RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12029
(81 letters)
>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is
composed of two C4-type zinc fingers. DNA-binding
domain of Tailless (TLX) is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom. TLX
interacts with specific DNA sites upstream of the
target gene and modulates the rate of transcriptional
initiation. TLX is an orphan receptor that is
expressed by neural stem/progenitor cells in the adult
brain of the subventricular zone (SVZ) and the dentate
gyrus (DG). It plays a key role in neural development
by promoting cell cycle progression and preventing
apoptosis in the developing brain. Like other members
of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, TLX has a
central well conserved DNA-binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 92
Score = 28.2 bits (63), Expect = 0.22
Identities = 11/35 (31%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 23 LFSCSGCARVYKNKKSLARHQTYECGQEPQYFCPL 57
+++C GC+ +K +S+ R++ Y C + Q CP+
Sbjct: 23 IYACDGCSGFFK--RSIRRNRQYVCKSKGQGGCPV 55
>gnl|CDD|150545 pfam09885, DUF2112, Uncharacterized protein conserved in archaea
(DUF2112). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 143
Score = 28.0 bits (63), Expect = 0.37
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 20 ADRLFSCSGCARVYKNKKSLAR 41
A LF C GCAR + K L R
Sbjct: 90 APILFGCMGCARTNELTKFLIR 111
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 27.8 bits (61), Expect = 0.57
Identities = 20/78 (25%), Positives = 27/78 (34%), Gaps = 24/78 (30%)
Query: 22 RLFSCS--GCARVYKNKKSLARH-------------------QTYECGQEPQYFCPLCPY 60
+ + C GC + YKN+ L H + +P Y C +C
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKP-YRCEVCDK 406
Query: 61 RAKQKTNLMTHMSIKHSH 78
R K L H KHSH
Sbjct: 407 RYKNLNGLKYH--RKHSH 422
>gnl|CDD|181171 PRK07928, PRK07928, NADH dehydrogenase subunit A; Validated.
Length = 119
Score = 25.8 bits (57), Expect = 1.7
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 40 ARHQTYECGQEP 51
A+ + YECG EP
Sbjct: 36 AKLEAYECGIEP 47
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 24.1 bits (53), Expect = 2.4
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 53 YFCPLCPYRAKQKTNLMTHMSIKH 76
Y C CPY + K L H+ + H
Sbjct: 1 YKCSHCPYSSTPK-KLERHLKLHH 23
>gnl|CDD|237884 PRK15020, PRK15020, ethanolamine utilization cobalamin
adenosyltransferase; Provisional.
Length = 267
Score = 25.7 bits (56), Expect = 3.2
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 51 PQYFCPLCPYRAKQKTNLMTHMS 73
PQ C LC +K + +TH+S
Sbjct: 76 PQACCELCRQPVAKKPDTLTHLS 98
>gnl|CDD|190760 pfam03811, Zn_Tnp_IS1, InsA N-terminal domain. This appears to
be a short zinc binding domain found in IS1 InsA family
protein. It is found at the N-terminus of the protein
and may be a DNA-binding domain.
Length = 36
Score = 23.7 bits (51), Expect = 4.4
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 25 SCSGCARVYKNKKSLARHQTYEC 47
CS VY++ +S A HQ Y C
Sbjct: 10 RCSSTEGVYRHGQSTAGHQRYRC 32
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 23.2 bits (50), Expect = 5.9
Identities = 9/22 (40%), Positives = 10/22 (45%)
Query: 53 YFCPLCPYRAKQKTNLMTHMSI 74
Y CP C K K+ L HM
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|131958 TIGR02912, sulfite_red_C, sulfite reductase, subunit C. Members of
this protein family include the C subunit, one of three
subunits, of the anaerobic sulfite reductase of
Salmonella, and close homologs from various Clostridum
species, where the three-gene neighborhood is preserved.
Two such gene clusters are found in Clostridium
perfringens, but it may be that these sets of genes
correspond to the distinct assimilatory and
dissimilatory forms as seen in Clostridium pasteurianum.
Note that any one of these enzymes may have secondary
substates such as NH2OH, SeO3(2-), and SO3(2-).
Heterologous expression of the anaerobic sulfite
reductase of Salmonella confers on Escherichia coli the
ability to produce hydrogen sulfide gas from sulfite
[Central intermediary metabolism, Sulfur metabolism].
Length = 314
Score = 24.4 bits (53), Expect = 7.3
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 13 ITESSYFADRLFSCSGCARVYKNK 36
+TE Y ADR C C +V K K
Sbjct: 161 MTEPQYDADRCIGCGACVKVCKKK 184
>gnl|CDD|232871 TIGR00201, comF, comF family protein. This protein is found in
species that do (Bacillus subtilis, Haemophilus
influenzae) or do not (E. coli, Borrelia burgdorferi)
have described systems for natural transformation with
exogenous DNA. It is involved in competence for
transformation in Bacillus subtilis [Cellular
processes, DNA transformation].
Length = 190
Score = 24.4 bits (53), Expect = 7.9
Identities = 9/29 (31%), Positives = 12/29 (41%), Gaps = 4/29 (13%)
Query: 26 CSGCARVYKNKKSLARHQTYECGQEPQYF 54
CS C R Y++ +L R CG
Sbjct: 1 CSLCGRPYQSVHALCRQ----CGSWRTRI 25
>gnl|CDD|215958 pfam00507, Oxidored_q4, NADH-ubiquinone/plastoquinone
oxidoreductase, chain 3.
Length = 102
Score = 24.0 bits (53), Expect = 8.3
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 33 YKNKKSLARHQTYECGQEP 51
K + YECG +P
Sbjct: 15 PKKPSDREKLSPYECGFDP 33
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 23.8 bits (52), Expect = 8.5
Identities = 5/23 (21%), Positives = 8/23 (34%)
Query: 55 CPLCPYRAKQKTNLMTHMSIKHS 77
C C + + + HM H
Sbjct: 2 CLFCNHTSDTVEENLEHMFKSHG 24
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and
recognises the first three GAG bases of the consensus
in a manner similar to that seen in other classical
zinc finger-DNA complexes. The second basic region
forms a helix that interacts in the major groove
recognising the last G of the consensus, while the
first basic region wraps around the DNA in the minor
groove and recognises the A in the fourth position of
the consensus sequence.
Length = 54
Score = 23.4 bits (50), Expect = 9.7
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 55 CPLCPYRAKQKTNLMTHMSIKH 76
CP+C +Q NL H+ ++H
Sbjct: 27 CPICQAVIRQSRNLRRHLELRH 48
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
0.326 0.135 0.435
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,698,755
Number of extensions: 251863
Number of successful extensions: 322
Number of sequences better than 10.0: 1
Number of HSP's gapped: 320
Number of HSP's successfully gapped: 24
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.3 bits)