RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12278
(300 letters)
>gnl|CDD|190542 pfam03145, Sina, Seven in absentia protein family. The seven in
absentia (sina) gene was first identified in Drosophila.
The Drosophila Sina protein is essential for the
determination of the R7 pathway in photoreceptor cell
development: the loss of functional Sina results in the
transformation of the R7 precursor cell to a non-
neuronal cell type. The Sina protein contains an
N-terminal RING finger domain pfam00097. Through this
domain, Sina binds E2 ubiquitin-conjugating enzymes
(UbcD1) Sina also interacts with Tramtrack (TTK88) via
PHYL. Tramtrack is a transcriptional repressor that
blocks photoreceptor determination, while PHYL
down-regulates the activity of TTK88. In turn, the
activity of PHYL requires the activation of the
Sevenless receptor tyrosine kinase, a process essential
for R7 determination. It is thought that thus Sina
targets TTK88 for degradation, therefore promoting the
R7 pathway. Murine and human homologues of Sina have
also been identified. The human homologue Siah-1 also
binds E2 enzymes (UbcH5) and through a series of
physical interactions, targets beta-catenin for
ubiquitin degradation. Siah-1 expression is enhanced by
p53, itself promoted by DNA damage. Thus this pathway
links DNA damage to beta-catenin degradation. Sina
proteins, therefore, physically interact with a variety
of proteins. The N-terminal RING finger domain that
binds ubiquitin conjugating enzymes is described in
pfam00097, and does not form part of the alignment for
this family. The remainder C-terminal part is involved
in interactions with other proteins, and is included in
this alignment. In addition to the Drosophila protein
and mammalian homologues, whose similarity was noted
previously, this family also includes putative
homologues from Caenorhabditis elegans, Arabidopsis
thaliana.
Length = 198
Score = 270 bits (692), Expect = 8e-92
Identities = 107/199 (53%), Positives = 133/199 (66%), Gaps = 3/199 (1%)
Query: 100 IRNLAMEKVAGTMWFPCRYQMNGCGISLLHTEKPEHEDTCEHRPYLCPCPGASCKWGGAL 159
IRNLA+EKVA + FPC++ GC + L K HE+ CE++PY CP PGA CKW G
Sbjct: 1 IRNLAVEKVASKVLFPCKHAALGCPVRLPLQLKDWHEERCEYKPYFCPMPGAKCKWQGDE 60
Query: 160 DQVMAHLNQSHKSITTLQGE-DIVFLATDINLPGAVDWVMMQ-SCFGHHFMLVLEKQEKF 217
D +M HL HK ITT GE DIV+LA +NL GA WVM+Q SCFG HF L LEK +
Sbjct: 61 DDLMPHLTADHKVITTEGGEFDIVYLAAAVNLVGAPTWVMVQFSCFGRHFNLYLEKYDL- 119
Query: 218 DGHQHFFAIVQLIGSRKQSENFTYRLELNGHRRRLTWEATPRSIHEGVASAIMNSDCLVF 277
G Q +FA++QLIG RK++ENF Y LEL G+RR+LTW+A PRSI + AI DCL+F
Sbjct: 120 GGTQMYFAVIQLIGERKEAENFAYELELGGNRRKLTWQAFPRSIRDDHKFAIDGRDCLIF 179
Query: 278 DTNIAQLFADNGNLGINVT 296
N A+ FA++ NL VT
Sbjct: 180 LRNAARFFAEDKNLHYRVT 198
>gnl|CDD|239753 cd03829, Sina, Seven in absentia (Sina) protein family, C-terminal
substrate binding domain; composed of the Drosophila
Sina protein, the mammalian Sina homolog (Siah), the
plant protein SINAT5, and similar proteins. Sina, Siah
and SINAT5 are RING-containing proteins that function as
E3 ubiquitin ligases, acting either as single proteins
or as a part of multiprotein complexes. Sina is
expressed in many cells in the developing eye but is
essential specifically for R7 photoreceptor cell
development. Sina cooperates with Phyllopod (Phyl), Ebi
and the E2 ubiquitin-conjugating enzyme Ubcd1 to
catalyze the ubiquitination and subsequent degradation
of Tramtrack (Ttk88); Ttk88 is a transcriptional
repressor that blocks photoreceptor differentiation.
Similarly, the mammalian homologue Siah1 cooperates with
SIP (Siah-interacting protein), Ebi and the adaptor
protein Skp1, to target beta-catenin for ubiquitination
and degradation via a p53-dependent mechanism. SINAT5
targets NAC1 for ubiquitin-mediated degradation
resulting in the downregulation of auxin, a hormone that
controls many aspects of plant development. Other
targets of Sina family proteins include c-Myb,
synaptophysin, group 1 glutamate receptors,
promyelocytic leukemia protein, alpha-synuclein,
synphilin-1 and alpha-ketoglutarate dehydrogenase, among
others. Sina proteins also bind proteins that are not
targets for ubiquitination such as Phyl, adenomatous
polyposis coli, VAV, BAG-1 and Dab-1. Siah binds to a
consensus motif, PXAXVXP, which is present in
Siah-binding proteins. Siah is a dimeric protein
consisting of an N-terminal RING domain, two zinc finger
motifs and a C-terminal substrate-binding domain (SBD);
this SBD contains an eight-stranded antiparallel
beta-sandwich fold similar to the MATH (meprin and
TRAF-C homology) domain.
Length = 127
Score = 248 bits (634), Expect = 6e-84
Identities = 107/125 (85%), Positives = 116/125 (92%)
Query: 173 ITTLQGEDIVFLATDINLPGAVDWVMMQSCFGHHFMLVLEKQEKFDGHQHFFAIVQLIGS 232
+TTLQGEDIVFLATDINLPGA DWVMMQSCFGHHFMLVLEKQE ++GHQ FFA VQLIG+
Sbjct: 1 VTTLQGEDIVFLATDINLPGATDWVMMQSCFGHHFMLVLEKQELYEGHQQFFAFVQLIGT 60
Query: 233 RKQSENFTYRLELNGHRRRLTWEATPRSIHEGVASAIMNSDCLVFDTNIAQLFADNGNLG 292
KQ+ENFTYRLELNG+RRRLTWEATPRSI EG AS I NSDCLVFDT+IAQLF++NGNLG
Sbjct: 61 EKQAENFTYRLELNGNRRRLTWEATPRSIREGHASVIDNSDCLVFDTSIAQLFSENGNLG 120
Query: 293 INVTI 297
INVTI
Sbjct: 121 INVTI 125
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 42.9 bits (101), Expect = 4e-06
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 57 FECPVCFDYVLPPIIQCQSGHLVCSNCRPKL----SCCPTCR 94
ECP+C D + P++ GH+ C C + S CP CR
Sbjct: 3 LECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICR 44
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and
is likely to be a general function of this domain;
Various RING fingers exhibit binding activity towards
E2 ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 32.9 bits (75), Expect = 0.012
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 5/40 (12%)
Query: 59 CPVCFDYVLPPIIQCQSGHLVCSNC-----RPKLSCCPTC 93
CP+C + L + GH C +C + CP C
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain,
a specialized type of Zn-finger of 40 to 60 residues
that binds two atoms of zinc; defined by the
'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified
in a proteins with a wide range of functions such as
viral replication, signal transduction, and
development; has two variants, the C3HC4-type and a
C3H2C3-type (RING-H2 finger), which have different
cysteine/histidine pattern; a subset of RINGs are
associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 32.8 bits (75), Expect = 0.014
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 58 ECPVCFDYVLPPIIQCQSGHLVCSNC-----RPKLSCCPTCRGPL 97
ECP+C + P++ GH+ C +C + + CP CR P+
Sbjct: 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 34.6 bits (79), Expect = 0.048
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 7/49 (14%)
Query: 53 LASLFECPVCFDYVLPPII-QCQSGHLVCSNC-RPKLSC---CPTCRGP 96
L + C +C D+ P++ C H CS C R LS CP CR
Sbjct: 23 LDTSLRCHICKDFFDVPVLTSC--SHTFCSLCIRRCLSNQPKCPLCRAE 69
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 29.7 bits (67), Expect = 0.16
Identities = 13/40 (32%), Positives = 16/40 (40%), Gaps = 5/40 (12%)
Query: 59 CPVCFDYVLPPIIQCQSGHLVCSNC-----RPKLSCCPTC 93
CP+C + P+ GHL CS C CP C
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 29.3 bits (66), Expect = 0.28
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 57 FECPVCFDYVLP--PIIQCQSGHLVCSNC-RPKL---SCCPTCRGP 96
ECP+C D P ++ GH+ C L + CP CR P
Sbjct: 1 DECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46
>gnl|CDD|226399 COG3882, FkbH, Predicted enzyme involved in methoxymalonyl-ACP
biosynthesis [Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 574
Score = 32.1 bits (73), Expect = 0.36
Identities = 19/78 (24%), Positives = 28/78 (35%), Gaps = 18/78 (23%)
Query: 216 KFDGHQHFFAIVQLIGSRKQSENFTYRLELNGHRRRLTWEATPRSIHEGVASAIMNSDCL 275
KFD + I QL Q N T + R E V + + L
Sbjct: 418 KFDEV-NIPRISQLTQKTNQF-NLTTK--------RYN--------EEDVRQMQEDPNFL 459
Query: 276 VFDTNIAQLFADNGNLGI 293
+F ++ F DNG +G+
Sbjct: 460 IFSVSLKDKFGDNGIIGV 477
>gnl|CDD|219500 pfam07655, Secretin_N_2, Secretin N-terminal domain. This is a
short domain found in bacterial type II/III secretory
system proteins. The architecture of these proteins
suggest that this family may be functionally analogous
to pfam03958.
Length = 95
Score = 28.8 bits (65), Expect = 1.1
Identities = 13/48 (27%), Positives = 20/48 (41%)
Query: 10 VDSNPNHTVGIVGSKKHGPGNGLNNISPSSSSNSSNSAGTSTDLASLF 57
V S + G S + + S SSS +SS+ +T+ S F
Sbjct: 21 VTSGSVSSSGSNSSSSSSNSSNGGSSSSSSSGDSSSGTRITTESESDF 68
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 30.8 bits (70), Expect = 1.2
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 48 GTSTDLASLFECPVCFDYVLPPIIQCQSGHLVCSNCRPKLSCCPTCRGPLGNIRNLAMEK 107
GT T+ ++ CP C V P +SG + C C +L+ + A+E
Sbjct: 686 GTHTEP--VYVCPDCGAEVPPD----ESGRVECPRCDVELTPYQRRTINVKEEYRSALEN 739
Query: 108 V 108
V
Sbjct: 740 V 740
>gnl|CDD|221480 pfam12238, MSA-2c, Merozoite surface antigen 2c. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 263 and 318 amino acids in length.
There is a conserved SFT sequence motif. MSA-2 is a
plasma membrane glycoprotein which can be found in
Babesia bovis species.
Length = 201
Score = 29.0 bits (65), Expect = 2.4
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 23 SKKHGPGNGLNNISPSSSSNSSNSAGTST 51
S KH G + PS S + N++ T
Sbjct: 143 SPKHSSSQGTSTTRPSDGSATPNTSAPPT 171
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 26.2 bits (58), Expect = 3.1
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 5/43 (11%)
Query: 58 ECPVCFDYVLPPIIQCQSGHLV-CSNCRPKL---SCCPTCRGP 96
C +C + ++ GHL C C +L CP CR P
Sbjct: 4 LCVICLERP-RNVVFLPCGHLCLCEECAKRLRSKKKCPICRQP 45
>gnl|CDD|237844 PRK14873, PRK14873, primosome assembly protein PriA; Provisional.
Length = 665
Score = 29.1 bits (66), Expect = 3.2
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 78 LVCSNCRPKLSCCPTCRGPLG 98
L C+ CR + C C GPLG
Sbjct: 384 LACARCR-TPARCRHCTGPLG 403
>gnl|CDD|224886 COG1975, XdhC, Xanthine and CO dehydrogenases maturation factor,
XdhC/CoxF family [Posttranslational modification,
protein turnover, chaperones].
Length = 278
Score = 28.9 bits (65), Expect = 3.6
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 224 FAIVQLIGSRKQSENFTYRLELNGHRR 250
V L+GSRK++ RL G
Sbjct: 197 AFYVGLLGSRKRAALRLERLRQAGLDE 223
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2;
Provisional.
Length = 193
Score = 28.1 bits (62), Expect = 4.5
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 49 TSTDLASLFECPVCFDYVLPPIIQCQSGHLVCSNC 83
T D F+C +C D V P++ GHL C C
Sbjct: 11 TLVDSGGDFDCNICLDQVRDPVVTL-CGHLFCWPC 44
>gnl|CDD|72673 pfam09257, BCMA-Tall_bind, BCMA, TALL-1 binding. Members of this
family, which are predominantly found in the tumour
necrosis factor receptor superfamily member 17, BCMA,
are required for binding to tumour necrosis factor
ligand TALL-1.
Length = 39
Score = 25.5 bits (55), Expect = 4.9
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 73 CQSGHLVCSNCRPKLSCCPTC 93
C L CS+ P L+C C
Sbjct: 14 CIPCQLRCSSNTPPLTCQRYC 34
>gnl|CDD|218612 pfam05501, DUF755, Domain of unknown function (DUF755). This
family is predominated by ORFs from Circoviridae. The
function of this family remains to be determined.
Length = 122
Score = 27.0 bits (60), Expect = 7.0
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 36 SPSSSSNSSNSAGTSTD 52
S SSSS+SS+S+ +S++
Sbjct: 104 SSSSSSSSSSSSSSSSE 120
>gnl|CDD|217320 pfam03016, Exostosin, Exostosin family. The EXT family is a family
of tumour suppressor genes. Mutations of EXT1 on 8q24.1,
EXT2 on 11p11-13, and EXT3 on 19p have been associated
with the autosomal dominant disorder known as hereditary
multiple exostoses (HME). This is the most common known
skeletal dysplasia. The chromosomal locations of other
EXT genes suggest association with other forms of
neoplasia. EXT1 and EXT2 have both been shown to encode
a heparan sulphate polymerase with both D-glucuronyl
(GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC)
transferase activities. The nature of the defect in
heparan sulphate biosynthesis in HME is unclear.
Length = 292
Score = 27.8 bits (62), Expect = 8.0
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 6/53 (11%)
Query: 239 FTYRL-----ELNGHRRRLTWEATPRSIHEG-VASAIMNSDCLVFDTNIAQLF 285
+ Y L L +W T + E + +I+NS C D + A LF
Sbjct: 8 YVYDLPRRFNLLEDVLPETSWYLTHQYAAESILHKSILNSRCRTLDPDEADLF 60
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
0.321 0.136 0.438
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,491,085
Number of extensions: 1287327
Number of successful extensions: 1110
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1091
Number of HSP's successfully gapped: 24
Length of query: 300
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 204
Effective length of database: 6,679,618
Effective search space: 1362642072
Effective search space used: 1362642072
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: 59 (26.7 bits)