RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17710
(75 letters)
>gnl|CDD|236629 PRK09849, PRK09849, putative oxidoreductase; Provisional.
Length = 702
Score = 29.6 bits (67), Expect = 0.11
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 37 KLVDYLMDWVLGSANQVTIPPTP---GESFVSISR 68
+L DY++ ++G+ N +P TP E SR
Sbjct: 220 RLNDYMLTELIGANNNHVVPSTPQSWAEYSDPGSR 254
>gnl|CDD|237416 PRK13532, PRK13532, nitrate reductase catalytic subunit;
Provisional.
Length = 830
Score = 29.5 bits (67), Expect = 0.11
Identities = 11/26 (42%), Positives = 12/26 (46%), Gaps = 4/26 (15%)
Query: 54 TIPPTPGESFVSISRDL----LKFIW 75
TIPP PG V+ R L L W
Sbjct: 454 TIPPKPGYHAVAQDRMLKDGKLNAYW 479
>gnl|CDD|162284 TIGR01282, nifD, nitrogenase molybdenum-iron protein alpha chain.
Nitrogenase consists of alpha (NifD) and beta (NifK)
subunits of the molybdenum-iron protein and an
ATP-binding iron-sulfur protein (NifH). This model
describes a large clade of NifD proteins, but excludes a
lineage that contains putative NifD and NifD homologs
from species with vanadium-dependent nitrogenases
[Central intermediary metabolism, Nitrogen fixation].
Length = 466
Score = 26.9 bits (60), Expect = 0.87
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 40 DYLMDWVLGSANQVTIPPTP 59
D + DWVLG ++ PTP
Sbjct: 188 DAVRDWVLGKGDKEKFEPTP 207
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 26.2 bits (58), Expect = 1.5
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 16 IEAMMRRRDDLAFRREMSFR 35
E RR +L RE+ FR
Sbjct: 196 PEEAKARRAELRKMRELLFR 215
>gnl|CDD|130767 TIGR01706, NAPA, periplasmic nitrate reductase, large subunit.
This model represents the large subunit of a family of
nitrate reductases found in proteobacteria which are
localized to the periplasm. This subunit binds
molybdopterin and contains a twin-arginine motif at the
N-terminus. The protein associates with NapB, a soluble
heme-containing protein and NapC, a membrane-bound
cytochrome c. The periplasmic nitrate reductases are not
involved in the assimilation of nitrogen, and are not
directly involved in the formation of electrochemical
gradients (i.e. respiration) either. Rather, the purpose
of this enzyme is either dissimilatory (i.e. to dispose
of excess reductive equivalents) or indirectly
respiratory by virtue of the consumption of electrons
derived from NADH via the proton translocating NADH
dehydrogenase. The enzymes from Alicagenes eutrophus and
Paracoccus pantotrophus have been characterized. In E.
coli (as well as other organisms) this gene is part of a
large nitrate reduction operon (napFDAGHBC) [Energy
metabolism, Aerobic, Energy metabolism, Electron
transport, Central intermediary metabolism, Nitrogen
metabolism].
Length = 830
Score = 26.4 bits (58), Expect = 1.5
Identities = 11/26 (42%), Positives = 12/26 (46%), Gaps = 4/26 (15%)
Query: 54 TIPPTPGESFVSISRDL----LKFIW 75
TIP PG V+ R L L F W
Sbjct: 454 TIPEKPGLHAVAQDRALKDGKLNFYW 479
>gnl|CDD|239391 cd03117, alpha_CA_IV_XV_like, Carbonic anhydrase alpha, CA_IV,
CA_XV, like isozymes. Carbonic anhydrases (CAs) are
zinc-containing enzymes that catalyze the reversible
hydration of carbon dioxide in a two-step mechanism: a
nucleophilic attack of a zinc-bound hydroxide ion on
carbon dioxide, followed by the regeneration of the
active site by ionization of the zinc-bound water
molecule and removal of a proton from the active site.
They are ubiquitous enzymes involved in fundamental
processes like photosynthesis, respiration, pH
homeostasis and ion transport. There are three
evolutionary distinct groups - alpha, beta and gamma
carbonic anhydrases - which show no significant sequence
identity or structural similarity. Most alpha CAs are
monomeric enzymes. The zinc ion is complexed by three
histidine residues. This subgroup, restricted to
animals, contains isozyme IV and similar proteins such
as mouse CA XV. Isozymes IV is attached to membranes via
a glycosylphosphatidylinositol (GPI) tail. In mammals,
Isozyme IV plays crucial roles in kidney and lung
function, amongst others. This subgroup also contains
the dual domain CA from the giant clam, Tridacna gigas.
T. gigas CA plays a role in the movement of inorganic
carbon from the surrounding seawater to the symbiotic
algae found in the clam's tissues. CA XV is expressed in
several species but not in humans or chimps. Similar to
isozyme CA IV, CA XV attaches to membranes via a GPI
tail.
Length = 234
Score = 25.7 bits (57), Expect = 2.6
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 11/81 (13%)
Query: 1 MTVHAVHIKTKLCNLIEAMMRRRDDLA----FRREMSFRNK----LVDYLMDWVLGSANQ 52
M +H VHIK +L+EA+ D LA F E N L+ L + +
Sbjct: 91 MELHIVHIKESYNSLLEALK-DSDGLAVLGFFIEEGEEENTNFDPLISALSN-IPQKGGS 148
Query: 53 VTIPPTPGESFVSISRDLLKF 73
+ P S + S L K+
Sbjct: 149 TNLTPFSLRSLLP-SVLLTKY 168
>gnl|CDD|221293 pfam11890, DUF3410, Domain of unknown function (DUF3410). This
domain is functionally uncharacterized. This domain is
found in bacteria. This presumed domain is about 90
amino acids in length. This domain is found associated
with pfam02826, pfam00389. This domain has a conserved
RRE sequence motif.
Length = 81
Score = 24.6 bits (54), Expect = 3.4
Identities = 10/21 (47%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 22 RRDDLAFRREMSFRNKLVDYL 42
RRDD A RR + DYL
Sbjct: 32 RRDDAALRRNLERPGGF-DYL 51
>gnl|CDD|130819 TIGR01758, MDH_euk_cyt, malate dehydrogenase, NAD-dependent. This
model represents the NAD-dependent cytosolic malate
dehydrogenase from eukaryotes. The enzyme from pig has
been studied by X-ray crystallography.
Length = 324
Score = 25.2 bits (55), Expect = 3.7
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 9/38 (23%)
Query: 30 REMSFRNKLVDYLMDWVLGSANQVTIPPTPGESFVSIS 67
+S VD + DWVLG TP +FVS+
Sbjct: 237 SALSAAKAAVDQMHDWVLG---------TPEGTFVSMG 265
>gnl|CDD|143456 cd07138, ALDH_CddD_SSP0762, Rhodococcus ruber 6-oxolauric acid
dehydrogenase-like. The 6-oxolauric acid dehydrogenase
(CddD) from Rhodococcus ruber SC1 which converts
6-oxolauric acid to dodecanedioic acid, and the
aldehyde dehydrogenase (locus SSP0762) from
Staphylococcus saprophyticus subsp. saprophyticus ATCC
15305 and other similar sequences, are included in this
CD.
Length = 466
Score = 25.2 bits (56), Expect = 4.0
Identities = 8/20 (40%), Positives = 10/20 (50%), Gaps = 2/20 (10%)
Query: 15 LIEAMMRRRDDLA--FRREM 32
+ EA R D+LA EM
Sbjct: 67 IAEAYEARADELAQAITLEM 86
>gnl|CDD|133421 cd01336, MDH_cytoplasmic_cytosolic, Cytoplasmic and cytosolic
Malate dehydrogenases. MDH is one of the key enzymes in
the citric acid cycle, facilitating both the conversion
of malate to oxaloacetate and replenishing levels of
oxalacetate by reductive carboxylation of pyruvate.
Members of this subfamily are eukaryotic MDHs localized
to the cytoplasm and cytosol. MDHs are part of the
NAD(P)-binding Rossmann fold superfamily, which includes
a wide variety of protein families including the
NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding potassium
channel domains, among others.
Length = 325
Score = 24.5 bits (54), Expect = 5.7
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 9/36 (25%)
Query: 32 MSFRNKLVDYLMDWVLGSANQVTIPPTPGESFVSIS 67
MS + D++ DW G TP FVS+
Sbjct: 242 MSAAKAICDHVHDWWFG---------TPEGEFVSMG 268
>gnl|CDD|224471 COG1554, ATH1, Trehalose and maltose hydrolases (possible
phosphorylases) [Carbohydrate transport and metabolism].
Length = 772
Score = 24.2 bits (53), Expect = 7.2
Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 20 MRRRDDLAFRREMSFRNKLVDYLMDWVLGSANQVTIPPTPGESFVSISR 68
+ + L++ RE+ + L+ + W + Q+T+ E FVS+++
Sbjct: 98 LSAGEVLSYERELDMKKGLLTRSLRWRSPAGKQITL---TSERFVSLAQ 143
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
0.328 0.138 0.429
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,913,350
Number of extensions: 299930
Number of successful extensions: 330
Number of sequences better than 10.0: 1
Number of HSP's gapped: 330
Number of HSP's successfully gapped: 12
Length of query: 75
Length of database: 10,937,602
Length adjustment: 45
Effective length of query: 30
Effective length of database: 8,941,672
Effective search space: 268250160
Effective search space used: 268250160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)