RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11807
(88 letters)
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 30.3 bits (68), Expect = 0.074
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 12 CIFIFHEFCIRGWCIVGKKQICPYCKEKV 40
C I H C++ W ++Q CP C+ V
Sbjct: 318 CGHILHLHCLKNWL--ERQQTCPICRRPV 344
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 29.8 bits (68), Expect = 0.13
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 7/30 (23%)
Query: 29 KKQICPYCKEK-VDLKLMFVNLWEKPHVFY 57
K+ +CP+C EK +K EKP FY
Sbjct: 144 KRMVCPHCGEKQYKIKF------EKPTTFY 167
>gnl|CDD|204746 pfam11793, FANCL_C, FANCL C-terminal domain. This domain is
found at the C-terminus of the Fancl protein in humans
which is the putative E3 ubiquitin ligase subunit of
the FA complex (Fanconi anaemia). Eight subunits of the
Fanconi anaemia gene products form a multisubunit
nuclear complex which is required for
mono-ubiquitination of a downstream FA protein, FANCD2.
Length = 70
Score = 27.0 bits (60), Expect = 0.52
Identities = 13/44 (29%), Positives = 16/44 (36%), Gaps = 15/44 (34%)
Query: 12 CIFIFHEFCIRGW------------CIVGKKQICPYCKEKVDLK 43
C FH C+ W G CPYCK K+ +K
Sbjct: 28 CGLPFHIACLYEWLRTLRDSRQSFNVSFGT---CPYCKAKISVK 68
>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 = 24.7 bits (54), Expect = 2.4
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 15 IFHEFCIRGWCIVGKKQICPYCKEKV 40
+F CI W GK CP C+ +
Sbjct: 21 VFCRSCIDKWLKSGKNT-CPLCRTPI 45
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 26.0 bits (57), Expect = 2.5
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 10 TYCIFIFHEFCIRGWCIVGKKQICPYCKEKVDLK 43
T C +F C+ K + CP C+ KV K
Sbjct: 231 TPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPK 264
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 26.2 bits (57), Expect = 3.1
Identities = 10/31 (32%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 7 TCKTYCIFIFHEFCIRGWCIVGKKQICPYCK 37
C T C FH C+ W + CP C+
Sbjct: 1490 RCAT-CKNKFHTRCLYKWFASSARSNCPLCR 1519
>gnl|CDD|218888 pfam06087, Tyr-DNA_phospho, Tyrosyl-DNA phosphodiesterase.
Covalent intermediates between topoisomerase I and DNA
can become dead-end complexes that lead to cell death.
Tyrosyl-DNA phosphodiesterase can hydrolyse the bond
between topoisomerase I and DNA.
Length = 433
Score = 25.8 bits (57), Expect = 3.6
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 5 IMTCKTYCIFIFHEFCIRGWCIVG 28
KTY F +F W +V
Sbjct: 341 PPHIKTYIRFNDEDFKDLDWALVT 364
>gnl|CDD|218547 pfam05303, DUF727, Protein of unknown function (DUF727). This
family consists of several uncharacterized eukaryotic
proteins of unknown function.
Length = 108
Score = 25.0 bits (55), Expect = 3.8
Identities = 6/19 (31%), Positives = 9/19 (47%), Gaps = 4/19 (21%)
Query: 10 TYCIFIFHEFCIRGWCIVG 28
YC+ E +G+ IV
Sbjct: 44 RYCV----ELTEKGFRIVS 58
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 23.9 bits (52), Expect = 5.0
Identities = 7/23 (30%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 15 IFHEFCIRGWCIVGKKQICPYCK 37
+FH+ C+ W CP C+
Sbjct: 24 VFHKECLDKWL--RSSNTCPLCR 44
>gnl|CDD|220192 pfam09345, DUF1987, Domain of unknown function (DUF1987). This
family of proteins are functionally uncharacterized.
Length = 99
Score = 24.4 bits (54), Expect = 5.7
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 51 EKPHVFYGQLLDWLR 65
E FY +LDWL
Sbjct: 21 ENAFEFYEPILDWLE 35
>gnl|CDD|227282 COG4946, COG4946, Uncharacterized protein related to the
periplasmic component of the Tol biopolymer transport
system [Function unknown].
Length = 668
Score = 24.8 bits (54), Expect = 7.5
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 8 CKTYCIFIFHEFCIRGW 24
C Y FHEFC++ +
Sbjct: 26 CAKYYYIGFHEFCMKNY 42
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
0.334 0.148 0.547
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,524,441
Number of extensions: 351692
Number of successful extensions: 724
Number of sequences better than 10.0: 1
Number of HSP's gapped: 722
Number of HSP's successfully gapped: 30
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.5 bits)
S2: 53 (24.2 bits)