RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4065
(348 letters)
>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 = 37.7 bits (88), Expect = 2e-04
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 44 SCSVCGKTFTRREHLRRHQQIH 65
C CGK+F+R+ +L+RH + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 37.7 bits (88), Expect = 2e-04
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 152 SCSVCGKTFTRREHLRRHQQIH 173
C CGK+F+R+ +L+RH + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 34.2 bits (79), Expect = 0.003
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 289 KCDVCKKVFSRRSHLLRHLKR 309
KC C K FSR+S+L RHL+
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
Score = 28.9 bits (65), Expect = 0.28
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 8 QCDVCNQGFVRKEHLVRHRKR 28
+C C + F RK +L RH +
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
Score = 28.9 bits (65), Expect = 0.28
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 116 QCDVCNQGFVRKEHLVRHRKR 136
+C C + F RK +L RH +
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 42.4 bits (99), Expect = 2e-04
Identities = 45/179 (25%), Positives = 67/179 (37%), Gaps = 37/179 (20%)
Query: 6 PFQCDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSC--SVCGKTFTRREHLRRHQQ 63
P + CN F R L RH + + G KPFSC S+CGK F+R + L+RH
Sbjct: 289 PIKSKQCNISFSRSSPLTRHLRSVNH----SGESLKPFSCPYSLCGKLFSRNDALKRHIL 344
Query: 64 IH-----ARELLQSSM--DMSALTGLAEEVFPTPLRLDENVRRWVACQRIEGIDVVRPFQ 116
+H A+E L +S L + Q+ + + + +
Sbjct: 345 LHTSISPAKEKLLNSSSKFSPLLNNEPPQSL----------------QQYKDLKNDKKSE 388
Query: 117 CDV--CNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSVCGKTFTRREHLRRHQQIH 173
C + F R +L H H P C K+F R +L H++IH
Sbjct: 389 TLSNSCIRNFKRDSNLSLHIIT-HLSFRP-----YNCKNPPCSKSFNRHYNLIPHKKIH 441
Score = 34.3 bits (78), Expect = 0.085
Identities = 24/63 (38%), Positives = 28/63 (44%), Gaps = 10/63 (15%)
Query: 5 RPFQCDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSV--CGKTFTRREHLRRHQ 62
RP C C F R EHL RH + G KP CS C K+F+R L RH
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRH------IRSHTG--EKPSQCSYSGCDKSFSRPLELSRHL 83
Query: 63 QIH 65
+ H
Sbjct: 84 RTH 86
Score = 34.3 bits (78), Expect = 0.085
Identities = 24/63 (38%), Positives = 28/63 (44%), Gaps = 10/63 (15%)
Query: 113 RPFQCDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSV--CGKTFTRREHLRRHQ 170
RP C C F R EHL RH + G KP CS C K+F+R L RH
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRH------IRSHTG--EKPSQCSYSGCDKSFSRPLELSRHL 83
Query: 171 QIH 173
+ H
Sbjct: 84 RTH 86
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 37.4 bits (87), Expect = 3e-04
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 43 FSCSVCGKTFTRREHLRRHQQIH 65
+ C CGK F + LR H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 37.4 bits (87), Expect = 3e-04
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 151 FSCSVCGKTFTRREHLRRHQQIH 173
+ C CGK F + LR H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 30.9 bits (70), Expect = 0.048
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 289 KCDVCKKVFSRRSHLLRHLKR 309
+C C KVF +S L H++
Sbjct: 2 RCPECGKVFKSKSALREHMRT 22
Score = 29.0 bits (65), Expect = 0.27
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 7 FQCDVCNQGFVRKEHLVRHRKR 28
++C C + F K L H +
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
Score = 29.0 bits (65), Expect = 0.27
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 115 FQCDVCNQGFVRKEHLVRHRKR 136
++C C + F K L H +
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>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 = 33.4 bits (76), Expect = 0.006
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 43 FSCSVCGKTFTRREHLRRHQQIH 65
F C +CGK+F+ ++ L+RH + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 33.4 bits (76), Expect = 0.006
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 151 FSCSVCGKTFTRREHLRRHQQIH 173
F C +CGK+F+ ++ L+RH + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 32.6 bits (74), Expect = 0.015
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 289 KCDVCKKVFSRRSHLLRHLKRLH 311
KC +C K FS + L RHL++ H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKHH 24
Score = 31.5 bits (71), Expect = 0.038
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 7 FQCDVCNQGFVRKEHLVRHRKRAH 30
F+C +C + F K+ L RH ++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 31.5 bits (71), Expect = 0.038
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 115 FQCDVCNQGFVRKEHLVRHRKRAH 138
F+C +C + F K+ L RH ++ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|214746 smart00614, ZnF_BED, BED zinc finger. DNA-binding domain in
chromatin-boundary-element-binding proteins and
transposases.
Length = 50
Score = 33.9 bits (78), Expect = 0.007
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 278 IPRERPPKPIPKCDVCKKVFSRR-----SHLLRHLKRLH 311
I + K KC C K SR S+L RHL+R H
Sbjct: 9 ILEKDNGKQRAKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 35.5 bits (81), Expect = 0.038
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 13/70 (18%)
Query: 5 RPFQCDV--CNQGFVRKEHLVRHRKRAH---------DLDPPEG--AEAKPFSCSVCGKT 51
+P++C V CN+ + + L H H + A+ KP+ C VC K
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKR 407
Query: 52 FTRREHLRRH 61
+ L+ H
Sbjct: 408 YKNLNGLKYH 417
Score = 35.5 bits (81), Expect = 0.038
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 13/70 (18%)
Query: 113 RPFQCDV--CNQGFVRKEHLVRHRKRAH---------DLDPPEG--AEAKPFSCSVCGKT 159
+P++C V CN+ + + L H H + A+ KP+ C VC K
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKR 407
Query: 160 FTRREHLRRH 169
+ L+ H
Sbjct: 408 YKNLNGLKYH 417
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a
zinc-finger domain with the CxxCx(12)Hx(6)H motif,
found in multiple copies in a wide range of proteins
from plants to metazoans. Some member proteins,
particularly those from plants, are annotated as being
RNA-binding.
Length = 25
Score = 29.4 bits (67), Expect = 0.15
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 43 FSCSVCGKTFTRREHLRRHQQ 63
F C +C TFT L+ H +
Sbjct: 1 FYCELCNVTFTSESQLKSHLR 21
Score = 29.4 bits (67), Expect = 0.15
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 151 FSCSVCGKTFTRREHLRRHQQ 171
F C +C TFT L+ H +
Sbjct: 1 FYCELCNVTFTSESQLKSHLR 21
Score = 29.4 bits (67), Expect = 0.17
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 290 CDVCKKVFSRRSHLLRHLK 308
C++C F+ S L HL+
Sbjct: 3 CELCNVTFTSESQLKSHLR 21
>gnl|CDD|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein
(LMP2) protein. This family consists of several
Gammaherpesvirus latent membrane protein (LMP2)
proteins. Epstein-Barr virus is a human Gammaherpesvirus
that infects and establishes latency in B lymphocytes in
vivo. The latent membrane protein 2 (LMP2) gene is
expressed in latently infected B cells and encodes two
protein isoforms, LMP2A and LMP2B, that are identical
except for an additional N-terminal 119 aa cytoplasmic
domain which is present in the LMP2A isoform. LMP2A is
thought to play a key role in either the establishment
or the maintenance of latency and/or the reactivation of
productive infection from the latent state. The
significance of LMP2B and its role in pathogenesis
remain unclear.
Length = 489
Score = 33.7 bits (77), Expect = 0.15
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 5/50 (10%)
Query: 207 MPEISMSSGGSGNSSPRVKKEGDDGSEDPMEVELPPPEASSSPLNRPAAP 256
M + M G+G +GD+G +P P + S +RP P
Sbjct: 1 MVSLEMQPLGAGGPRSHGGPDGDEGDSNPY-----YPSSFGSSWDRPGPP 45
>gnl|CDD|202452 pfam02892, zf-BED, BED zinc finger.
Length = 43
Score = 29.1 bits (66), Expect = 0.32
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 289 KCDVCKKVFSRR---SHLLRHLKRLH 311
+C C K+ S S+L RHL R
Sbjct: 17 RCKYCGKILSGGGGTSNLKRHLVRKC 42
>gnl|CDD|226830 COG4395, COG4395, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 281
Score = 30.5 bits (69), Expect = 1.1
Identities = 22/121 (18%), Positives = 32/121 (26%), Gaps = 17/121 (14%)
Query: 172 IHARELLQSSMDMSALTGLAGMGGELQMPLFAASLMPEISMSSGGSGNSSPRVKKEGDDG 231
+ + + L L G L+M F + + + +
Sbjct: 50 GGLFFGIAAFLIFLLLITLIGFVIMLEMRFFDPYRPQRPAYDAAQASVAPDNY------- 102
Query: 232 SEDPMEVELPPPEASSSPLNRPAAPAALTALGGIPLAVREKLMRPVIPRERPPKPIPKCD 291
P E P S + PAA A G PLA R V P P
Sbjct: 103 VTLPRAPEAQPA----SAADIPAAGDA-IGGAGGPLA---AGARAV--HNADPSFDPARF 152
Query: 292 V 292
+
Sbjct: 153 L 153
>gnl|CDD|177288 PHA00616, PHA00616, hypothetical protein.
Length = 44
Score = 27.8 bits (62), Expect = 1.1
Identities = 6/27 (22%), Positives = 14/27 (51%)
Query: 289 KCDVCKKVFSRRSHLLRHLKRLHNIDP 315
+C C +F ++ ++ HL +H +
Sbjct: 3 QCLRCGGIFRKKKEVIEHLLSVHKQNK 29
>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 = 27.7 bits (62), Expect = 1.2
Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 9 CDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSVCGKTFTRREHL 58
C C+QG + LVR RA D F+C VC K + E L
Sbjct: 1 CAGCDQG-ISPNDLVR---RARDK----VFHLNCFTCMVCRKQLSTGEEL 42
Score = 27.7 bits (62), Expect = 1.2
Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 117 CDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSVCGKTFTRREHL 166
C C+QG + LVR RA D F+C VC K + E L
Sbjct: 1 CAGCDQG-ISPNDLVR---RARDK----VFHLNCFTCMVCRKQLSTGEEL 42
>gnl|CDD|192286 pfam09416, UPF1_Zn_bind, RNA helicase (UPF2 interacting domain).
UPF1 is an essential RNA helicase that detects mRNAs
containing premature stop codons and triggers their
degradation. This domain contains 3 zinc binding motifs
and forms interactions with another protein (UPF2) that
is also involved nonsense-mediated mRNA decay (NMD).
Length = 152
Score = 29.7 bits (67), Expect = 1.2
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 15/47 (31%)
Query: 284 PKPIPKCDVCKKVF------SRRSHLLRHLKRLHNIDPPPSSRNKQV 324
P + KC+ C K F + SH++ HL + S++K+V
Sbjct: 11 PACVVKCNSCNKWFCNGKGGTSGSHIVNHLVK---------SKHKEV 48
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 26.4 bits (59), Expect = 2.0
Identities = 10/23 (43%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 289 KCDVCKKVFSRRSHLLRHLKRLH 311
C VC K FS L H K+ H
Sbjct: 3 TCGVCGKTFSSLQALGGH-KKSH 24
Score = 26.4 bits (59), Expect = 2.1
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 43 FSCSVCGKTFTRREHLRRHQQIH 65
+C VCGKTF+ + L H++ H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
Score = 26.4 bits (59), Expect = 2.1
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 151 FSCSVCGKTFTRREHLRRHQQIH 173
+C VCGKTF+ + L H++ H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX
protein family. The second LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved
members of this family. Proteins in this group 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. Isl-1 is one of
the LHX proteins isolated originally by virtue of its
ability to bind DNA sequences from the 5'-flanking
region of the rat insulin gene in pancreatic
insulin-producing cells. Mice deficient in Isl-1 fail
to form the dorsal exocrine pancreas and islet cells
fail to differentiate. On the other hand, Isl-1 takes
part in the pituitary development by activating the
gonadotropin-releasing hormone receptor gene together
with LHX3 and steroidogenic factor 1. Mouse Isl2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Same as Isl1, Isl2 may also be able
to bind to the insulin gene enhancer to promote gene
activation. 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 = 55
Score = 27.4 bits (61), Expect = 2.0
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 14/55 (25%)
Query: 9 CDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSVC------GKTFTRREH 57
C C Q F + + ++R R + + ++ F CS C G F R+
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIE--------CFRCSACSRQLIPGDEFALRDD 47
Score = 27.4 bits (61), Expect = 2.0
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 14/55 (25%)
Query: 117 CDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSVC------GKTFTRREH 165
C C Q F + + ++R R + + ++ F CS C G F R+
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIE--------CFRCSACSRQLIPGDEFALRDD 47
>gnl|CDD|140258 PTZ00231, PTZ00231, variable surface protein Vir17; Provisional.
Length = 385
Score = 29.9 bits (67), Expect = 2.2
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 3/40 (7%)
Query: 227 EGDDGSEDPMEVELPPPEASSSPLNRPAAP---AALTALG 263
E + +D E+ LP + N P+ P A L+ G
Sbjct: 280 EQEVILDDIPELFLPSSTDVNLTDNGPSKPIYYAGLSVSG 319
>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 = 26.0 bits (58), Expect = 2.5
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 290 CDVCKKVFSRRSHLLRHLK 308
C C K F + L HLK
Sbjct: 4 CVACDKYFKSENALENHLK 22
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 28.7 bits (64), Expect = 2.5
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 289 KCDVCKKVFSRRSHLLRHLKRLHNI 313
C VC K F L H+ + HNI
Sbjct: 101 VCPVCGKEFRNTDSTLDHVCKKHNI 125
Score = 27.1 bits (60), Expect = 6.8
Identities = 16/59 (27%), Positives = 20/59 (33%), Gaps = 12/59 (20%)
Query: 4 VRPFQCDVCNQGFVRKEHLVRH-RKRAHDLDPPEGAEAKPFSCSVCGKTFTRREHLRRH 61
V P+ C +C F L +H R H C VCGK F + H
Sbjct: 71 VSPYVCPLCLMPFSSSVSLKQHIRYTEHSK-----------VCPVCGKEFRNTDSTLDH 118
Score = 27.1 bits (60), Expect = 6.8
Identities = 16/59 (27%), Positives = 20/59 (33%), Gaps = 12/59 (20%)
Query: 112 VRPFQCDVCNQGFVRKEHLVRH-RKRAHDLDPPEGAEAKPFSCSVCGKTFTRREHLRRH 169
V P+ C +C F L +H R H C VCGK F + H
Sbjct: 71 VSPYVCPLCLMPFSSSVSLKQHIRYTEHSK-----------VCPVCGKEFRNTDSTLDH 118
>gnl|CDD|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type)
[DNA replication, recombination, and repair].
Length = 1444
Score = 29.6 bits (67), Expect = 3.3
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 8/41 (19%)
Query: 304 LRHLKRLHNIDPPPSSRNKQVPTY--YLLKLLSKTPMLGVT 342
++ L+ L IDP K +P ++K+ S T LGVT
Sbjct: 1106 IKMLQDLTGIDP------KTIPMDDPEVMKIFSSTESLGVT 1140
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 25.8 bits (57), Expect = 3.8
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 41 KPFSCSVCGKTFTR 54
KP+ C VCGK+F+
Sbjct: 13 KPYKCPVCGKSFSS 26
Score = 25.8 bits (57), Expect = 3.8
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 149 KPFSCSVCGKTFTR 162
KP+ C VCGK+F+
Sbjct: 13 KPYKCPVCGKSFSS 26
>gnl|CDD|180750 PRK06921, PRK06921, hypothetical protein; Provisional.
Length = 266
Score = 29.0 bits (65), Expect = 4.0
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 24 RHRKRAHDLDPPEGAEAKPFSCSVC---GKTFTRREHLRRHQQIHARE 68
R+R PE ++A+ + C C G RR +Q E
Sbjct: 14 LMRERPSTTTKPEESDAERYDCPKCKDRGIIIYRRNTAEVWRQCECVE 61
Score = 29.0 bits (65), Expect = 4.0
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 132 RHRKRAHDLDPPEGAEAKPFSCSVC---GKTFTRREHLRRHQQIHARE 176
R+R PE ++A+ + C C G RR +Q E
Sbjct: 14 LMRERPSTTTKPEESDAERYDCPKCKDRGIIIYRRNTAEVWRQCECVE 61
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 29.0 bits (65), Expect = 4.6
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 2 DVVRPFQCDVCNQGFVRKEHLVRHRKRAHDLDPPEGAE 39
D + + C+ C + RKE L RH K+ DL P G E
Sbjct: 194 DCSKLYFCEFCLKFMKRKEQLQRHMKKC-DLKHPPGDE 230
Score = 29.0 bits (65), Expect = 4.6
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 110 DVVRPFQCDVCNQGFVRKEHLVRHRKRAHDLDPPEGAE 147
D + + C+ C + RKE L RH K+ DL P G E
Sbjct: 194 DCSKLYFCEFCLKFMKRKEQLQRHMKKC-DLKHPPGDE 230
Score = 28.2 bits (63), Expect = 7.2
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 290 CDVCKKVFSRRSHLLRHLKRLHNIDPP 316
C+ C K R+ L RH+K+ PP
Sbjct: 201 CEFCLKFMKRKEQLQRHMKKCDLKHPP 227
>gnl|CDD|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9. The second
LIM domain of Lhx9: Lhx9 belongs to the 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.
Lhx9 is highly homologous to Lhx2. It is expressed in
several regions of the developing mouse brain, the
spinal cord, the pancreas, in limb mesenchyme, and in
the urogenital region. Lhx9 plays critical roles in
gonad development. Homozygous mice lacking functional
Lhx9 alleles exhibit numerous urogenital defects, such
as gonadal agenesis, infertility, and undetectable
levels of testosterone and estradiol coupled with high
FSH levels. Lhx9 null mice have reduced levels of the
Sf1 nuclear receptor that is required for
gonadogenesis, and recent studies have shown that Lhx9
is able to activate the Sf1/FtzF1 gene. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
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.
Length = 59
Score = 26.2 bits (57), Expect = 4.8
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 8 QCDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSVCGKTFTRREHL 58
+C C+ G E ++R R+ + L F+C+ C KT T +H
Sbjct: 4 RCARCHLGISASEMVMRARESVYHL--------SCFTCTTCNKTLTTGDHF 46
Score = 26.2 bits (57), Expect = 4.8
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 116 QCDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSVCGKTFTRREHL 166
+C C+ G E ++R R+ + L F+C+ C KT T +H
Sbjct: 4 RCARCHLGISASEMVMRARESVYHL--------SCFTCTTCNKTLTTGDHF 46
>gnl|CDD|219837 pfam08430, Fork_head_N, Forkhead N-terminal region. The region
described in this family is found towards the N-terminus
of various eukaryotic fork head/HNF-3-related
transcription factors (which contain the pfam00250
domain). These proteins play key roles in embryogenesis,
maintenance of differentiated cell states, and
tumorigenesis.
Length = 137
Score = 27.6 bits (61), Expect = 5.4
Identities = 7/42 (16%), Positives = 15/42 (35%)
Query: 180 SSMDMSALTGLAGMGGELQMPLFAASLMPEISMSSGGSGNSS 221
+ + G++ MG L ++ P + S G +
Sbjct: 69 GAGSPMGMMGMSSMGTSLSPSGTMGAMGPMPAGSGGSLSPNM 110
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 25.3 bits (56), Expect = 5.5
Identities = 7/24 (29%), Positives = 10/24 (41%), Gaps = 1/24 (4%)
Query: 7 FQCDVCNQGFVRKEHLVRHRKRAH 30
++C C + L RH K H
Sbjct: 1 YKCSHCPY-SSTPKKLERHLKLHH 23
Score = 25.3 bits (56), Expect = 5.5
Identities = 7/24 (29%), Positives = 10/24 (41%), Gaps = 1/24 (4%)
Query: 115 FQCDVCNQGFVRKEHLVRHRKRAH 138
++C C + L RH K H
Sbjct: 1 YKCSHCPY-SSTPKKLERHLKLHH 23
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 26.7 bits (59), Expect = 6.1
Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 13/55 (23%)
Query: 7 FQCDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSVCGKTFTRREHLRRH 61
F+C +C V L +H +R H L C VC K++ L +H
Sbjct: 2 FKCPICGFTTVTLFALKQHARRNHTLT----------KCPVCNKSYR---RLNQH 43
Score = 26.7 bits (59), Expect = 6.1
Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 13/55 (23%)
Query: 115 FQCDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSVCGKTFTRREHLRRH 169
F+C +C V L +H +R H L C VC K++ L +H
Sbjct: 2 FKCPICGFTTVTLFALKQHARRNHTLT----------KCPVCNKSYR---RLNQH 43
>gnl|CDD|183745 PRK12787, fliX, flagellar assembly regulator FliX; Reviewed.
Length = 138
Score = 27.3 bits (61), Expect = 7.3
Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 4/59 (6%)
Query: 213 SSGGSGNSSPRVKKEGDDGSEDPMEVELPPPEASSSPLNRPAAPAALTALGGIPLAVRE 271
G+ + S + E + ++ P A A + AL LA++
Sbjct: 5 GPNGTTAAGGSRSARRTGSSGFSLPDESASGAGEARAVSAPKAVAGVDAL----LALQG 59
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 28.3 bits (64), Expect = 7.5
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 8/41 (19%)
Query: 304 LRHLKRLHNIDPPPSSRNKQVPTY--YLLKLLSKTPMLGVT 342
+R L+ L IDP K +P ++KL S T LGVT
Sbjct: 1100 IRMLQDLTGIDP------KTIPMDDPKVMKLFSSTEALGVT 1134
>gnl|CDD|224443 COG1526, FdhD, Uncharacterized protein required for formate
dehydrogenase activity [Energy production and
conversion].
Length = 266
Score = 27.7 bits (62), Expect = 9.7
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 9/55 (16%)
Query: 106 IEGIDVVRPFQCDVCNQGFVRKEHLVRHRKRAHDLDPPEGAEAKPFSCSVCGKTF 160
IE ++V D + V+ V KRA+ L A A C VCG+
Sbjct: 72 IESVEVD-----DQGSGNEVQ----VELSKRANPLKARRRALAGRSGCGVCGRES 117
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 0.136 0.415
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: 18,458,865
Number of extensions: 1800227
Number of successful extensions: 2334
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2320
Number of HSP's successfully gapped: 89
Length of query: 348
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 250
Effective length of database: 6,590,910
Effective search space: 1647727500
Effective search space used: 1647727500
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 (21.8 bits)
S2: 59 (26.6 bits)