RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17006
(446 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 = 266 bits (681), Expect = 5e-88
Identities = 111/198 (56%), Positives = 135/198 (68%), Gaps = 2/198 (1%)
Query: 248 IRNLAMEKVAETVTFPCRYQMNGCNVVLLHTEKPEHEDACEYRPYHCPCPGASCKWSGAL 307
IRNLA+EKVA V FPC++ GC V L K HE+ CEY+PY CP PGA CKW G
Sbjct: 1 IRNLAVEKVASKVLFPCKHAALGCPVRLPLQLKDWHEERCEYKPYFCPMPGAKCKWQGDE 60
Query: 308 DQVMGHLNQSHKTITTLQGE-DIVFLATDINLAGAVDWVMMQ-SCFGHHFMLVLEKQEID 365
D +M HL HK ITT GE DIV+LA +NL GA WVM+Q SCFG HF L LEK ++
Sbjct: 61 DDLMPHLTADHKVITTEGGEFDIVYLAAAVNLVGAPTWVMVQFSCFGRHFNLYLEKYDLG 120
Query: 366 GRQHFFAIVQLIGSRKQAEHFTYRLELNGHRRRLTWEATPRSIHEGIASAIMNSDCLVFD 425
G Q +FA++QLIG RK+AE+F Y LEL G+RR+LTW+A PRSI + AI DCL+F
Sbjct: 121 GTQMYFAVIQLIGERKEAENFAYELELGGNRRKLTWQAFPRSIRDDHKFAIDGRDCLIFL 180
Query: 426 SNIAQLFADNKNLGINVT 443
N A+ FA++KNL VT
Sbjct: 181 RNAARFFAEDKNLHYRVT 198
Score = 189 bits (482), Expect = 3e-58
Identities = 82/143 (57%), Positives = 98/143 (68%), Gaps = 2/143 (1%)
Query: 80 IRNLAMEKVAETVTFPCRYQMNGCNVVLLHTEKPEHEDACEYRPYHCPCPGASCKWSGAL 139
IRNLA+EKVA V FPC++ GC V L K HE+ CEY+PY CP PGA CKW G
Sbjct: 1 IRNLAVEKVASKVLFPCKHAALGCPVRLPLQLKDWHEERCEYKPYFCPMPGAKCKWQGDE 60
Query: 140 DQVMGHLNQSHKTITTLQGE-DIVFLATDINLAGAVDWVMMQ-SCFGHHFMLVLEKQEID 197
D +M HL HK ITT GE DIV+LA +NL GA WVM+Q SCFG HF L LEK ++
Sbjct: 61 DDLMPHLTADHKVITTEGGEFDIVYLAAAVNLVGAPTWVMVQFSCFGRHFNLYLEKYDLG 120
Query: 198 GRQHFFAIVQLIGSRKQAEHFTY 220
G Q +FA++QLIG RK+AE+F Y
Sbjct: 121 GTQMYFAVIQLIGERKEAENFAY 143
>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 = 228 bits (582), Expect = 3e-74
Identities = 103/127 (81%), Positives = 114/127 (89%), Gaps = 1/127 (0%)
Query: 321 ITTLQGEDIVFLATDINLAGAVDWVMMQSCFGHHFMLVLEKQEI-DGRQHFFAIVQLIGS 379
+TTLQGEDIVFLATDINL GA DWVMMQSCFGHHFMLVLEKQE+ +G Q FFA VQLIG+
Sbjct: 1 VTTLQGEDIVFLATDINLPGATDWVMMQSCFGHHFMLVLEKQELYEGHQQFFAFVQLIGT 60
Query: 380 RKQAEHFTYRLELNGHRRRLTWEATPRSIHEGIASAIMNSDCLVFDSNIAQLFADNKNLG 439
KQAE+FTYRLELNG+RRRLTWEATPRSI EG AS I NSDCLVFD++IAQLF++N NLG
Sbjct: 61 EKQAENFTYRLELNGNRRRLTWEATPRSIREGHASVIDNSDCLVFDTSIAQLFSENGNLG 120
Query: 440 INVTIAT 446
INVTI+
Sbjct: 121 INVTISG 127
Score = 123 bits (311), Expect = 4e-34
Identities = 57/69 (82%), Positives = 62/69 (89%), Gaps = 1/69 (1%)
Query: 153 ITTLQGEDIVFLATDINLAGAVDWVMMQSCFGHHFMLVLEKQEI-DGRQHFFAIVQLIGS 211
+TTLQGEDIVFLATDINL GA DWVMMQSCFGHHFMLVLEKQE+ +G Q FFA VQLIG+
Sbjct: 1 VTTLQGEDIVFLATDINLPGATDWVMMQSCFGHHFMLVLEKQELYEGHQQFFAFVQLIGT 60
Query: 212 RKQAEHFTY 220
KQAE+FTY
Sbjct: 61 EKQAENFTY 69
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 35.5 bits (82), Expect = 0.002
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 37 FECPVCFDYVLPPIIQCQSGHLVCSNCRPKL----SCCSTCR 74
ECP+C D + P++ GH+ C C + S C CR
Sbjct: 3 LECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICR 44
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 35.8 bits (83), Expect = 0.049
Identities = 27/97 (27%), Positives = 41/97 (42%), Gaps = 18/97 (18%)
Query: 5 TMNNTVGI----VGSRR-----HEPTHPSMCP--GTSTDLASLFECPVCFDYVLPPIIQC 53
M++ G+ VG RR E T+ + CP GT T+ ++ CP C V P
Sbjct: 653 DMSDEGGVIEVEVGRRRCPSCGTE-TYENRCPDCGTHTEP--VYVCPDCGAEVPPD---- 705
Query: 54 QSGHLVCSNCRPKLSCCSTCRGPLGNIRNLAMEKVAE 90
+SG + C C +L+ + A+E V E
Sbjct: 706 ESGRVECPRCDVELTPYQRRTINVKEEYRSALENVGE 742
>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 = 27.9 bits (62), Expect = 1.0
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 39 CPVCFDYVLPPIIQCQSGHLVCSNC 63
CP+C + L + GH C +C
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSC 25
>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 = 31.1 bits (70), Expect = 1.1
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 33 LASLFECPVCFDYVLPPII-QCQSGHLVCSNC-RPKLSC---CSTCRGP 76
L + C +C D+ P++ C H CS C R LS C CR
Sbjct: 23 LDTSLRCHICKDFFDVPVLTSC--SHTFCSLCIRRCLSNQPKCPLCRAE 69
>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 = 30.9 bits (70), Expect = 1.3
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 6/53 (11%)
Query: 386 FTYRL-----ELNGHRRRLTWEATPRSIHEGI-ASAIMNSDCLVFDSNIAQLF 432
+ Y L L +W T + E I +I+NS C D + A LF
Sbjct: 8 YVYDLPRRFNLLEDVLPETSWYLTHQYAAESILHKSILNSRCRTLDPDEADLF 60
>gnl|CDD|219493 pfam07638, Sigma70_ECF, ECF sigma factor. These proteins are
probably RNA polymerase sigma factors belonging to the
extra-cytoplasmic function (ECF) subfamily and show
sequence similarity to pfam04542 and pfam04545.
Length = 185
Score = 29.3 bits (66), Expect = 2.7
Identities = 19/76 (25%), Positives = 30/76 (39%), Gaps = 11/76 (14%)
Query: 362 QEIDGRQHFFAIVQLIGSRKQAEHF--TYRLELNGHRRRLTWEATPRSIHEGIASAIMNS 419
+ GR HFFA R +H R + G +R R + E + + +
Sbjct: 67 PDWSGRGHFFAAAAEAMRRILIDHARRRQRQKRGGDVQR-------RELDEVVDNGDSPN 119
Query: 420 DCLVFDSNIA--QLFA 433
L+ D + A QLF+
Sbjct: 120 PDLLLDLDEALEQLFS 135
>gnl|CDD|198290 cd03181, GST_C_EF1Bgamma_like, Glutathione S-transferase
C-terminal-like, alpha helical domain of the Gamma
subunit of Elongation Factor 1B and similar proteins.
Glutathione S-transferase (GST) C-terminal domain
family, Gamma subunit of Elongation Factor 1B
(EF1Bgamma) subfamily; EF1Bgamma is part of the
eukaryotic translation elongation factor-1 (EF1) complex
which plays a central role in the elongation cycle
during protein biosynthesis. EF1 consists of two
functionally distinct units, EF1A and EF1B. EF1A
catalyzes the GTP-dependent binding of aminoacyl-tRNA to
the ribosomal A site concomitant with the hydrolysis of
GTP. The resulting inactive EF1A:GDP complex is recycled
to the active GTP form by the guanine-nucleotide
exchange factor EF1B, a complex composed of at least two
subunits, alpha and gamma. Metazoan EFB1 contain a third
subunit, beta. The EF1B gamma subunit contains a GST
fold consisting of an N-terminal thioredoxin-fold domain
and a C-terminal alpha helical domain. The GST-like
domain of EF1Bgamma is believed to mediate the
dimerization of the EF1 complex, which in yeast is a
dimer of the heterotrimer EF1A:EF1Balpha:EF1Bgamma. In
addition to its role in protein biosynthesis, EF1Bgamma
may also display other functions. The recombinant rice
protein has been shown to possess GSH conjugating
activity. The yeast EF1Bgamma binds to membranes in a
calcium dependent manner and is also part of a complex
that binds to the msrA (methionine sulfoxide reductase)
promoter suggesting a function in the regulation of its
gene expression. Also included in this subfamily is the
GST_C-like domain at the N-terminus of human valyl-tRNA
synthetase (ValRS) and its homologs. Metazoan ValRS
forms a stable complex with Elongation Factor-1H
(EF-1H), and together, they catalyze consecutive steps
in protein biosynthesis, tRNA aminoacylation and its
transfer to EF.
Length = 123
Score = 28.7 bits (65), Expect = 2.7
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 138 ALDQVMGHLNQSHKTITTLQGEDIVFLATDINLAGAVDWVMMQSCFGHHF 187
L + +G L + T T L GE I LA DI +A A+ ++ F
Sbjct: 44 DLKRALGVLEEHLLTRTYLVGERI-TLA-DIFVASALLRG-FETVLDPEF 90
Score = 28.7 bits (65), Expect = 2.7
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 306 ALDQVMGHLNQSHKTITTLQGEDIVFLATDINLAGAVDWVMMQSCFGHHF 355
L + +G L + T T L GE I LA DI +A A+ ++ F
Sbjct: 44 DLKRALGVLEEHLLTRTYLVGERI-TLA-DIFVASALLRG-FETVLDPEF 90
>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 = 26.6 bits (59), Expect = 3.4
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 38 ECPVCFDYVLPPIIQCQSGHLVCSNC-----RPKLSCCSTCRGPL 77
ECP+C + P++ GH+ C +C + + C CR P+
Sbjct: 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 29.5 bits (67), Expect = 5.2
Identities = 16/71 (22%), Positives = 25/71 (35%), Gaps = 9/71 (12%)
Query: 26 CP--GTSTDLASLFECPVCFDYVLP----PIIQCQSGHLVCSNCRPKLSCCSTCRGPLGN 79
CP G T CP C + P P + C C + + S + L
Sbjct: 629 CPSCGKET---FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTPYSKRKIDLKE 685
Query: 80 IRNLAMEKVAE 90
+ + A+E + E
Sbjct: 686 LYDRALENLGE 696
>gnl|CDD|234438 TIGR03999, thiol_BshA, N-acetyl-alpha-D-glucosaminyl L-malate
synthase BshA. Members of this protein family are BshA,
a glycosyltransferase required for bacillithiol
biosynthesis. This enzyme combines UDP-GlcNAc and
L-malate to form N-acetyl-alpha-D-glucosaminyl L-malate
synthase. Bacillithiol is a low-molecular-weight thiol,
an analog of glutathione and mycothiol, and is found
largely in the Firmicutes [Biosynthesis of cofactors,
prosthetic groups, and carriers, Glutathione and
analogs].
Length = 374
Score = 28.7 bits (65), Expect = 6.5
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 141 QVMGHLNQSHKTITTLQGEDIVFLATDINLAGAVDWVMMQS 181
Q++G +TTL G DI + D + AV + + +S
Sbjct: 105 QMLGKEGIDIPIVTTLHGTDITLVGADPSFKPAVRFSIEKS 145
Score = 28.7 bits (65), Expect = 6.5
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 309 QVMGHLNQSHKTITTLQGEDIVFLATDINLAGAVDWVMMQS 349
Q++G +TTL G DI + D + AV + + +S
Sbjct: 105 QMLGKEGIDIPIVTTLHGTDITLVGADPSFKPAVRFSIEKS 145
>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 = 25.1 bits (55), Expect = 9.2
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 39 CPVCFDYVLPPIIQCQSGHLVCSNC 63
CP+C + P+ GHL CS C
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKC 25
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2;
Provisional.
Length = 193
Score = 27.7 bits (61), Expect = 9.7
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 29 TSTDLASLFECPVCFDYVLPPIIQCQSGHLVCSNCRPKLSCCS 71
T D F+C +C D V P++ GHL C C K + S
Sbjct: 11 TLVDSGGDFDCNICLDQVRDPVVTL-CGHLFCWPCIHKWTYAS 52
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
0.324 0.136 0.447
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: 21,627,431
Number of extensions: 1988777
Number of successful extensions: 1873
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1864
Number of HSP's successfully gapped: 24
Length of query: 446
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 346
Effective length of database: 6,502,202
Effective search space: 2249761892
Effective search space used: 2249761892
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 (21.6 bits)
S2: 61 (27.5 bits)