RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8804
(114 letters)
>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of
transcription factors; members include CAP (or cAMP
receptor protein (CRP)), which binds cAMP, FNR
(fumarate and nitrate reduction), which uses an
iron-sulfur cluster to sense oxygen) and CooA, a heme
containing CO sensor. In all cases binding of the
effector leads to conformational changes and the
ability to activate transcription. Cyclic
nucleotide-binding domain similar to CAP are also
present in cAMP- and cGMP-dependent protein kinases
(cAPK and cGPK) and vertebrate cyclic nucleotide-gated
ion-channels. Cyclic nucleotide-monophosphate binding
domain; proteins that bind cyclic nucleotides (cAMP or
cGMP) share a structural domain of about 120 residues;
the best studied is the prokaryotic catabolite gene
activator, CAP, where such a domain is known to be
composed of three alpha-helices and a distinctive
eight-stranded, antiparallel beta-barrel structure;
three conserved glycine residues are thought to be
essential for maintenance of the structural integrity
of the beta-barrel; CooA is a homodimeric transcription
factor that belongs to CAP family; cAMP- and
cGMP-dependent protein kinases (cAPK and cGPK) contain
two tandem copies of the cyclic nucleotide-binding
domain; cAPK's are composed of two different subunits,
a catalytic chain and a regulatory chain, which
contains both copies of the domain; cGPK's are single
chain enzymes that include the two copies of the domain
in their N-terminal section; also found in vertebrate
cyclic nucleotide-gated ion-channels.
Length = 115
Score = 43.1 bits (102), Expect = 2e-06
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 4/68 (5%)
Query: 23 DSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFIDGSMFLPQSRNFVFNVFS 82
D L L + R A +V+ G+ + S YI+LSGSV + R +
Sbjct: 7 DEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEV--YKLDEDGREQIVGFLG 64
Query: 83 P--VFGLI 88
P +FG +
Sbjct: 65 PGDLFGEL 72
>gnl|CDD|197516 smart00100, cNMP, Cyclic nucleotide-monophosphate binding domain.
Catabolite gene activator protein (CAP) is a
prokaryotic homologue of eukaryotic cNMP-binding
domains, present in ion channels, and cNMP-dependent
kinases.
Length = 120
Score = 37.8 bits (88), Expect = 2e-04
Identities = 13/45 (28%), Positives = 22/45 (48%)
Query: 18 LAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSV 62
LR L + R+ A +V+ G++ S+YI++SG V
Sbjct: 2 FKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEV 46
>gnl|CDD|223736 COG0664, Crp, cAMP-binding proteins - catabolite gene activator
and regulatory subunit of cAMP-dependent protein
kinases [Signal transduction mechanisms].
Length = 214
Score = 36.3 bits (84), Expect = 0.001
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 4/79 (5%)
Query: 12 LHGLEALAPYRDSVLRSLCRVVRYERHQANDVLYYTGELSTSWYILLSGSVFIDGSMFLP 71
L L +L L + + +VL+ GE + S YI+LSG V +
Sbjct: 2 LKENPLLNLLPSELLELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKL--YANTE 59
Query: 72 QSRNFVFNVFSP--VFGLI 88
R + P FG +
Sbjct: 60 DGREIILGFLGPGDFFGEL 78
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 31.9 bits (73), Expect = 0.017
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 36 ERHQANDVLYYTGELSTSWYILLSGSVFIDGSMFLPQSRNFVFNVFSP--VFGLI 88
+ +V++ G+ + S YI+LSG V + R + P FG +
Sbjct: 2 RSFKKGEVIFREGDPADSLYIVLSGKVKV--YKLDEDGREQILAFLGPGDFFGEL 54
>gnl|CDD|193600 cd09986, LOTUS_1_TDRD7, The first LOTUS domain on
Tudor-containing protein 7 (TDRD7). The first LOTUS
domain on Tudor-containing protein 7 (TDRD7): TDRD7
contains three N-terminal LOTUS domains and three Tudor
domain repeats at the C-terminus. It belongs to the
evolutionary conserved Tudor domain-containing protein
(TDRD) family involved in germ cell development. In
mice, TDRD7 together with TDRD1/MTR-1, TDRD5 and TDRD6
forms a ribonucleoprotein complex in the
intermitochondrial cements (IMCs) and the chromatoid
bodies (CBs) involving in RNA processing for
spermatogenesis. TDRD7 is functionally essential for
the differentiation of germ cells. The exact molecular
function of LOTUS domain on TDRD7 remains to be
characterized. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 88
Score = 27.1 bits (60), Expect = 0.95
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 9/52 (17%)
Query: 4 DLQIIYYGLHGLEALAPYR-------DSVLRSLCRVVRYERHQANDVLYYTG 48
LQ Y L G P++ D++LRS+ VVR ER ++ +V+ +
Sbjct: 23 RLQGEYKELTG--EQIPFKQLGYHTLDALLRSMPSVVRLERSRSGEVMCFAS 72
>gnl|CDD|235970 PRK07217, PRK07217, replication factor A; Reviewed.
Length = 311
Score = 25.7 bits (57), Expect = 7.0
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 93 VSMAAKVSTLWDPGS 107
V + AKV LW+P S
Sbjct: 85 VDVTAKVVQLWEPSS 99
>gnl|CDD|236539 PRK09490, metH, B12-dependent methionine synthase; Provisional.
Length = 1229
Score = 25.1 bits (56), Expect = 9.6
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 60 GSVFIDGSMFLPQ 72
G +F +G MFLPQ
Sbjct: 707 GDLFGEGKMFLPQ 719
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
0.325 0.139 0.427
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,909,684
Number of extensions: 508715
Number of successful extensions: 578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 578
Number of HSP's successfully gapped: 29
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
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: 53 (24.3 bits)