RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14799
(230 letters)
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 36.5 bits (84), Expect = 0.007
Identities = 28/112 (25%), Positives = 39/112 (34%), Gaps = 25/112 (22%)
Query: 35 SFQC--DECDMSFGTHQALGRHKQCKHMDISLRPFPCDLC---------EQRFLNKSHLA 83
SF+C +C G+ + L +H + +H C C E R S L
Sbjct: 151 SFKCPKSKCHRRCGSLKELKKHYKAQH-----GFVLCSECIGNKKDFWNEIRLFRSSTLR 205
Query: 84 YHVKTHTGER----DVTCGLCFQSFYSKADLVRHMKGRHLNIRSFTCHLCNK 131
H E C C FY +L RH + RH CH+C+
Sbjct: 206 DHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRHE-----ACHICDM 252
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 29.5 bits (67), Expect = 0.10
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 36 FQCDECDMSFGTHQALGRHKQCKH 59
C C +F + QALG HK+
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSHC 25
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 31.6 bits (71), Expect = 0.33
Identities = 22/76 (28%), Positives = 31/76 (40%), Gaps = 2/76 (2%)
Query: 65 RPFPCDLCEQRFLNKSHLAYHVKTHTGERDVTCGL--CFQSFYSKADLVRHMKGRHLNIR 122
RP C C F HL H+++HTGE+ C C +SF +L RH++ H N
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPS 91
Query: 123 SFTCHLCNKGFFRKSY 138
+ S
Sbjct: 92 DLNSKSLPLSNSKASS 107
>gnl|CDD|180315 PRK05933, PRK05933, type III secretion system protein; Validated.
Length = 372
Score = 31.0 bits (70), Expect = 0.46
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 11/63 (17%)
Query: 62 ISLRPFPCDLCEQRFLNKSHLAYHVKTHTGERDVTCGLCFQSFYSKADLVRHMKGRHLNI 121
+S FP +LC+Q+ K L DV + + S A V+ G HL +
Sbjct: 29 VSFPVFPKELCQQKLKEKFRL----------EDVELSIESRGSLSAAAAVQEF-GEHLLL 77
Query: 122 RSF 124
+ F
Sbjct: 78 QPF 80
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 27.0 bits (60), Expect = 0.87
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 23 LEAHITTVHGDKSFQCDECDMSF 45
L H+ T G+K ++C C SF
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSF 24
Score = 26.2 bits (58), Expect = 1.8
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 81 HLAYHVKTHTGERDVTCGLCFQSF 104
+L H++THTGE+ C +C +SF
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSF 24
>gnl|CDD|222020 pfam13278, DUF4066, Putative amidotransferase. This domain
contains similarities to other amidotransferase families
such as pfam00117. Some members of the family lack the
likely catalytic residues.
Length = 164
Score = 28.4 bits (64), Expect = 2.4
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 92 ERDVTCGLCFQSFY-SKADLVRHMKGRHLNIRSFTCHLCNKGFFRKSYLKVHL 143
+ +C + ++A L L+ R T H K + R++ KV L
Sbjct: 91 AGQLLGAVCSGALLLAEAGL--------LDGRPATTHWTLKPWLREAGPKVLL 135
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 28.9 bits (64), Expect = 2.5
Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 18/79 (22%)
Query: 30 VHGDKSFQCD--ECDMSFGTHQALGRHKQCKHMDISL----------------RPFPCDL 71
V K ++C C+ + L H H + L +P+ C++
Sbjct: 344 VKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEV 403
Query: 72 CEQRFLNKSHLAYHVKTHT 90
C++R+ N + L YH K
Sbjct: 404 CDKRYKNLNGLKYHRKHSH 422
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.5 bits (56), Expect = 3.1
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 67 FPCDLCEQRFLNKSHLAYHVKTH 89
+ C C + F +KS L H++TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 28.4 bits (64), Expect = 3.4
Identities = 9/39 (23%), Positives = 13/39 (33%), Gaps = 2/39 (5%)
Query: 36 FQCDECDMSFGTHQALGRHKQCKHMDISLR-PFPCDLCE 73
+C CD H+A +C + P C C
Sbjct: 445 AECPNCDSPLTLHKA-TGQLRCHYCGYQEPIPQSCPECG 482
>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The second LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Lhx1 is required for regulating
the vertebrate head organizer, the nervous system, and
female reproductive tract development. During
embryogenesis in the mouse, Lhx1 is expressed early in
mesodermal tissue, then later during urogenital, kidney,
liver, and nervous system development. In the adult,
expression is restricted to the kidney and brain. A
mouse embryos with Lhx1 gene knockout cannot grow normal
anterior head structures, kidneys, and gonads, but with
normally developed trunk and tail morphology. In the
developing nervous system, Lhx1 is required to direct
the trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 56
Score = 25.8 bits (57), Expect = 3.9
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 97 CGLCFQSFYSKADLVRHMKGRHLNIRSFTCHLCNK 131
C C Q S DLVR + + ++ FTC +C K
Sbjct: 1 CAGCDQGI-SPNDLVRRARDKVFHLNCFTCMVCRK 34
>gnl|CDD|143531 cd07156, NR_DBD_VDR_like, The DNA-binding domain of vitamin D
receptors (VDR) like nuclear receptor family is composed
of two C4-type zinc fingers. The DNA-binding domain of
vitamin D receptors (VDR) like nuclear receptor family
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. This domain interacts
with specific DNA site upstream of the target gene and
modulates the rate of transcriptional initiation. This
family includes three types of nuclear receptors:
vitamin D receptors (VDR), constitutive androstane
receptor (CAR) and pregnane X receptor (PXR). VDR
regulates calcium metabolism, cellular proliferation and
differentiation. PXR and CAR function as sensors of
toxic byproducts of cell metabolism and of exogenous
chemicals, to facilitate their elimination. The DNA
binding activity is regulated by their corresponding
ligands. VDR is activated by Vitamin D; CAR and PXR
respond to a diverse array of chemically distinct
ligands, including many endogenous compounds and
clinical drugs. Like other nuclear receptors, xenobiotic
receptors have 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 = 72
Score = 25.8 bits (57), Expect = 5.2
Identities = 23/63 (36%), Positives = 26/63 (41%), Gaps = 5/63 (7%)
Query: 113 HMKGRHLNIRSFTCHLCNKGFFRKSYLKVHLLTIHMQPADEAQNAIHR-CYACRCAGHCL 171
G H N + TC C KGFFR+S + T E R C ACR CL
Sbjct: 7 RATGYHFN--AMTCEGC-KGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLK-KCL 62
Query: 172 QIG 174
IG
Sbjct: 63 DIG 65
>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 = 24.9 bits (54), Expect = 5.4
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 67 FPCDLCEQRFLNKSHLAYHVKTH 89
F C LC + F +K L H++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|227480 COG5151, SSL1, RNA polymerase II transcription
initiation/nucleotide excision repair factor TFIIH,
subunit SSL1 [Transcription / DNA replication,
recombination, and repair].
Length = 421
Score = 27.7 bits (61), Expect = 6.0
Identities = 25/124 (20%), Positives = 37/124 (29%), Gaps = 29/124 (23%)
Query: 57 CKHMDISLRPFPCDLCEQRFLNKSHLA--YH----------VKTHTGERDVTCGLCFQSF 104
CK SL P C +C + + +HLA YH T + C +C Q
Sbjct: 314 CKTKVCSL-PISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVC-QGP 371
Query: 105 YSKADLVRHMKGRHLNIRSFTCHLCNKGFFRKSYLKVHLLTIHMQPADEAQNAIHRCYAC 164
+ K + + C LC F + +H +H C C
Sbjct: 372 FPK--PPVSPFDESTSSGRYQCELCKSTFCSDCDVFIH-------------ETLHFCIGC 416
Query: 165 RCAG 168
Sbjct: 417 ELPH 420
>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 = 24.2 bits (53), Expect = 8.8
Identities = 12/21 (57%), Positives = 12/21 (57%)
Query: 125 TCHLCNKGFFRKSYLKVHLLT 145
C C K F RKS LK HL T
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
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
0.329 0.140 0.484
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,140,177
Number of extensions: 951421
Number of successful extensions: 991
Number of sequences better than 10.0: 1
Number of HSP's gapped: 989
Number of HSP's successfully gapped: 56
Length of query: 230
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 136
Effective length of database: 6,768,326
Effective search space: 920492336
Effective search space used: 920492336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 57 (25.9 bits)