RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14089
(333 letters)
>gnl|CDD|192445 pfam10018, Med4, Vitamin-D-receptor interacting Mediator subunit 4.
Members of this family function as part of the Mediator
(Med) complex, which links DNA-bound transcriptional
regulators and the general transcription machinery,
particularly the RNA polymerase II enzyme. They play a
role in basal transcription by mediating activation or
repression according to the specific complement of
transcriptional regulators bound to the promoter.
Length = 176
Score = 79.4 bits (196), Expect = 1e-17
Identities = 39/95 (41%), Positives = 46/95 (48%), Gaps = 10/95 (10%)
Query: 188 NEATAIFQAKQKLQSINKANKRPVSSEELIKYAHRISSSNAV--------CAPLTWQP-- 237
EA + L SINKANKR VSSEEL+KYAHRIS + AP W
Sbjct: 53 KEAEKELRTLPDLSSINKANKRKVSSEELLKYAHRISKFTSAPPTVSSGAIAPNNWIAPL 112
Query: 238 GDPRRPYPTDIEMRVGFLGRLNDSPLNGHLLPQQS 272
GD RP+P + EMR G L + + G P
Sbjct: 113 GDLFRPWPAEDEMRRGLLAQSSLLSKEGIEPPGFD 147
>gnl|CDD|133450 cd05211, NAD_bind_Glu_Leu_Phe_Val, NAD(P) binding domain of
glutamate dehydrogenase, leucine dehydrogenase,
phenylalanine dehydrogenase, and valine dehydrogenase.
Amino acid dehydrogenase (DH) is a widely distributed
family of enzymes that catalyzes the oxidative
deamination of an amino acid to its keto acid and
ammonia with concomitant reduction of NAD(P)+. This
subfamily includes glutamate, leucine, phenylalanine,
and valine DHs. Glutamate DH is a multi-domain enzyme
that catalyzes the reaction from glutamate to
2-oxyoglutarate and ammonia in the presence of NAD or
NADP. It is present in all organisms. Enzymes involved
in ammonia assimilation are typically NADP+-dependent,
while those involved in glutamate catabolism are
generally NAD+-dependent. As in other NAD+-dependent
DHs, monomers in this family have 2 domains separated by
a deep cleft. Here the c-terminal domain contains a
modified NAD-binding Rossmann fold with 7 rather than
the usual 6 beta strands and one strand anti-parrallel
to the others. Amino acid DH-like NAD(P)-binding domains
are members of the Rossmann fold superfamily and include
glutamate, leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 217
Score = 31.0 bits (70), Expect = 0.58
Identities = 15/79 (18%), Positives = 23/79 (29%)
Query: 119 IDDIELVAKKKQEAHNHLQKTVVYFNKNEVVKQSFRIEIEEFTKKSKNASTAGFEDAHGV 178
I EL+ + K YF ++ I + A A V
Sbjct: 64 ITTEELINYAVALGGSARVKVQDYFPGEAILGLDVDIFAPCALGNVIDLENAKKLKAKVV 123
Query: 179 WESASGSNKNEATAIFQAK 197
E A+ +EA I +
Sbjct: 124 AEGANNPTTDEALRILHER 142
>gnl|CDD|237037 PRK12285, PRK12285, tryptophanyl-tRNA synthetase; Reviewed.
Length = 368
Score = 30.6 bits (70), Expect = 1.2
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 85 KPSRTQIFSRYTPGYHFSNMSSKNISTGEKLLSLIDDIELVAKK 128
KPS + ++ PG MSS S E + L DD E V KK
Sbjct: 235 KPS--STYHKFMPGLTGGKMSS---SKPESAIYLTDDPETVKKK 273
>gnl|CDD|143420 cd07102, ALDH_EDX86601, Uncharacterized aldehyde dehydrogenase of
Synechococcus sp. PCC 7335 (EDX86601). Uncharacterized
aldehyde dehydrogenase of Synechococcus sp. PCC 7335
(locus EDX86601) and other similar sequences, are
present in this CD.
Length = 452
Score = 29.9 bits (68), Expect = 2.1
Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 10/71 (14%)
Query: 194 FQAKQKLQSINKANK--RPVSSEELIKYAHR-----ISSSNAVCAPLTWQPGDPRRPYPT 246
+ L+ A K R V EE R ++++ + LTWQ G P
Sbjct: 18 EAVRAALERARAAQKGWRAVPLEERKAIVTRAVELLAANTDEIAEELTWQMGRPIAQAGG 77
Query: 247 DIEMRVGFLGR 257
+I G L R
Sbjct: 78 EIR---GMLER 85
>gnl|CDD|237609 PRK14096, pgi, glucose-6-phosphate isomerase; Provisional.
Length = 528
Score = 28.7 bits (65), Expect = 5.5
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 10/90 (11%)
Query: 150 KQSFRIEIEEFTKKSKNASTAGFEDAHGVWESASGSN----------KNEATAIFQAKQK 199
+QS I I E ++ A A FE A G++ S N K A AI ++K
Sbjct: 408 RQSITITIPEVNPRTLGALIALFERAVGLYASLVNINAYHQPGVEAGKKAAAAILDLQKK 467
Query: 200 LQSINKANKRPVSSEELIKYAHRISSSNAV 229
++ + K + +S EE+ +
Sbjct: 468 VEELLKEDGGELSIEEIAAALGAPEQVETI 497
>gnl|CDD|234774 PRK00464, nrdR, transcriptional regulator NrdR; Validated.
Length = 154
Score = 27.8 bits (63), Expect = 5.9
Identities = 12/29 (41%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 197 KQKL-QSINKA-NKRPVSSEELIKYAHRI 223
++KL + + +A KRPVSSE++ RI
Sbjct: 63 REKLRRGLRRACEKRPVSSEQIEAAVSRI 91
>gnl|CDD|215999 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family. This
family includes Ribosomal L4/L1 from eukaryotes and
archaebacteria and L4 from eubacteria. L4 from yeast has
been shown to bind rRNA.
Length = 190
Score = 27.8 bits (63), Expect = 6.0
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 113 EKLLSLIDDIELVAKKKQEAHNHLQK--------TVVYFNKNEVVKQSFR 154
E L ++DD EL K ++A L+ +V K+E + S R
Sbjct: 104 EGKLVVVDDFELEIPKTKDAVKLLKNLGLKNKKVLIVVDEKDENLYLSAR 153
>gnl|CDD|240641 cd12164, GDH_like_2, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
also known as hydroxypyruvate reductase) and other
enzymes of the 2-hydroxyacid dehydrogenase family. GDH
catalyzes the reversible reaction of (R)-glycerate +
NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid
dehydrogenases catalyze the conversion of a wide variety
of D-2-hydroxy acids to their corresponding keto acids.
The general mechanism is (R)-lactate + acceptor to
pyruvate + reduced acceptor. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 306
Score = 28.2 bits (64), Expect = 6.3
Identities = 9/22 (40%), Positives = 10/22 (45%), Gaps = 4/22 (18%)
Query: 235 WQPGDPRRPYPTDIEMRVGFLG 256
W+P R E RVG LG
Sbjct: 122 WKPLPQRPAA----ERRVGVLG 139
>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 = 28.1 bits (63), Expect = 6.6
Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 4/25 (16%)
Query: 118 LI-DDIELVAKKKQEAHNHLQKTVV 141
LI DDIE VAKK + K VV
Sbjct: 146 LIGDDIEAVAKKASKELG---KPVV 167
>gnl|CDD|238935 cd01976, Nitrogenase_MoFe_alpha, Nitrogenase_MoFe_alpha_II:
Nitrogenase MoFe protein, beta subunit. A group of
proteins similar to the alpha subunit of the MoFe
protein of the molybdenum (Mo-) nitrogenase. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen to ammonia. The Mo-nitrogenase is the most
widespread and best characterized of these systems.
Mo-nitrogenase consists of the MoFe protein (component
1) and the Fe protein (component 2). MoFe is an
alpha2beta2 tetramer. Each alphabeta pair of MoFe
contains one P-cluster (at the alphabeta interface) and,
one molecule of iron molybdenum cofactor (FeMoco)
contained within the alpha subunit. The Fe protein
contains a single [4Fe-4S] cluster. Electrons are
transferred from the [4Fe-4S] cluster of the Fe protein
to the P-cluster of the MoFe and in turn to FeMoCo, the
site of substrate reduction.
Length = 421
Score = 27.7 bits (62), Expect = 10.0
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 4/28 (14%)
Query: 118 LI-DDIELVAKKKQEAHNHLQKTVVYFN 144
LI DDIE VA+K + VV
Sbjct: 113 LIGDDIEAVARKASKEL---GIPVVPVR 137
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
0.309 0.123 0.343
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,575,291
Number of extensions: 1398842
Number of successful extensions: 980
Number of sequences better than 10.0: 1
Number of HSP's gapped: 978
Number of HSP's successfully gapped: 19
Length of query: 333
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 236
Effective length of database: 6,635,264
Effective search space: 1565922304
Effective search space used: 1565922304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 59 (26.6 bits)