RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8691
(211 letters)
>gnl|CDD|217926 pfam04146, YTH, YT521-B-like domain. A protein of the YTH family
has been shown to selectively remove transcripts of
meiosis-specific genes expressed in mitotic cells. It
has been speculated that in higher eukaryotic YTH-family
members may be involved in similar mechanisms to
suppress gene regulation during gametogenesis or general
silencing. The rat protein YT521-B is a
tyrosine-phosphorylated nuclear protein, that interacts
with the nuclear transcriptosomal component scaffold
attachment factor B, and the 68-kDa Src substrate
associated during mitosis, Sam68. In vivo splicing
assays demonstrated that YT521-B modulates alternative
splice site selection in a concentration-dependent
manner. The YTH domain has been identified as part of
the PUA superfamily.
Length = 135
Score = 113 bits (286), Expect = 2e-32
Identities = 49/154 (31%), Positives = 69/154 (44%), Gaps = 45/154 (29%)
Query: 50 RFFVIKSNNSENVDIAKSQGVWSTLPQNEQKLNQAYRESRDVLLIFSNYYVSNELNFKVY 109
RFF+IKS N +NV ++ Y
Sbjct: 1 RFFIIKSYNEDNVHLSIK-----------------------------------------Y 19
Query: 110 GVWSTLPQNEQKLNQAYRESRNVLLIFSVRESGKFSGFARLASEADHGVSPVKWVLPPGL 169
GVW++ N +KLN+A++E+ V LIFSV +SGKF G+AR+ S D +
Sbjct: 20 GVWASTSHNNKKLNKAFKEAEPVYLIFSVNKSGKFCGYARMTSPIDFDSTANSQ----DS 75
Query: 170 SGKVLNGVFKIDWVSRKELPFTSTLHLYNSWNEG 203
S + G FK++W+S K+LPF HL N NE
Sbjct: 76 SSQKWGGPFKVEWLSVKDLPFHRLRHLKNPNNEN 109
>gnl|CDD|221346 pfam11967, RecO_N, Recombination protein O N terminal.
Recombination protein O (RecO) is involved in DNA repair
and pfam00470 pathway recombination. This domain forms a
beta barrel structure.
Length = 80
Score = 28.3 bits (64), Expect = 0.72
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 124 QAYRESRNVLLIFSVRESGKFSGFAR 149
+ Y ES ++ +F+ RE GK SG AR
Sbjct: 14 RDYGESDKIVTLFT-REHGKISGVAR 38
>gnl|CDD|177158 MTH00095, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 527
Score = 28.3 bits (64), Expect = 3.0
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 93 LIFSNYYVSNELNFKVY 109
L+FS+YY++ ELNF +
Sbjct: 62 LVFSSYYMNGELNFNYF 78
>gnl|CDD|119131 pfam10611, DUF2469, Protein of unknown function (DUF2469). Member
proteins often found in Actinomycetes clustered with
signal peptidase and/or RNAse-HII.
Length = 101
Score = 26.2 bits (58), Expect = 5.5
Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 7/33 (21%)
Query: 83 QAYRESRDVLLIFS-------NYYVSNELNFKV 108
YRE RDV+ +FS +Y++N ++ +V
Sbjct: 16 SLYREYRDVVGLFSYVVETERRFYLANSVDLQV 48
>gnl|CDD|143509 cd06842, PLPDE_III_Y4yA_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Y4yA. This subfamily is composed
of the hypothetical Rhizobium sp. protein Y4yA and
similar uncharacterized bacterial proteins. These
proteins are homologous to eukaryotic ornithine
decarboxylase (ODC) and diaminopimelate decarboxylase
(DapDC). ODC and DapDC are fold type III PLP-dependent
enzymes that contain an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain,
similar to bacterial alanine racemases. ODC participates
in the formation of putrescine by catalyzing the
decarboxylation of ornithine, the first step in
polyamine biosynthesis. DapDC participates in the last
step of lysine biosynthesis, the conversion of
meso-2,6-diaminoheptanedioate to L-lysine. Proteins in
this subfamily may function as PLP-dependent
decarboxylases.
Length = 423
Score = 27.6 bits (62), Expect = 6.0
Identities = 10/45 (22%), Positives = 16/45 (35%)
Query: 114 TLPQNEQKLNQAYRESRNVLLIFSVRESGKFSGFARLASEADHGV 158
T +N L ++ R++ K R A+ A GV
Sbjct: 19 TFRENIAALRAVLDRHGVDGRVYFARKANKSLALVRAAAAAGIGV 63
>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
Length = 590
Score = 27.4 bits (61), Expect = 6.7
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 179 KIDWVSRKELPFTSTLHLYNSWNEGE 204
+I WV E+P HL+N+W E E
Sbjct: 390 EIQWV---EVPDCFCFHLWNAWEEPE 412
>gnl|CDD|224653 COG1739, COG1739, Uncharacterized conserved protein [Function
unknown].
Length = 203
Score = 26.5 bits (59), Expect = 8.5
Identities = 6/71 (8%), Positives = 20/71 (28%), Gaps = 1/71 (1%)
Query: 57 NNSENVDIAKSQGVWSTLPQNEQKLNQAYRESRDVLLIFSNYYVSNELNFKVYGVWSTLP 116
+E ++ +++ L + + D + + Y + V +
Sbjct: 125 EAAEAIEKKEAKANHVGCAYRILGLLERLLKQNDDDVEEARYS-GGSVLLTVRFRHIVIE 183
Query: 117 QNEQKLNQAYR 127
+ L +
Sbjct: 184 AVSRLLKGNHI 194
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
0.317 0.132 0.399
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,577,541
Number of extensions: 939088
Number of successful extensions: 755
Number of sequences better than 10.0: 1
Number of HSP's gapped: 754
Number of HSP's successfully gapped: 16
Length of query: 211
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 118
Effective length of database: 6,812,680
Effective search space: 803896240
Effective search space used: 803896240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.7 bits)