RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3400
(417 letters)
>gnl|CDD|197673 smart00352, POU, Found in Pit-Oct-Unc transcription factors.
Length = 75
Score = 170 bits (432), Expect = 8e-53
Identities = 64/75 (85%), Positives = 67/75 (89%)
Query: 205 EDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNM 264
+D +LEAFAKQFKQRRIKLGFTQADVGLALG LYG FSQTTICRFEALQLSFKNM
Sbjct: 1 DDDTDPRELEAFAKQFKQRRIKLGFTQADVGLALGALYGPAFSQTTICRFEALQLSFKNM 60
Query: 265 CKLKPLLQKWLEEAD 279
CKLKPLLQKWLEEA+
Sbjct: 61 CKLKPLLQKWLEEAE 75
>gnl|CDD|189427 pfam00157, Pou, Pou domain - N-terminal to homeobox domain.
Length = 75
Score = 163 bits (414), Expect = 4e-50
Identities = 62/75 (82%), Positives = 68/75 (90%)
Query: 205 EDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNM 264
+D D+LE FAK+FKQRRIKLG+TQADVGLALG LYG VFSQTTICRFEALQLSFKNM
Sbjct: 1 DDTTDLDELEQFAKEFKQRRIKLGYTQADVGLALGALYGPVFSQTTICRFEALQLSFKNM 60
Query: 265 CKLKPLLQKWLEEAD 279
CKLKPLL+KWLEEA+
Sbjct: 61 CKLKPLLEKWLEEAE 75
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 90.2 bits (225), Expect = 1e-22
Identities = 26/57 (45%), Positives = 31/57 (54%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354
R+KRT+ LE F K PSA+E LA L L + V+VWF NRR K KR
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 79.2 bits (196), Expect = 1e-18
Identities = 27/57 (47%), Positives = 31/57 (54%)
Query: 297 KRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353
KR+KRTS LE F K P PS +E LA L L + V+VWF NRR K K
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 76.9 bits (190), Expect = 6e-18
Identities = 25/58 (43%), Positives = 30/58 (51%)
Query: 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355
R+KRT LE F K P PS +E LA L L + V++WF NRR K KR
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 50.5 bits (121), Expect = 1e-07
Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 276 EEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQ 335
E ADS D + KR++ T ++ V LE F P PS+ L+ L
Sbjct: 33 EAADSEMKLERKQDGSSPPKSKRRRTTDEQLMV---LEREFEINPYPSSITRIKLSLLLN 89
Query: 336 LEKEVVRVWFCNRRQKEKR 354
+ + V++WF N+R KEK+
Sbjct: 90 MPPKSVQIWFQNKRAKEKK 108
>gnl|CDD|222221 pfam13560, HTH_31, Helix-turn-helix domain. This domain is a
helix-turn-helix domain that probably binds to DNA.
Length = 63
Score = 35.2 bits (82), Expect = 0.004
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 6/41 (14%)
Query: 215 AFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
+ ++ R + G TQA++ LG S++T+ R E
Sbjct: 1 ELGARLRRLRERAGLTQAELAERLG------VSRSTLSRIE 35
>gnl|CDD|238045 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Prokaryotic DNA binding proteins belonging to the
xenobiotic response element family of transcriptional
regulators.
Length = 58
Score = 32.5 bits (75), Expect = 0.034
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 217 AKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE 255
++ K+ R + G TQ ++ LG S++TI R E
Sbjct: 1 GERLKELRKEKGLTQEELAEKLGV------SRSTISRIE 33
>gnl|CDD|213767 TIGR03070, couple_hipB, transcriptional regulator, y4mF family.
Members of this family belong to a clade of
helix-turn-helix DNA-binding proteins, among the larger
family pfam01381 (HTH_3; Helix-turn-helix). Members are
similar in sequence to the HipB protein of E. coli.
Genes for members of the seed alignment for this protein
family were found to be closely linked to genes encoding
proteins related to HipA. The HibBA operon appears to
have some features in common with toxin-antitoxin
post-segregational killing systems.
Length = 58
Score = 31.9 bits (73), Expect = 0.049
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 214 EAFAKQFKQRRIKLGFTQADVGLALGT 240
+ + RR LG TQAD+ G
Sbjct: 1 KQIGILVRARRKALGLTQADLADLAGV 27
>gnl|CDD|177328 PHA01929, PHA01929, putative scaffolding protein.
Length = 306
Score = 33.1 bits (75), Expect = 0.21
Identities = 18/68 (26%), Positives = 22/68 (32%), Gaps = 6/68 (8%)
Query: 54 QVPSSPSPNGHPVSLSAAHNPWVSLQPGAGAD---PWSSSMPGIHNHHHPHHHQQ---SP 107
VP + +P P + P QPGA P P + PH QQ P
Sbjct: 18 NVPPAAAPTPQPNPVIQPQAPVQPGQPGAPQQLAIPTQQPQPVPTSAMTPHVVQQAPAQP 77
Query: 108 VDIKPPPD 115
PP
Sbjct: 78 APAAPPAA 85
>gnl|CDD|218163 pfam04592, SelP_N, Selenoprotein P, N terminal region. SelP is the
only known eukaryotic selenoprotein that contains
multiple selenocysteine (Sec) residues, and accounts for
more than 50% of the selenium content of rat and human
plasma. It is thought to be glycosylated. SelP may have
antioxidant properties. It can attach to epithelial
cells, and may protect vascular endothelial cells
against peroxynitrite toxicity. The high selenium
content of SelP suggests that it may be involved in
selenium intercellular transport or storage. The
promoter structure of bovine SelP suggest that it may be
involved in countering heavy metal intoxication, and may
also have a developmental function. The N-terminal
region of SelP can exist independently of the C terminal
region. Zebrafish selenoprotein Pb lacks the C terminal
Sec-rich region, and a protein encoded by the rat SelP
gene and lacking this region has also been reported.
N-terminal region contains a conserved SecxxCys motif,
which is similar to the CysxxCys found in thioredoxins.
It is speculated that the N terminal region may adopt a
thioredoxin fold and catalyze redox reactions. The
N-terminal region also contains a His-rich region, which
is thought to mediate heparin binding. Binding to
heparan proteoglycans could account for the membrane
binding properties of SelP. The function of the
bacterial members of this family is uncharcterised.
Length = 238
Score = 32.9 bits (75), Expect = 0.23
Identities = 20/68 (29%), Positives = 25/68 (36%), Gaps = 7/68 (10%)
Query: 36 PDSGELKYQHHHHHHHHHQVP-SSPSPNGHPVSLSAAHNPWVSLQPGAGADPWSSSMPGI 94
P E + H HHH HH + P+GH H S DP + P
Sbjct: 176 PVEAEPRQDHPHHHSHHEHQGHAHHHPHGHH------HPGSNSHSESQQPDPDKPTEPPS 229
Query: 95 HNHHHPHH 102
HHH +H
Sbjct: 230 GLHHHHNH 237
>gnl|CDD|233974 TIGR02682, cas_csx11, CRISPR-associated protein, Csx11 family.
Members of this uncommon, sporadically distributed
protein family are large (>900 amino acids) and strictly
associated, so far, with CRISPR-associated (Cas) gene
clusters. Nearby Cas genes always include members of the
RAMP superfamily and the six-gene CRISPR-associated RAMP
module. Species in which it is found, so far, include
three archaea (Methanosarcina mazei, M. barkeri and
Methanobacterium thermoautotrophicum) and two bacteria
(Thermodesulfovibrio yellowstonii DSM 11347 and
Sulfurihydrogenibium azorense) [Mobile and
extrachromosomal element functions, Other].
Length = 918
Score = 33.7 bits (77), Expect = 0.23
Identities = 24/129 (18%), Positives = 36/129 (27%), Gaps = 20/129 (15%)
Query: 181 LRDIQAHSPSYSQSQHPDAPSGSEEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGT 240
L SPS+ S D E +D ++ K K ++
Sbjct: 22 LHLWGKLSPSFINSNSIDKQPNFEYFNENNDCWKSALKNSKIDFRLEVNSK--------- 72
Query: 241 LYGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEADSTTGSPTSIDKIAAQGRKRKK 300
T F L+ L Q L +GS DK + R++ K
Sbjct: 73 ------EFETWDNFIKKWRGHTKKNDLQGLCQ-IL---YGASGSLNGGDKKGS-PREKVK 121
Query: 301 RTSIEVTVK 309
+ E T
Sbjct: 122 KQPKEYTWI 130
>gnl|CDD|215173 PLN02304, PLN02304, probable pectinesterase.
Length = 379
Score = 30.6 bits (69), Expect = 1.4
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 25 TSIGYPSPRSVPDSGELKYQHHHHHHHHHQVPS 57
+ I + S + S HH HHHHHH+ P
Sbjct: 21 SLISFSSKIAT--SYPHSIHHHSHHHHHHKHPD 51
Score = 29.4 bits (66), Expect = 3.6
Identities = 16/39 (41%), Positives = 19/39 (48%), Gaps = 12/39 (30%)
Query: 94 IHNHHHPHHHQQSPVDIK------------PPPDMHRTS 120
IH+H H HHH + P D K PPPD + TS
Sbjct: 37 IHHHSHHHHHHKHPDDGKKVSICDDFPPDFPPPDTNTTS 75
Score = 28.7 bits (64), Expect = 5.6
Identities = 8/14 (57%), Positives = 8/14 (57%)
Query: 45 HHHHHHHHHQVPSS 58
HHH HHHHH
Sbjct: 38 HHHSHHHHHHKHPD 51
>gnl|CDD|236641 PRK10019, PRK10019, nickel/cobalt efflux protein RcnA; Provisional.
Length = 279
Score = 29.0 bits (65), Expect = 5.0
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 43 YQHHHHHHHHHQVPSSPSPNGHPVSLSAAH 72
++HHH H HHH + + + AH
Sbjct: 133 HEHHHDHGHHHHHEHGATAEEYQDAHERAH 162
Score = 27.8 bits (62), Expect = 9.0
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 40 ELKYQHHHHHHHHHQ 54
+ ++ H H HHHHH+
Sbjct: 132 DHEHHHDHGHHHHHE 146
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 29.1 bits (65), Expect = 5.6
Identities = 5/30 (16%), Positives = 7/30 (23%)
Query: 43 YQHHHHHHHHHQVPSSPSPNGHPVSLSAAH 72
Y + H P+ L H
Sbjct: 212 YPSIRKNSRHSSNSMPSFPHSSTAVLLKRH 241
>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed.
Length = 324
Score = 28.5 bits (64), Expect = 7.3
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 192 SQSQHP---DAPSGSEEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTL 241
S+ P D P GS+E+AP D +E + + G D+ L TL
Sbjct: 211 EHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATL 263
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 28.5 bits (64), Expect = 7.5
Identities = 21/95 (22%), Positives = 27/95 (28%), Gaps = 1/95 (1%)
Query: 56 PSSPSPNGHPVSL-SAAHNPWVSLQPGAGADPWSSSMPGIHNHHHPHHHQQSPVDIKPPP 114
P+S SP+ P S P P + +D P P +SP + PPP
Sbjct: 179 PASASPSDPPSSSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPSPPP 238
Query: 115 DMHRTSHQHGGMGSPHSWHTPVVSSHYIPSGNSGA 149
P S P S G
Sbjct: 239 GPAAPPPPPVQQVPPLSTAKPTPPSASATPAPIGG 273
>gnl|CDD|176163 cd08474, PBP2_CrgA_like_5, The C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator CrgA-like, contains the type 2 periplasmic
binding fold. This CD represents the substrate binding
domain of an uncharacterized LysR-type transcriptional
regulator (LTTR) CrgA-like 5. The LTTRs are acting as
both auto-repressors and activators of target promoters,
controlling operons involved in a wide variety of
cellular processes such as amino acid biosynthesis, CO2
fixation, antibiotic resistance, degradation of aromatic
compounds, nodule formation of nitrogen-fixing bacteria,
and synthesis of virulence factors, to name a few. In
contrast to the tetrameric form of other LTTRs, CrgA
from Neisseria meningitides assembles into an octameric
ring, which can bind up to four 63-bp DNA
oligonucleotides. Phylogenetic cluster analysis showed
that the CrgA-like regulators form a subclass of the
LTTRs that function as octamers. The CrgA is an
auto-repressor of its own gene and activates the
expression of the mdaB gene which coding for an
NADPH-quinone reductase and that its action is increased
by MBL (alpha-methylene-gamma-butyrolactone), an inducer
of NADPH-quinone oxidoreductase. The structural
topology of this substrate-binding domain is most
similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 202
Score = 27.8 bits (63), Expect = 7.9
Identities = 6/23 (26%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 85 DPWSSSMPGIHNHHHPHHHQQSP 107
+ WS PG + ++P + P
Sbjct: 172 EDWSPPFPGGY-LYYPSRRRVPP 193
>gnl|CDD|238499 cd01017, AdcA, Metal binding protein AcdA. These proteins have
been shown to function in the ABC uptake of Zn2+ and
Mn2+ and in competence for genetic transformation and
adhesion. The AcdA proteins belong to the TroA
superfamily of helical backbone metal receptor proteins
that share a distinct fold and ligand binding mechanism.
They are comprised of two globular subdomains connected
by a long alpha helix and they bind their ligand in the
cleft between these domains. In addition, many of these
proteins have a low complexity region containing metal
binding histidine-rich motif (repetitive HDH sequence).
Length = 282
Score = 28.0 bits (63), Expect = 8.3
Identities = 10/43 (23%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 14 ASDLDGMNIVNTSIGYPSPRSVPDSGELKYQHHHHHHHHHQVP 56
+ + +V S G + +G ++ H H H HHH
Sbjct: 73 SLQNKKLKVVEASKGIK----LLKAGGAEHDHDHSHSHHHGDY 111
>gnl|CDD|217089 pfam02535, Zip, ZIP Zinc transporter. The ZIP family consists of
zinc transport proteins and many putative metal
transporters. The main contribution to this family is
from the Arabidopsis thaliana ZIP protein family these
proteins are responsible for zinc uptake in the plant.
Also found within this family are C. elegans proteins of
unknown function which are annotated as being similar to
human growth arrest inducible gene product, although
this protein in not found within this family.
Length = 314
Score = 28.1 bits (63), Expect = 8.7
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 44 QHHHHHHHHHQVPSSPSPNGHPVSLSA 70
HHHHH H+ S +G V A
Sbjct: 142 GPHHHHHEGHEKGESDKESGLRVRDIA 168
>gnl|CDD|133478 cd07153, Fur_like, Ferric uptake regulator(Fur) and related
metalloregulatory proteins; typically iron-dependent,
DNA-binding repressors and activators. Ferric uptake
regulator (Fur) and related metalloregulatory proteins
are iron-dependent, DNA-binding repressors and
activators mainly involved in iron metabolism. A
general model for Fur repression under iron-rich
conditions is that activated Fur (a dimer having one
Fe2+ coordinated per monomer) binds to specific DNA
sequences (Fur boxes) in the promoter region of
iron-responsive genes, hindering access of RNA
polymerase, and repressing transcription. Positive
regulation by Fur can be direct or indirect, as in the
Fur repression of an anti-sense regulatory small RNA.
Some members sense metal ions other than Fe2+. For
example, the zinc uptake regulator (Zur) responds to
Zn2+, the manganese uptake regulator (Mur) responds to
Mn2+, and the nickel uptake regulator (Nur) responds to
Ni2+. Other members sense signals other than metal
ions. For example, PerR, a metal-dependent sensor of
hydrogen peroxide. PerR regulates DNA-binding activity
through metal-based protein oxidation, and co-ordinates
Mn2+ or Fe2+ at its regulatory site. Fur family
proteins contain an N-terminal winged-helix DNA-binding
domain followed by a dimerization domain; this CD spans
both those domains.
Length = 116
Score = 26.8 bits (60), Expect = 9.4
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 37 DSGELKYQHHHHHHHHH 53
G+ +Y+ + HHHH
Sbjct: 57 GDGKARYELNTDEHHHH 73
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
0.314 0.128 0.401
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,113,654
Number of extensions: 1987794
Number of successful extensions: 2469
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2214
Number of HSP's successfully gapped: 139
Length of query: 417
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 318
Effective length of database: 6,546,556
Effective search space: 2081804808
Effective search space used: 2081804808
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: 60 (27.1 bits)