RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16400
(145 letters)
>gnl|CDD|234471 TIGR04104, cxxc_20_cxxc, cxxc_20_cxxc protein. This small,
uncommon, poorly conserved protein is found primarily
in the Firmicutes. It features are pair of CxxC motifs
separated by about 20 amino acids, followed by a highly
hydrophobic region of about 45 amino acids. It has no
conserved gene neighborhood, and its function is
unknown.
Length = 94
Score = 33.1 bits (76), Expect = 0.010
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 52 SCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHC 86
C++C +++ +K LK +F P+ CP+C
Sbjct: 2 ICKNCNEKFSYKELLKS--LF--SLYRPIK-CPNC 31
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys.
The C2H2 zinc finger is composed of two short beta
strands followed by an alpha helix. The amino terminal
part of the helix binds the major groove in DNA binding
zinc fingers. The accepted consensus binding sequence
for Sp1 is usually defined by the asymmetric
hexanucleotide core GGGCGG but this sequence does not
include, among others, the GAG (=CTC) repeat that
constitutes a high-affinity site for Sp1 binding to the
wt1 promoter.
Length = 22
Score = 28.9 bits (65), Expect = 0.093
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 52 SCQHCGKRYRWKSTLKRH 69
C CGK + KS LKRH
Sbjct: 1 KCPDCGKSFSRKSNLKRH 18
Score = 27.3 bits (61), Expect = 0.46
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 82 QCPHCDYRAKQSGNLRVHIRK 102
+CP C + NL+ H+R
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 28.0 bits (62), Expect = 0.24
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 81 HQCPHCDYRAKQSGNLRVHIRKYH 104
+CP C L+ H+RK+H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 25.7 bits (56), Expect = 1.4
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 51 YSCQHCGKRYRWKSTLKRH 69
+ C CGK + K LKRH
Sbjct: 1 FKCPLCGKSFSSKDALKRH 19
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 27.8 bits (62), Expect = 0.28
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 81 HQCPHCDYRAKQSGNLRVHIRK 102
++CP C K LR H+R
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
Score = 27.8 bits (62), Expect = 0.29
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 51 YSCQHCGKRYRWKSTLKRH 69
Y C CGK ++ KS L+ H
Sbjct: 1 YRCPECGKVFKSKSALREH 19
>gnl|CDD|234777 PRK00481, PRK00481, NAD-dependent deacetylase; Provisional.
Length = 242
Score = 30.1 bits (69), Expect = 0.33
Identities = 12/48 (25%), Positives = 15/48 (31%), Gaps = 16/48 (33%)
Query: 53 CQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHI 100
C CG+ Y L K +CP C G LR +
Sbjct: 125 CTKCGQTYDLDEYL----------KPEPPRCPKC------GGILRPDV 156
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 27.6 bits (62), Expect = 0.36
Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 81 HQCPHCDYRAKQSGNLRVHIRKYH 104
++C HC Y + L H++ +H
Sbjct: 1 YKCSHCPYSSTPK-KLERHLKLHH 23
>gnl|CDD|222109 pfam13408, Zn_ribbon_recom, Recombinase zinc beta ribbon domain.
This short bacterial protein contains a zinc ribbon
domain that is likely to be DNA-binding. This domain is
found in site specific recombinase proteins. This
family appears most closely related to pfam04606.
Length = 57
Score = 28.0 bits (63), Expect = 0.46
Identities = 6/40 (15%), Positives = 15/40 (37%)
Query: 53 CQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQ 92
C CG ++ ++ + C + +C + R +
Sbjct: 8 CGECGSPMTRRTRKGKYRYYRCSTRRKKGKCSNHSIREEV 47
>gnl|CDD|220661 pfam10263, SprT-like, SprT-like family. This family represents a
domain found in eukaryotes and prokaryotes. The domain
contains a characteristic motif of the zinc
metallopeptidases. This family includes the bacterial
SprT protein.
Length = 153
Score = 29.3 bits (66), Expect = 0.47
Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 9/61 (14%)
Query: 19 GVFTAALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRH--EVFECGG 76
G +T RF +Y+ Y C CG+ Y K ++RH CGG
Sbjct: 95 GAGPLEPTTTHRFDIEVVSGRKRYI-------YRCGSCGQLYPRKRRIRRHKYRCGRCGG 147
Query: 77 K 77
K
Sbjct: 148 K 148
>gnl|CDD|151678 pfam11236, DUF3037, Protein of unknown function (DUF3037). This
bacterial family of proteins has no known function.
Length = 118
Score = 28.7 bits (65), Expect = 0.65
Identities = 9/31 (29%), Positives = 10/31 (32%)
Query: 5 ALNSLSGFAFFFPRGVFTAALSTLARFHWLN 35
AL + AAL RF WL
Sbjct: 56 ALEAFEAICAGGKAAGPIAALDIRERFRWLT 86
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 29.5 bits (67), Expect = 0.71
Identities = 9/60 (15%), Positives = 19/60 (31%), Gaps = 7/60 (11%)
Query: 51 YSCQHCGKR-YRWK------STLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIRKY 103
C CGK + + T + CG + +C C ++ +++
Sbjct: 627 RKCPSCGKETFYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTPYSKRKIDLKEL 686
>gnl|CDD|220362 pfam09723, CxxC_CxxC_SSSS, Zinc ribbon domain. This entry
represents a region of about 41 amino acids found in a
number of small proteins in a wide range of bacteria.
The region usually begins with the initiator Met and
contains two CxxC motifs separated by 17 amino acids.
One protein in this entry has been noted as a putative
regulatory protein, designated FmdB. Most proteins in
this entry have a C-terminal region containing highly
degenerate sequence.
Length = 42
Score = 26.8 bits (60), Expect = 0.92
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 9/36 (25%)
Query: 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHC 86
Y C+ CG + EV + +P+ CP C
Sbjct: 6 YRCEDCGHTF---------EVLQKISDDPLATCPEC 32
>gnl|CDD|238552 cd01132, F1_ATPase_alpha, F1 ATP synthase alpha, central domain.
The F-ATPase is found in bacterial plasma membranes,
mitochondrial inner membranes and in chloroplast
thylakoid membranes. It has also been found in the
archaea Methanosarcina barkeri. It uses a proton
gradient to drive ATP synthesis and hydrolyzes ATP to
build the proton gradient. The extrinisic membrane
domain, F1, is composed of alpha, beta, gamma, delta and
epsilon subunits with a stoichiometry of 3:3:1:1:1. The
alpha subunit of the F1 ATP synthase can bind
nucleotides, but is non-catalytic.
Length = 274
Score = 28.0 bits (63), Expect = 1.7
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 107 IELQSPSPAPRKPIVNPMQT 126
IE ++P PRK + P+QT
Sbjct: 36 IESKAPGIIPRKSVNEPLQT 55
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 27.8 bits (63), Expect = 2.1
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 7/38 (18%)
Query: 53 CQHCGKRY---RWKSTLKRHEVFECGGKEPV-HQCPHC 86
C HC R++ L+ H CG +EP+ CP C
Sbjct: 393 CPHCDASLTLHRFQRRLRCHH---CGYQEPIPKACPEC 427
>gnl|CDD|177582 PHA03312, PHA03312, helicase-primase subunit BBLF2/3; Provisional.
Length = 709
Score = 27.7 bits (61), Expect = 2.2
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 78 EPVHQCPHCDYRAKQSGNLRVHIRKYHTSIELQS------PSPAPRKPIVNPM 124
E CPH ++ G L V+IR + S PSP P + I+ P+
Sbjct: 161 EGEQTCPHAQRHSESPGQLDVYIRTPRGDVFTYSTETPDDPSPVPFRDILRPV 213
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 27.8 bits (62), Expect = 2.3
Identities = 13/58 (22%), Positives = 18/58 (31%), Gaps = 20/58 (34%)
Query: 52 SCQHCGKRY---------RWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHI 100
SC HCG R+ R +++ CP C K + R H
Sbjct: 92 SCTHCGPRFTIIEALPYDRENTSMA-----------DFPLCPDCAKEYKDPLDRRFHA 138
>gnl|CDD|187761 cd09321, TDT_like_3, The Tellurite-resistance/Dicarboxylate
Transporter (TDT) family. The
Tellurite-resistance/Dicarboxylate Transporter (TDT)
family includes members from all three kingdoms, but
only three members of the family have been functionally
characterized: the TehA protein of E. coli functioning
as a tellurite-resistance uptake permease, the Mae1
protein of S. pombe functioning in the uptake of malate
and other dicarboxylates, and the sulfite efflux pump
(SSU1) of Saccharomyces cerevisiae. In plants, the
plasma membrane protein SLAC1 (Slow Anion
Channel-Associated 1), which is preferentially expressed
in guard cells, encodes a distant homolog of fungal and
bacterial dicarboxylate/malic acid transport proteins.
SLAC1 is essential in mediating stomatal responses to
physiological and stress stimuli. Members of the TDT
family exhibit 10 putative transmembrane a-helical
spanners (TMSs).
Length = 327
Score = 27.7 bits (62), Expect = 2.5
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 8 SLSGFAFFFPRGVFTAALSTLARFHWLNW 36
SL +AF FP G +T ++T LN+
Sbjct: 275 SLGWWAFIFPLGAYT--IATYLVAKVLNF 301
>gnl|CDD|177288 PHA00616, PHA00616, hypothetical protein.
Length = 44
Score = 25.5 bits (56), Expect = 2.6
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 51 YSCQHCGKRYRWKSTLKRH 69
Y C CG +R K + H
Sbjct: 2 YQCLRCGGIFRKKKEVIEH 20
>gnl|CDD|224245 COG1326, COG1326, Uncharacterized archaeal Zn-finger protein
[General function prediction only].
Length = 201
Score = 27.0 bits (60), Expect = 2.9
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 6/43 (13%)
Query: 46 TQENQYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDY 88
T+E C CG + HEV + G+EP+ +C C
Sbjct: 2 TEEIYIECPSCGS----EEVS--HEVIKERGREPLVRCEECGT 38
>gnl|CDD|236448 PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated.
Length = 502
Score = 27.3 bits (62), Expect = 2.9
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 107 IELQSPSPAPRKPIVNPMQT 126
+E ++P RK + P+QT
Sbjct: 129 VERKAPGVIDRKSVHEPLQT 148
>gnl|CDD|238698 cd01407, SIR2-fam, SIR2 family of proteins includes silent
information regulator 2 (Sir2) enzymes which catalyze
NAD+-dependent protein/histone deacetylation, where the
acetyl group from the lysine epsilon-amino group is
transferred to the ADP-ribose moiety of NAD+, producing
nicotinamide and the novel metabolite
O-acetyl-ADP-ribose. Sir2 proteins, also known as
sirtuins, are found in all eukaryotes and many archaea
and prokaryotes and have been shown to regulate gene
silencing, DNA repair, metabolic enzymes, and life span.
The most-studied function, gene silencing, involves the
inactivation of chromosome domains containing key
regulatory genes by packaging them into a specialized
chromatin structure that is inaccessible to DNA-binding
proteins. The oligomerization state of Sir2 appears to
be organism-dependent, sometimes occurring as a monomer
and sometimes as a multimer.
Length = 218
Score = 27.1 bits (61), Expect = 2.9
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 6/37 (16%)
Query: 50 QYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHC 86
+ C CGK Y E+ +E V +CP C
Sbjct: 109 RVRCTKCGKEYPR------DELQADIDREEVPRCPKC 139
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 27.4 bits (60), Expect = 3.4
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 35 NWDPNPKYVRTTQENQYSCQHCGKRYRWKSTLKRH 69
N P + + ++ Y C+ C KRY+ + LK H
Sbjct: 383 NPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYH 417
Score = 26.6 bits (58), Expect = 5.7
Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 2/50 (4%)
Query: 55 HCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCDYRAKQSGNLRVHIRKYH 104
H ++ + ++ +F K ++C CD R K L+ H + H
Sbjct: 375 HQNQKLHENPSPEKMNIFSAKDKP--YRCEVCDKRYKNLNGLKYHRKHSH 422
>gnl|CDD|149126 pfam07884, VKOR, Vitamin K epoxide reductase family. Vitamin K
epoxide reductase (VKOR) recycles reduced vitamin K,
which is used subsequently as a co-factor in the
gamma-carboxylation of glutamic acid residues in blood
coagulation enzymes. VKORC1 is a member of a large
family of predicted enzymes that are present in
vertebrates, Drosophila, plants, bacteria and archaea.
Four cysteine residues and one residue, which is either
serine or threonine, are identified as likely
active-site residues. In some plant and bacterial
homologues the VKORC1 homologous domain is fused with
domains of the thioredoxin family of oxidoreductases.
Length = 138
Score = 26.5 bits (59), Expect = 4.5
Identities = 10/34 (29%), Positives = 12/34 (35%), Gaps = 4/34 (11%)
Query: 3 IPALNSLSGFAFFFPRGVFTAALSTLARFHWLNW 36
IP NSL G + V + LA W
Sbjct: 57 IP--NSLLGILAYL--VVLLLGVLGLAGVTLSRW 86
>gnl|CDD|212061 cd11492, SLC5sbd_NIS-SMVT, Na(+)/iodide (NIS) and
Na(+)/multivitamin (SMVT) cotransporters, and related
proteins; solute binding domain. NIS (encoded by the
SLC5A5 gene) transports I-, and other anions including
ClO4-, SCN-, and Br-. SMVT (encoded by the SLC5A6 gene)
transports biotin, pantothenic acid and lipoate. This
subfamily also includes SMCT1 and -2. SMCT1(encoded by
the SLC5A8 gene) is a high-affinity transporter of
various monocarboxylates including lactate and pyruvate,
short-chain fatty acids, ketone bodies, nicotinate and
its structural analogs, pyroglutamate, benzoate and its
derivatives, and iodide. SMCT2 (encoded by the SLC5A12
gene) is a low-affinity transporter for short-chain
fatty acids, lactate, pyruvate, and nicotinate. This
subgroup belongs to the solute carrier 5 (SLC5)
transporter family.
Length = 522
Score = 26.7 bits (60), Expect = 4.8
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 1 MKIPALNSLSGFAFFFPRGVFTAALSTLA 29
M I L L G F G+F+AALSTL+
Sbjct: 316 MDI--LGHLPGLPGLFVAGIFSAALSTLS 342
>gnl|CDD|238704 cd01413, SIR2_Af2, SIR2_Af2: Archaeal and prokaryotic group which
includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus
solfataricus ssSir2, and several bacterial homologs; and
are members of the SIR2 family of proteins, silent
information regulator 2 (Sir2) enzymes which catalyze
NAD+-dependent protein/histone deacetylation. Sir2
proteins have been shown to regulate gene silencing, DNA
repair, metabolic enzymes, and life span. The Sir2
homolog from the archaea Sulfolobus solftaricus
deacetylates the non-specific DNA protein Alba to
mediate transcription repression.
Length = 222
Score = 26.6 bits (59), Expect = 5.1
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 51 YSCQHCGKRYRWKSTL--KRHEVFEC 74
C +CG +Y + K+HEV C
Sbjct: 114 AYCVNCGSKYDLEEVKYAKKHEVPRC 139
>gnl|CDD|239124 cd02659, peptidase_C19C, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 334
Score = 26.5 bits (59), Expect = 5.5
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 3/21 (14%)
Query: 48 ENQYSCQHCGKRYRWKSTLKR 68
+N+Y C+ CGK+ K
Sbjct: 169 DNKYFCEKCGKKVD---AEKG 186
>gnl|CDD|218514 pfam05231, MASE1, MASE1. Predicted integral membrane sensory
domain found in histidine kinases, diguanylate cyclases
and other bacterial signaling proteins. This entry also
includes members of the 8 transmembrane UhpB type
(8TMR-UT) domain family.
Length = 298
Score = 26.3 bits (58), Expect = 5.9
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 5 ALNSLSGFAFFFPRGVFTAALSTLARFHWLNW 36
AL S A + P G+ AAL R +W
Sbjct: 22 ALVSSGIAAIWLPTGLRLAALLLFGRRYWPGI 53
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 26.6 bits (59), Expect = 6.4
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 73 ECGG-KEPVHQCPHC--DYRAKQSGNLR 97
+CG EPV+ CP C + +SG +
Sbjct: 684 DCGTHTEPVYVCPDCGAEVPPDESGRVE 711
>gnl|CDD|172627 PRK14138, PRK14138, NAD-dependent deacetylase; Provisional.
Length = 244
Score = 26.3 bits (58), Expect = 6.5
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 6/37 (16%)
Query: 50 QYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHC 86
+Y C CGKRY + +++ E K V +C C
Sbjct: 119 EYYCVRCGKRYTVEDVIEKLE------KSDVPRCDDC 149
>gnl|CDD|233604 TIGR01863, cas_Csd1, CRISPR-associated protein Cas8c/Csd1, subtype
I-C/DVULG. CRISPR loci appear to be mobile elements
with a wide host range. This model represents a protein
that tends to be found near CRISPR repeats of the DVULG
subtype of CRISPR/Cas locus. We designate this family
Csd1 (CRISPR/Cas Subtype DVULG protein 1). The species
range for this subtype, so far, is exclusively bacterial
and mesophilic, although CRISPR loci in general are
particularly common among archaea and thermophilic
bacteria. In a few species (Xanthomonas axonopodis pv.
citri str. 306 and Streptococcus mutans UA159), homology
to this protein family is split across two tandem genes;
the trusted cutoff to this family is set low enough to
capture at least the longer of the two [Mobile and
extrachromosomal element functions, Other].
Length = 584
Score = 26.2 bits (58), Expect = 7.1
Identities = 8/56 (14%), Positives = 21/56 (37%), Gaps = 4/56 (7%)
Query: 87 DYRAKQSGNLRVHIRKYHTSIELQSP---SPAPR-KPIVNPMQTQQQASNLSTNQT 138
+R G L ++ ++ +E + P I++ Q ++ N+ +
Sbjct: 345 YWRELTVGELLENLERHFDDLEWEPRPKDDGPPSLWRILSATAGQGKSENVPPDLA 400
>gnl|CDD|213729 TIGR02605, CxxC_CxxC_SSSS, putative regulatory protein, FmdB
family. This model represents a region of about 50
amino acids found in a number of small proteins in a
wide range of bacteria. The region begins usually with
the initiator Met and contains two CxxC motifs
separated by 17 amino acids. One member of this family
is has been noted as a putative regulatory protein,
designated FmdB (SP:Q50229, PMID:8841393 ). Most
members of this family have a C-terminal region
containing highly degenerate sequence, such as
SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in
Mycobacterium tuberculosis and
VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces
avermitilis. These low complexity regions, which are
not included in the model, resemble low-complexity
C-terminal regions of some heterocycle-containing
bacteriocin precursors [Regulatory functions, DNA
interactions].
Length = 52
Score = 24.6 bits (54), Expect = 7.2
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 9/37 (24%)
Query: 50 QYSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHC 86
+Y C CG R+ EV + +P+ CP C
Sbjct: 5 EYRCTACGHRF---------EVLQKMSDDPLATCPEC 32
>gnl|CDD|187758 cd09318, TDT_SSU1, Tellurite-resistance/Dicarboxylate Transporter
(TDT) family includes sulfite sensitivity protein
(sulfite efflux pump; SSU1). This family contains the
sulfite sensitivity protein (sulfite efflux pump; SSU1)
and belongs to the tellurite-resistance/dicarboxylate
transporter (TDT) family. The SSU1 gene encodes the
sulfite pump required for efficient sulfite efflux.
Mutations in the SSU1 gene cause sensitivity to sulfite
while overexpression confers heightened resistance to
sulfite toxicity. In dematophytes and other filamentous
fungi, sulfite is excreted as a reducing agent during
keratin degradation; thus sulfite transporters in
keratinolytic fungi could be a new target for antifungal
drugs in dermatology. The number of genes encoding
sulfite efflux pumps in fungal genomes varies from
species to species.
Length = 341
Score = 26.0 bits (58), Expect = 7.3
Identities = 8/21 (38%), Positives = 10/21 (47%), Gaps = 1/21 (4%)
Query: 11 GF-AFFFPRGVFTAALSTLAR 30
G+ F FP GV A L +
Sbjct: 295 GWWGFTFPLGVMALATIELGK 315
>gnl|CDD|143430 cd07112, ALDH_GABALDH-PuuC, Escherichia coli NADP+-dependent
gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
PuuC-like. NADP+-dependent,
gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
(GABALDH) PuuC of Escherichia coli which catalyzes the
conversion of putrescine to 4-aminobutanoate and other
similar sequences are present in this CD.
Length = 462
Score = 26.4 bits (59), Expect = 7.5
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 59 RYRWKSTLKRHEVF-ECGGKEP---VHQCPHCDYRAKQSGN 95
Y +S LKR V+ ECGGK P P D A+ +
Sbjct: 221 EYSGQSNLKR--VWLECGGKSPNIVFADAPDLDAAAEAAAA 259
>gnl|CDD|215642 PLN03238, PLN03238, probable histone acetyltransferase MYST;
Provisional.
Length = 290
Score = 26.0 bits (57), Expect = 7.7
Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHCD-YRAKQSGNLRVH 99
Y C++C K R K +L RH K + Q P Y A G L V
Sbjct: 49 YICEYCLKYMRKKKSLLRHLA-----KCDIRQPPGGGIYGAVTEGPLSVF 93
>gnl|CDD|197903 smart00834, CxxC_CXXC_SSSS, Putative regulatory protein.
CxxC_CXXC_SSSS represents a region of about 41 amino
acids found in a number of small proteins in a wide
range of bacteria. The region usually begins with the
initiator Met and contains two CxxC motifs separated by
17 amino acids. One protein in this entry has been
noted as a putative regulatory protein, designated
FmdB. Most proteins in this entry have a C-terminal
region containing highly degenerate sequence.
Length = 41
Score = 24.1 bits (53), Expect = 8.0
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 9/36 (25%)
Query: 51 YSCQHCGKRYRWKSTLKRHEVFECGGKEPVHQCPHC 86
Y C+ CG + EV + +P+ CP C
Sbjct: 6 YRCEDCGHTF---------EVLQKISDDPLTTCPEC 32
>gnl|CDD|227812 COG5525, COG5525, Phage terminase, large subunit GpA [Replication,
recombination and repair].
Length = 611
Score = 26.2 bits (58), Expect = 8.1
Identities = 15/80 (18%), Positives = 23/80 (28%), Gaps = 19/80 (23%)
Query: 22 TAALSTLARFHWLNWDPNPKYVRTTQENQYSCQHCGKRYR----WKSTLKRHEVFECGGK 77
T + YV C HCG+ + KS + + + +
Sbjct: 212 TTIERAYNAGDQRRF-----YVP--------CPHCGEEQQLKFGEKSGPRG--LKDTPAE 256
Query: 78 EPVHQCPHCDYRAKQSGNLR 97
QC HC + N R
Sbjct: 257 AAFIQCEHCGCVIRPKLNGR 276
>gnl|CDD|214746 smart00614, ZnF_BED, BED zinc finger. DNA-binding domain in
chromatin-boundary-element-binding proteins and
transposases.
Length = 50
Score = 24.3 bits (53), Expect = 9.0
Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 12/44 (27%)
Query: 31 FHWLNWDPNPKYVRTTQENQYSCQHCGKRYR-----WKSTLKRH 69
F + N K C++CGK+ S L+RH
Sbjct: 6 FTLILEKDNGKQRAK-------CKYCGKKLSRSSKGGTSNLRRH 42
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus,
particularly the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 23.7 bits (52), Expect = 9.3
Identities = 6/21 (28%), Positives = 12/21 (57%)
Query: 50 QYSCQHCGKRYRWKSTLKRHE 70
Q+ C C K ++ ++ L+ H
Sbjct: 1 QFYCVACDKYFKSENALENHL 21
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This
protein contains an ATP/GTP binding P-loop motif. It is
found associated with IS21 family insertion sequences.
The function of this protein is unknown, but it may
perform a transposase function.
Length = 178
Score = 25.7 bits (57), Expect = 9.6
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 2 KIPALNSLSGFAFFFPRGVFTAALSTLARFHWLN 35
K+PA +L F F RG+ ++ LA W+
Sbjct: 12 KLPARKTLEDFDFRAARGLDRRLIAELAGLDWIE 45
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
0.320 0.131 0.427
Gapped
Lambda K H
0.267 0.0804 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,072,882
Number of extensions: 572865
Number of successful extensions: 740
Number of sequences better than 10.0: 1
Number of HSP's gapped: 735
Number of HSP's successfully gapped: 55
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
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: 54 (24.4 bits)