RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2601
(132 letters)
>gnl|CDD|202715 pfam03645, Tctex-1, Tctex-1 family. Tctex-1 is a dynein light
chain. It has been shown that Tctex-1 can bind to the
cytoplasmic tail of rhodopsin. C-terminal rhodopsin
mutations responsible for retinitis pigmentosa inhibit
this interaction.
Length = 101
Score = 128 bits (324), Expect = 7e-40
Identities = 43/101 (42%), Positives = 69/101 (68%), Gaps = 1/101 (0%)
Query: 33 VDEISCIIKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLD-KPFKYVVNGTVMQK 91
D++ IIKE +E+ +GG Y+ KV + ++ E I+ L +L K +KYVV T+ QK
Sbjct: 1 PDKVKEIIKEVLEEKLGGVEYDHEKVQQWSKEISEEILKRLKELGFKRYKYVVQVTIGQK 60
Query: 92 LGAGLHTSSSCLWDDNTDGSCTVRWENKTMYCIVSVYALAL 132
G G+H +S CLWD NTDGS +V++ENK+++C+V+V+ + +
Sbjct: 61 NGQGIHVASRCLWDPNTDGSASVKYENKSLFCVVTVFGVYI 101
>gnl|CDD|239362 cd03064, TRX_Fd_NuoE, TRX-like [2Fe-2S] Ferredoxin (Fd) family,
NADH:ubiquinone oxidoreductase (Nuo) subunit E
subfamily; Nuo, also called respiratory chain Complex
1, is the entry point for electrons into the
respiratory chains of bacteria and the mitochondria of
eukaryotes. It is a multisubunit complex with at least
14 core subunits. It catalyzes the electron transfer of
NADH to quinone coupled with the transfer of protons
across the membrane, providing the proton motive force
required for energy-consuming processes. Electrons are
transferred from NADH to quinone through a chain of
iron-sulfur clusters in Nuo, including the [2Fe-2S]
cluster present in NuoE core subunit, also called the
24 kD subunit of Complex 1. This subfamily also include
formate dehydrogenases, NiFe hydrogenases and
NAD-reducing hydrogenases, that contain a NuoE domain.
A subset of these proteins contain both NuoE and NuoF
in a single chain. NuoF, also called the 51 kD subunit
of Complex 1, contains one [4Fe-4S] cluster and also
binds the NADH substrate and FMN.
Length = 80
Score = 26.3 bits (59), Expect = 2.4
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 22 PGGTTEDSKFAVDEISCI 39
PG TT D +F ++E+ C+
Sbjct: 32 PGETTPDGRFTLEEVECL 49
>gnl|CDD|213409 cd12216, Csn2_like, CRISPR/Cas system-associated protein Csn2.
Csn2 is a Nmeni subtype-specific Cas protein, which may
function in the adaptation process which mediates the
incorporation of foreign nucleic acids into the
microbial host genome. Csn 2 may interact directly with
double-stranded DNA. CRISPR (Clustered Regularly
Interspaced Short Palindromic Repeats) and associated
Cas proteins comprise a system for heritable host
defense by prokaryotic cells against phage and other
foreign DNA. Csn2 has been predicted to be a functional
analog of Cas4 based on anti-correlated phyletic
patterns; also known as SPy1049 family.
Length = 217
Score = 26.6 bits (59), Expect = 3.7
Identities = 17/70 (24%), Positives = 27/70 (38%)
Query: 40 IKEAIEDCIGGNTYNSAKVSTYVSQVVETIMANLIKLDKPFKYVVNGTVMQKLGAGLHTS 99
I A+ I N + V Q+ I A LI ++ PF+ + + L A +
Sbjct: 78 IYSALSKSITDPQENKGHLEKLVEQITLIIEAELIDINLPFEVSYDLDLELLLKAKNISP 137
Query: 100 SSCLWDDNTD 109
S W + D
Sbjct: 138 ESGEWVNIFD 147
>gnl|CDD|143312 cd07688, IgC_TCR_alpha, T cell receptor (TCR) alpha chain
immunoglobulin domain. IgC_TCR_alpha: Constant domain
of the alpha chain of alpha/beta T-cell antigen
receptors (TCRs). TCRs mediate antigen recognition by T
lymphocytes, and are composed of alpha and beta, or
gamma and delta, polypeptide chains with variable (V)
and constant (C) regions. This group includes the
variable domain of the alpha chain. Alpha/beta TCRs
recognize antigen as peptide fragments presented by
major histocompatibility complex (MHC) molecules. The
antigen binding site is formed by the variable domains
of the alpha and beta chains, located at the N-terminus
of each chain. Alpha/beta TCRs recognize antigens
differently from gamma/delta TCRs.
Length = 81
Score = 25.6 bits (56), Expect = 3.9
Identities = 8/38 (21%), Positives = 14/38 (36%)
Query: 82 YVVNGTVMQKLGAGLHTSSSCLWDDNTDGSCTVRWENK 119
+ N TV+ ++ + W D TD C +
Sbjct: 39 FKTNTTVLDMSAMDSKSNGAVAWSDCTDFECESTFGGT 76
>gnl|CDD|216393 pfam01257, Complex1_24kDa, Respiratory-chain NADH dehydrogenase 24
Kd subunit.
Length = 145
Score = 26.2 bits (59), Expect = 3.9
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 22 PGGTTEDSKFAVDEISCI 39
PG TT D KF ++E+ C+
Sbjct: 96 PGETTPDGKFTLEEVECL 113
>gnl|CDD|188649 cd09817, linoleate_diol_synthase_like, Linoleate (8R)-dioxygenase
and related enzymes. These fungal enzymes, related to
animal heme peroxidases, catalyze the oxygenation of
linoleate and similar targets. Linoleate
(8R)-dioxygenase, also called linoleate:oxygen
7S,8S-oxidoreductase, generates
(9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate as a
product. Other members are 5,8-linoleate dioxygenase
(LDS, ppoA) and linoleate 10R-dioxygenase (ppoC),
involved in the biosynthesis of oxylipins.
Length = 550
Score = 26.9 bits (60), Expect = 3.9
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 27 EDSKFAVDEISCIIKEAIEDCIGG 50
D +F +++ I+K++IED G
Sbjct: 339 PDGRFRDEDLVRILKDSIEDPAGA 362
>gnl|CDD|239381 cd03083, TRX_Fd_NuoE_hoxF, TRX-like [2Fe-2S] Ferredoxin (Fd)
family, NADH:ubiquinone oxidoreductase (Nuo) subunit E
subfamily, hoxF; composed of proteins similar to the
NAD-reducing hydrogenase (hoxS) alpha subunit of
Alcaligenes eutrophus H16. HoxS is a cytoplasmic
hydrogenase catalyzing the oxidation of molecular
hydrogen accompanied by the reduction of NAD. It is
composed of four structural subunits encoded by the
genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or
alpha subunit) is a fusion protein containing an
N-terminal NuoE-like domain and a C-terminal NuoF
domain. NuoE and NuoF are components of Nuo, a
multisubunit complex catalyzing the electron transfer
of NADH to quinone coupled with the transfer of protons
across the membrane. Electrons are transferred from
NADH to quinone through a chain of iron-sulfur clusters
in Nuo, including the [2Fe-2S] cluster in NuoE and the
[4Fe-4S] cluster in NuoF. In addition, NuoF is also the
NADH- and FMN-binding subunit. HoxF may be involved in
the electron transport chain during the NAD-dependent
oxidation of hydrogen through its NuoF domain. The
NuoE-like domain of hoxF contains only one conserved
cysteine in its putative active site, compared to four
cysteines in NuoE, and may have lost the ability to
bind [2Fe-2S] clusters.
Length = 80
Score = 25.4 bits (56), Expect = 4.7
Identities = 5/18 (27%), Positives = 6/18 (33%)
Query: 22 PGGTTEDSKFAVDEISCI 39
G ED + SC
Sbjct: 32 FGEVDEDGMVGLFFTSCT 49
>gnl|CDD|181024 PRK07539, PRK07539, NADH dehydrogenase subunit E; Validated.
Length = 154
Score = 25.5 bits (57), Expect = 8.2
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 21 APGGTTEDSKFAVDEISCI 39
PG TT D +F + E+ C+
Sbjct: 104 KPGETTADGRFTLLEVECL 122
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 0.126 0.367
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,978,495
Number of extensions: 476130
Number of successful extensions: 280
Number of sequences better than 10.0: 1
Number of HSP's gapped: 279
Number of HSP's successfully gapped: 9
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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 (22.0 bits)
S2: 53 (24.1 bits)