RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12127
(263 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 = 67.4 bits (165), Expect = 1e-13
Identities = 33/122 (27%), Positives = 58/122 (47%), Gaps = 15/122 (12%)
Query: 68 RNVALERIFTKLELPCRNFRFGCKVYLPKAKRDKHEDKCKFRQLKCPMHA--CPWTNSVL 125
RN+A+E++ +K+ PC++ GC V LP +D HE++C+++ CPM C W
Sbjct: 2 RNLAVEKVASKVLFPCKHAALGCPVRLPLQLKDWHEERCEYKPYFCPMPGAKCKWQGDED 61
Query: 126 HLSEHLNQVHHLHLLKGNGVNIEISNFKTKVSESETKVHKYVILM---NCYSQYFICKLC 182
L HL H + +G +I ++ + V +M +C+ ++F
Sbjct: 62 DLMPHLTADHKVITTEGGEFDI------VYLAAAVNLVGAPTWVMVQFSCFGRHF----N 111
Query: 183 LY 184
LY
Sbjct: 112 LY 113
>gnl|CDD|238250 cd00443, ADA_AMPD, Adenosine/AMP deaminase. Adenosine deaminases
(ADAs) are present in pro- and eukaryotic organisms and
catalyze the zinc dependent irreversible deamination of
adenosine nucleosides to inosine nucleosides and
ammonia. The eukaryotic AMP deaminase catalyzes a
similar reaction leading to the hydrolytic removal of an
amino group at the 6 position of the adenine nucleotide
ring, a branch point in the adenylate catabolic pathway.
Length = 305
Score = 35.4 bits (82), Expect = 0.019
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 107 KFRQLKCPMHACPWTNSVLHLSEHLNQVHHLHLLKGNGVNIEISN-----FKTKVSESET 161
+ P+ CP +N VL + + H G+ + +S F T +SE +
Sbjct: 209 LVKLRNIPIEVCPTSNVVLGTVQSYEK-HPFMRFFKAGLPVSLSTDDPGIFGTSLSEEYS 267
Query: 162 KVHKYVIL 169
K L
Sbjct: 268 LAAKTFGL 275
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 33.9 bits (77), Expect = 0.090
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 11/62 (17%)
Query: 12 NCKELIASISECGVC---LEPLDRGITS--CQTCGNLVCTSCAARLLK------CPFCRI 60
N E + EC +C L+ +DR + S C TC N T C + CP CR
Sbjct: 1461 NIDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRS 1520
Query: 61 TI 62
I
Sbjct: 1521 EI 1522
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 29.7 bits (67), Expect = 0.18
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 5/43 (11%)
Query: 22 ECGVCLEPLDRGITSCQT-CGNLVCTSCAARLLK----CPFCR 59
EC +CL+ + G CG++ C + L+ CP CR
Sbjct: 2 ECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCR 44
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 29.4 bits (66), Expect = 0.21
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 19 SISECGVCLEPLDRGITSCQTCGNLVCTSCAARLL----KCPFCR 59
EC +CL+ L + CG++ C C R L KCP CR
Sbjct: 1 EELECPICLDLLRDPVVLTP-CGHVFCRECILRYLKKKSKCPICR 44
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 30.8 bits (69), Expect = 0.72
Identities = 30/121 (24%), Positives = 45/121 (37%), Gaps = 13/121 (10%)
Query: 23 CGVCLEPLDRGITSCQTCGNLVCTSCAARLL------KCPFCRITIDYSWQRNVALERIF 76
C +C ++ CG+ +C +CA RL CP CR + + I
Sbjct: 64 CQICAGSTT--YSARYPCGHQICHACAVRLRALYMQKGCPLCRTETEAVVFTASSPADIT 121
Query: 77 TKLELPCRNFRFGCKVYLPKAKRDKHEDKCKFRQLKCPMHACPWT-NSVLHLSEHLNQVH 135
+ + R + G Y + RD+ ED F KCP C S+ L +H H
Sbjct: 122 DRRQWKGREEKVGI-FYEGEDVRDEMEDLLSF---KCPKSKCHRRCGSLKELKKHYKAQH 177
Query: 136 H 136
Sbjct: 178 G 178
>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 = 27.8 bits (62), Expect = 0.76
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 22 ECGVCLEPLDRGITSCQTCGNLVCTSCAARLL-----KCPFCRITI 62
EC +CLE CG++ C SC + L CP CR I
Sbjct: 1 ECPICLEEFRE-PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 30.2 bits (68), Expect = 0.94
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 8/44 (18%)
Query: 22 ECGVCLEPLDRGITSCQTCGNLVCTSC------AARLLKCPFCR 59
+C +CLE + + SC CG+L C SC + CP CR
Sbjct: 217 KCFLCLEEPE--VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCR 258
>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional.
Length = 567
Score = 30.6 bits (69), Expect = 1.0
Identities = 19/53 (35%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 83 CRNFRFGCKVYLPKAKRDKHEDKCKFRQLKCPMHACPWTNSVLHLSEHLNQVH 135
CRN CK Y+P HE C + CP C VL + E N VH
Sbjct: 410 CRN----CKHYIPSRSIALHEAYCSRHNVVCPHDGC---GIVLRVEEAKNHVH 455
>gnl|CDD|237027 PRK12266, glpD, glycerol-3-phosphate dehydrogenase; Reviewed.
Length = 508
Score = 29.0 bits (66), Expect = 3.0
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 117 ACPWTNSVLHLSEHLNQVHHLHLLKG 142
A PW L L + + L+KG
Sbjct: 212 AGPWVKQFLDDGLGLPSPYGIRLVKG 237
>gnl|CDD|232935 TIGR00354, polC, DNA polymerase, archaeal type II, large subunit.
This model represents the large subunit, DP2, of a two
subunit novel Archaeal replicative DNA polymerase first
characterized for Pyrococcus furiosus. Structure of DP2
appears to be organized as a ~950 residue component
separated from a ~300 residue component by a ~150
residue intein. The other subunit, DP1, has sequence
similarity to the eukaryotic DNA polymerase delta small
subunit [DNA metabolism, DNA replication, recombination,
and repair].
Length = 1095
Score = 29.1 bits (65), Expect = 3.2
Identities = 9/50 (18%), Positives = 17/50 (34%), Gaps = 4/50 (8%)
Query: 30 LDRGITSCQTCGN----LVCTSCAARLLKCPFCRITIDYSWQRNVALERI 75
++ I C CG L C C + + + +D A+ +
Sbjct: 621 VEIAIRKCPQCGKESFWLKCPVCGELTEQLYYGKRKVDLRELYEEAIANL 670
>gnl|CDD|213914 TIGR04301, ODC_inducible, ornithine decarboxylase SpeF. Members of
this family are known or trusted examples of ornithine
decarboxylase, all encoded in the immediate vicinity of
an ornithine-putrescine antiporter. Decarboxylation of
ornithine to putrescine, followed by exchange of a
putrescine for a new ornithine, is a proton-motive cycle
that can be induced by low pH and protect a bacterium
against transient exposure to acidic conditions.
Length = 719
Score = 28.5 bits (64), Expect = 3.9
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 174 SQYFI--CKLCLYKKVLTMSFVQISNSSPFHFGVFVNIASNFKSMKGIVP 221
+QYF+ CKL +LT + FG+ I +NF GI+P
Sbjct: 487 NQYFVDPCKL-----LLTTPGIDAETGEYEDFGIPATILANFLRENGIIP 531
>gnl|CDD|220517 pfam10005, DUF2248, Uncharacterized protein conserved in bacteria
(DUF2248). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 340
Score = 28.4 bits (64), Expect = 4.1
Identities = 9/30 (30%), Positives = 10/30 (33%), Gaps = 6/30 (20%)
Query: 36 SCQTCGNLV------CTSCAARLLKCPFCR 59
C CG V C +C A L P
Sbjct: 1 HCPNCGQPVFFENTACLACGAALGFDPDRL 30
>gnl|CDD|165250 PHA02940, PHA02940, hypothetical protein; Provisional.
Length = 315
Score = 28.4 bits (63), Expect = 4.2
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 244 DNCVKIYLNIRYMNAPIRFM 263
DN +++Y N+ +NA +R +
Sbjct: 100 DNAIELYANLAAINALLRLI 119
>gnl|CDD|129290 TIGR00186, rRNA_methyl_3, rRNA methylase, putative, group 3. this
is part of the trmH (spoU) family of rRNA methylases
[Protein synthesis, tRNA and rRNA base modification].
Length = 237
Score = 27.3 bits (61), Expect = 8.7
Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 12/61 (19%)
Query: 121 TNSVLHLSEHLNQVHH------------LHLLKGNGVNIEISNFKTKVSESETKVHKYVI 168
N+VL + +V + L K G+NI++ + + ++ H+ +
Sbjct: 7 KNAVLEALLNQQRVFILKGLESKRLKKLIQLAKKQGINIQLVDRQKLDQLTKGGNHQGIA 66
Query: 169 L 169
Sbjct: 67 A 67
>gnl|CDD|204552 pfam10764, Gin, Inhibitor of sigma-G Gin. Gin allows sigma-F to
delay late forespore transcription by preventing
sigma-G to take over before the cell has reached a
critical stage of development. Gin is also known as
CsfB.
Length = 46
Score = 24.9 bits (55), Expect = 8.8
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 23 CGVCLEPLDRGITSCQTCGNLVCTSCAARLLKC 55
C +C +P + GI G +CT C +L+
Sbjct: 2 CIICEQPKNEGI---HLYGKFICTECEKKLVNT 31
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
0.327 0.138 0.463
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: 12,297,873
Number of extensions: 1073592
Number of successful extensions: 1177
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1163
Number of HSP's successfully gapped: 40
Length of query: 263
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 168
Effective length of database: 6,723,972
Effective search space: 1129627296
Effective search space used: 1129627296
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: 58 (26.3 bits)