTGDIEYPLKGHQKVAILR 46
K++ D +KV + + TG +E LK + KV I+R
Sbjct: 72 KAENVGIDFKKVQEWKNGVVNRLTGGVEGLLKKN-KVDIIR 111
>gnl|CDD|217492 pfam03321, GH3, GH3 auxin-responsive promoter.
Length = 513
Score = 24.2 bits (53), Expect = 8.1
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 43 AILRNIEKMVAEALQNQEEVSHLMRALVLGRYTE 76
+L+ IE + A++ QEEV L L TE
Sbjct: 1 KVLKEIELFTSNAVEVQEEV--LREILERNADTE 32
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 0.367
Gapped
Lambda K H
0.267 0.0617 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,822,536
Number of extensions: 281479
Number of successful extensions: 203
Number of sequences better than 10.0: 1
Number of HSP's gapped: 203
Number of HSP's successfully gapped: 14
Length of query: 76
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 30
Effective length of database: 8,897,318
Effective search space: 266919540
Effective search space used: 266919540
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: 53 (24.4 bits)