RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10675
(233 letters)
>gnl|CDD|218697 pfam05694, SBP56, 56kDa selenium binding protein (SBP56). This
family consists of several eukaryotic selenium binding
proteins as well as three sequences from archaea. The
exact function of this protein is unknown although it is
thought that SBP56 participates in late stages of
intra-Golgi protein transport. The Lotus japonicus
homologue of SBP56, LjSBP is thought to have more than
one physiological role and can be implicated in
controlling the oxidation/reduction status of target
proteins, in vesicular Golgi transport.
Length = 461
Score = 68.8 bits (169), Expect = 1e-13
Identities = 31/67 (46%), Positives = 43/67 (64%), Gaps = 6/67 (8%)
Query: 169 RQYFNFHNQLFYDLVDENFDWPE--ESGSALVKINVNTEQGGLTLDEDFIVDLGLEPNGP 226
R Y N L Y D+ F +P+ + G ++KI+V+ + GGL+LD +F VD G EP+GP
Sbjct: 387 RLYVT--NSL-YSAWDDQF-YPDGVKKGGWMLKIDVDPDNGGLSLDPNFFVDFGKEPDGP 442
Query: 227 ALAHEIR 233
A AHEIR
Sbjct: 443 ARAHEIR 449
>gnl|CDD|216059 pfam00685, Sulfotransfer_1, Sulfotransferase domain.
Length = 254
Score = 60.8 bits (148), Expect = 4e-11
Identities = 32/185 (17%), Positives = 63/185 (34%), Gaps = 40/185 (21%)
Query: 1 MNASIRLLVIVRDPVTRAISDYTQLKIHAAATSPGPVKRFEQLALRENGEINENYRPIAV 60
+ + +++ +VR+P A+S Y ++ +PG F + L N
Sbjct: 89 WDPNAKIIYLVRNPKDVAVSYYHFFRMAKILKAPGTPFEFVEDFLNGKV----NC----- 139
Query: 61 SMYHNFMYAWLEVSRVGVTKVRPATHYQVFPKEQILIVNGDRLIEDPVPELQRIERFLN- 119
Y + + W ++ P IL + + L +DP E+++I FL
Sbjct: 140 GSYFDHVKGWWKL----------------RPPGNILFLRYEDLKKDPRGEIKKIAEFLGI 183
Query: 120 ------LEPHINHDNFYFNHTKGFYC-----LKDNSMERCLRESKGR-KHVRVHPKVISK 167
L+ + H F + KG C L + + R+ + K
Sbjct: 184 PLTEEELDKIVKH--LSFENMKGNPCLNYSKLPKHEVSPFFRKGLVGDWKNYFTVEQAEK 241
Query: 168 MRQYF 172
+ +
Sbjct: 242 FDEIY 246
>gnl|CDD|227577 COG5252, COG5252, Uncharacterized conserved protein, contains
CCCH-type Zn-finger protein [General function prediction
only].
Length = 299
Score = 30.1 bits (67), Expect = 0.98
Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 3/95 (3%)
Query: 97 IVNGDRLIEDPVPELQRIERFLNLEPHINHDNFYFNHTKGFYCLKDNSMERCLRESKGRK 156
+++ D++ + E+ +E F+ LE + + F KD R L++ + ++
Sbjct: 180 VLSRDKIKDSTQVEIS-LEEFIELERQSLPEKLTPLTEENFKEWKDGRRLRILKQKEEKE 238
Query: 157 HVR--VHPKVISKMRQYFNFHNQLFYDLVDENFDW 189
R +K + F LF D V+ +W
Sbjct: 239 SARKVKGRATGTKGVELFETRRDLFKDDVEAGEEW 273
>gnl|CDD|185588 PTZ00385, PTZ00385, lysyl-tRNA synthetase; Provisional.
Length = 659
Score = 30.0 bits (67), Expect = 1.3
Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 23/95 (24%)
Query: 100 GDRLIEDPVP-ELQRIE------RFLNLEPHINHDNFYFNHTKGFYCLKDNSME------ 146
GD + D VP +QR E R L L P++ D + +GF L+DN ++
Sbjct: 162 GDIIGADGVPCRMQRGELSVAASRMLILSPYVCTDQVVCPNLRGFTVLQDNDVKYRYRFT 221
Query: 147 -----RCLRESKGRKHVRVHPKVISKMRQYFNFHN 176
C+ E+ ++HV ++ +R YFN N
Sbjct: 222 DMMTNPCVIETIKKRHV-----MLQALRDYFNERN 251
>gnl|CDD|238804 cd01570, NAPRTase_A, Nicotinate phosphoribosyltransferase
(NAPRTase), subgroup A. Nicotinate
phosphoribosyltransferase catalyses the formation of
NAMN and PPi from 5-phosphoribosy -1-pyrophosphate
(PRPP) and nicotinic acid, this is the first, and also
rate limiting, reaction in the NAD salvage synthesis.
This salvage pathway serves to recycle NAD degradation
products. This subgroup is present in bacteria and
eukaryota (except funghi).
Length = 327
Score = 28.7 bits (65), Expect = 3.0
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 10/40 (25%)
Query: 89 VFPKEQILIVNGDRLIEDPVPELQRIE-RFLNLEPHINHD 127
VFP E +L V G P+ E Q +E LNL IN
Sbjct: 98 VFPNEPLLTVEG------PLIEAQLLETLLLNL---INFQ 128
>gnl|CDD|239359 cd03061, GST_N_CLIC, GST_N family, Chloride Intracellular Channel
(CLIC) subfamily; composed of CLIC1-5, p64, parchorin
and similar proteins. They are auto-inserting,
self-assembling intracellular anion channels involved in
a wide variety of functions including regulated
secretion, cell division and apoptosis. They can exist
in both water-soluble and membrane-bound states, and are
found in various vesicles and membranes. Biochemical
studies of the C. elegans homolog, EXC-4, show that the
membrane localization domain is present in the
N-terminal part of the protein. The structure of soluble
human CLIC1 reveals that it is monomeric and it adopts a
fold similar to GSTs, containing an N-terminal domain
with a TRX fold and a C-terminal alpha helical domain.
Upon oxidation, the N-terminal domain of CLIC1 undergoes
a structural change to form a non-covalent dimer
stabilized by the formation of an intramolecular
disulfide bond between two cysteines that are far apart
in the reduced form. The CLIC1 dimer bears no similarity
to GST dimers. The redox-controlled structural
rearrangement exposes a large hydrophobic surface, which
is masked by dimerization in vitro. In vivo, this
surface may represent the docking interface of CLIC1 in
its membrane-bound state. The two cysteines in CLIC1
that form the disulfide bond in oxidizing conditions are
essential for dimerization and chloride channel
activity, however, in other subfamily members, the
second cysteine is not conserved.
Length = 91
Score = 27.0 bits (60), Expect = 3.0
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 11/59 (18%)
Query: 66 FMYAWLEVSRVGVT----KVRPATHYQVFPKEQ--ILIVNGDRLIEDPVPELQRIERFL 118
FM WL+ VT K +P + P Q L+ NG+ + D +IE FL
Sbjct: 29 FMVLWLKGVVFNVTTVDMKRKPEDLKDLAPGTQPPFLLYNGE-VKTD----NNKIEEFL 82
>gnl|CDD|153073 cd03603, CLECT_VCBS, A bacterial subgroup of the C-type lectin-like
(CTLD) domain; a subgroup of bacterial protein domains
homologous to the carbohydrate-recognition domains
(CRDs) of the C-type lectins. CLECT_VCBS: A bacterial
subgroup of the C-type lectin-like (CTLD) domain; a
subgroup of bacterial protein domains homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. Many CTLDs are calcium-dependent carbohydrate
binding modules; other CTLDs bind protein ligands,
lipids, and inorganic surfaces including CaCO3 and ice.
Bacterial CTLDs within this group are functionally
uncharacterized. Animal C-type lectins are involved in
such functions as extracellular matrix organization,
endocytosis, complement activation, pathogen
recognition, and cell-cell interactions. CTLDs may bind
a variety of carbohydrate ligands including mannose,
N-acetylglucosamine, galactose, N-acetylgalactosamine,
and fucose. CTLDs associate with each other through
several different surfaces to form dimers, trimers, or
tetramers from which ligand-binding sites project in
different orientations. In some CTLDs a loop extends to
the adjoining domain to form a loop-swapped dimer.
Length = 118
Score = 27.0 bits (60), Expect = 3.9
Identities = 12/35 (34%), Positives = 12/35 (34%), Gaps = 6/35 (17%)
Query: 179 FYDLVDENFDWP------EESGSALVKINVNTEQG 207
FY VD W E G LV IN E
Sbjct: 2 FYKFVDGGMTWEAAQTLAESLGGHLVTINSAEEND 36
>gnl|CDD|143505 cd06836, PLPDE_III_ODC_DapDC_like_1, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Uncharacterized Proteins with
similarity to Ornithine and Diaminopimelate
Decarboxylases. This subfamily contains uncharacterized
proteins with similarity to ornithine decarboxylase
(ODC) and diaminopimelate decarboxylase (DapDC). ODC and
DapDC are fold type III PLP-dependent enzymes that
contain an N-terminal PLP-binding TIM-barrel domain and
a C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. They exist as homodimers with active
sites that lie at the interface between the TIM barrel
domain of one subunit and the beta-sandwich domain of
the other subunit. ODC participates in the formation of
putrescine by catalyzing the decarboxylation of
ornithine, the first step in polyamine biosynthesis.
DapDC participates in the last step of lysine
biosynthesis, the conversion of
meso-2,6-diaminoheptanedioate to L-lysine. Proteins in
this subfamily may function as PLP-dependent
decarboxylases. Homodimer formation and the presence of
the PLP cofactor may be required for catalytic activity.
Length = 379
Score = 28.1 bits (63), Expect = 4.4
Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 20/71 (28%)
Query: 101 DRLIED-PVPELQRIERFLNLEPHINHDNFYFNHTKGFYCLKDNSMERC------LRESK 153
+R++ D P + L L IN DNF +ER +E+
Sbjct: 72 ERIVFDSPAKTRAELREALELGVAINIDNF-------------QELERIDALVAEFKEAS 118
Query: 154 GRKHVRVHPKV 164
R +RV+P+V
Sbjct: 119 SRIGLRVNPQV 129
>gnl|CDD|233696 TIGR02038, protease_degS, periplasmic serine pepetdase DegS. This
family consists of the periplasmic serine protease DegS
(HhoB), a shorter paralog of protease DO (HtrA, DegP)
and DegQ (HhoA). It is found in E. coli and several
other Proteobacteria of the gamma subdivision. It
contains a trypsin domain and a single copy of PDZ
domain (in contrast to DegP with two copies). A critical
role of this DegS is to sense stress in the periplasm
and partially degrade an inhibitor of sigma(E) [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Regulatory functions, Protein
interactions].
Length = 351
Score = 27.9 bits (62), Expect = 5.1
Identities = 13/28 (46%), Positives = 15/28 (53%)
Query: 200 INVNTEQGGLTLDEDFIVDLGLEPNGPA 227
IN QG D IV G++PNGPA
Sbjct: 264 INSVVAQGLGLPDLRGIVITGVDPNGPA 291
>gnl|CDD|234417 TIGR03958, monoFe_hyd_HmdC, 5,10-methenyltetrahydromethanopterin
hydrogenase cofactor biosynthesis protein HmdC. Members
of this protein family are HmdC, whose gene regularly
occurs in the context of genes for HmdA
(5,10-methenyltetrahydromethanopterin hydrogenase) and
the radical SAM protein HmdB involved in biosynthesis of
the HmdA cofactor. Bioinformatics suggests this protein,
a homolog of eukaryotic fibrillarin, may be involved in
biosynthesis of the guanylyl pyridinol cofactor in HmdA
[Protein fate, Protein modification and repair, Energy
metabolism, Methanogenesis].
Length = 505
Score = 27.4 bits (61), Expect = 6.9
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 13/50 (26%)
Query: 159 RVHPKVISKMRQYFNFHNQLFYDLVDENFDWPEESGSALVKINVNTEQGG 208
R+H ++I K ++Y +++ +W + S S V +NV EQGG
Sbjct: 162 RIHKRLIDKEKEY-----------LEDFEEWIKLSSS--VCVNVTEEQGG 198
>gnl|CDD|236101 PRK07803, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 626
Score = 27.7 bits (62), Expect = 7.1
Identities = 29/81 (35%), Positives = 38/81 (46%), Gaps = 18/81 (22%)
Query: 12 RDPVTRAISDYTQLKIHAAATSP-GPVKRFEQLALRENGEINENYRPIAVSMYHNFMYAW 70
RD V RAI +++K A SP G V + +A R E + P SMYH F
Sbjct: 322 RDEVARAI--NSEVK--AGRGSPHGGV--YLDIASRLPAEEIKRRLP---SMYHQFK--- 369
Query: 71 LEVSRVGVTK----VRPATHY 87
E++ V +TK V P HY
Sbjct: 370 -ELADVDITKEPMEVGPTCHY 389
>gnl|CDD|109787 pfam00743, FMO-like, Flavin-binding monooxygenase-like. This
family includes FMO proteins, cyclohexanone
mono-oxygenase and a number of different
mono-oxygenases.
Length = 532
Score = 27.5 bits (61), Expect = 7.8
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 27 IHAAATSPGPVKRF-EQLALRENGEINENYRPIAVSMYHNFMYAWLEVSRVGVTKVRPAT 85
+ A VK F E A+ E+G + E+ + + + F + +LE S V V + +
Sbjct: 292 LCGAVKVKPSVKEFTETSAIFEDGTVEEDIDVVIFATGYTFSFPFLEESLVKVETNKISL 351
Query: 86 HYQVFP 91
+ VFP
Sbjct: 352 YKYVFP 357
>gnl|CDD|239569 cd03487, RT_Bac_retron_II, RT_Bac_retron_II: Reverse transcriptases
(RTs) in bacterial retrotransposons or retrons. The
polymerase reaction of this enzyme leads to the
production of a unique RNA-DNA complex called msDNA
(multicopy single-stranded (ss)DNA) in which a small
ssDNA branches out from a small ssRNA molecule via a
2'-5'phosphodiester linkage. Bacterial retron RTs
produce cDNA corresponding to only a small portion of
the retron genome.
Length = 214
Score = 26.8 bits (60), Expect = 8.7
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 100 GDRLIEDPVPELQRIERFL--NLEPHINHDNFYFNHTKG 136
G R I P PEL+ I+R + NL + + KG
Sbjct: 5 GFRTIYAPKPELKAIQRKILSNLLSKLPVHDAAHGFVKG 43
>gnl|CDD|165792 PLN00413, PLN00413, triacylglycerol lipase.
Length = 479
Score = 26.9 bits (59), Expect = 9.7
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 9/48 (18%)
Query: 177 QLFYDLVDENFDWPEESGSALVKINVNTEQGGLTLDEDFIVDLGLEPN 224
++F +L NF WPE++ + IN N +Q V+LGL P
Sbjct: 94 KIFLNLFKGNFIWPEKASATFASINGNLDQK---------VELGLGPK 132
>gnl|CDD|217617 pfam03567, Sulfotransfer_2, Sulfotransferase family. This family
includes a variety of sulfotransferase enzymes.
Chondroitin 6-sulfotransferase catalyzes the transfer of
sulfate to position 6 of the N-acetylgalactosamine
residue of chondroitin. This family also includes
Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan
sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS)
is a co-receptor for a number of growth factors,
morphogens, and adhesion proteins. HS biosynthetic
modifications may determine the strength and outcome of
HS-ligand interactions. Mice that lack HS2ST undergo
developmental failure only after midgestation,the most
dramatic effect being the complete failure of kidney
development. Heparan sulphate 6- O -sulfotransferase
(HS6ST) catalyzes the transfer of sulphate from
adenosine 3'-phosphate, 5'-phosphosulphate to the 6th
position of the N -sulphoglucosamine residue in heparan
sulphate.
Length = 238
Score = 26.6 bits (59), Expect = 9.7
Identities = 11/45 (24%), Positives = 15/45 (33%), Gaps = 1/45 (2%)
Query: 9 VIVRDPVTRAISDYTQLKIHAAATSPGPVKRFEQLALRENGEINE 53
VRDP R +S Y K A + + +G E
Sbjct: 79 AFVRDPFERFVSAYRN-KCVGANYGSDMRCKGRKPTDDGSGVSFE 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
0.321 0.139 0.417
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,360,140
Number of extensions: 1185367
Number of successful extensions: 925
Number of sequences better than 10.0: 1
Number of HSP's gapped: 924
Number of HSP's successfully gapped: 26
Length of query: 233
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 139
Effective length of database: 6,768,326
Effective search space: 940797314
Effective search space used: 940797314
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.7 bits)