RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14742
(66 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 = 48.1 bits (115), Expect = 4e-09
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 5 ILSKGRVEVSREN-----KYLSTLAPGKVFGELAILYNCKRTATIK 45
I+ G VEV + + + + L PG +FGELA+L N R+AT++
Sbjct: 40 IVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPRSATVR 85
>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 = 45.1 bits (107), Expect = 7e-08
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 5 ILSKGRVEVSR-----ENKYLSTLAPGKVFGELAILYNCKRTATIKV 46
I+ G VEV + E + + TL PG FGELA+L N +R A+
Sbjct: 40 IIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRRAASAAA 86
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 41.1 bits (97), Expect = 1e-06
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 5 ILSKGRVEVSRENK-----YLSTLAPGKVFGELAILYNCKRTATIKV 46
I+ G+V+V + ++ L+ L PG FGELA+L R+AT+
Sbjct: 22 IVLSGKVKVYKLDEDGREQILAFLGPGDFFGELALLGGEPRSATVVA 68
>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 = 33.7 bits (77), Expect = 0.002
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 5 ILSKGRVEVSREN-----KYLSTLAPGKVFGELAILYNCKRTATIKV 46
I+ G V++ L L PG FGELA+L R+A+
Sbjct: 46 IILSGIVKLYANTEDGREIILGFLGPGDFFGELALLGGDPRSASAVA 92
>gnl|CDD|223822 COG0751, GlyS, Glycyl-tRNA synthetase, beta subunit [Translation,
ribosomal structure and biogenesis].
Length = 691
Score = 25.6 bits (57), Expect = 1.7
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 4 RILSKGRVEVSRENKYLSTLAPGKVFGELAILYNCKRTATIK 45
R L G + + + Y+ L GKV I +R A I
Sbjct: 192 RFLGPGEITIDSADDYVEKLREGKV-----IADPEERKAIIL 228
>gnl|CDD|233578 TIGR01787, squalene_cyclas, squalene/oxidosqualene cyclases. This
family of enzymes catalyzes the cyclization of the
triterpenes squalene or 2-3-oxidosqualene to a variety
of products including hopene , lanosterol ,
cycloartenol, amyrin, lupeol and isomultiflorenol.
Length = 621
Score = 25.5 bits (56), Expect = 1.8
Identities = 11/58 (18%), Positives = 21/58 (36%), Gaps = 3/58 (5%)
Query: 1 MRDRILSKGRVEVSRENKYLSTLAPGKVFGELAILYNCKRTATIKVHWTLNLKSWGSR 58
M+ + ++L L P +VFG++ I + L ++G R
Sbjct: 400 MQSSNGGFAAYDPDNTGEWLELLNPSEVFGDIMIDPP---YVDVTARVIQALGAFGHR 454
>gnl|CDD|215880 pfam00370, FGGY_N, FGGY family of carbohydrate kinases, N-terminal
domain. This domain adopts a ribonuclease H-like fold
and is structurally related to the C-terminal domain.
Length = 245
Score = 25.0 bits (55), Expect = 2.8
Identities = 9/29 (31%), Positives = 11/29 (37%), Gaps = 2/29 (6%)
Query: 33 AILYNCKRTATIKVHWT--LNLKSWGSRT 59
AIL+N RTA I + T
Sbjct: 95 AILWNDTRTAEIVENLKEEGGADKLYEIT 123
>gnl|CDD|225902 COG3367, COG3367, Uncharacterized conserved protein [Function
unknown].
Length = 339
Score = 25.1 bits (55), Expect = 2.8
Identities = 4/28 (14%), Positives = 10/28 (35%)
Query: 39 KRTATIKVHWTLNLKSWGSRTSGDNEMG 66
KRT +++ + + + G
Sbjct: 162 KRTTALELREAAREEGIKAGFVATGQTG 189
>gnl|CDD|237225 PRK12843, PRK12843, putative FAD-binding dehydrogenase; Reviewed.
Length = 578
Score = 25.1 bits (55), Expect = 3.4
Identities = 10/23 (43%), Positives = 11/23 (47%)
Query: 21 STLAPGKVFGELAILYNCKRTAT 43
TL P VF LA + KRT
Sbjct: 552 ITLGPAIVFAYLAARHAAKRTLA 574
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 0.397
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: 3,122,602
Number of extensions: 208668
Number of successful extensions: 141
Number of sequences better than 10.0: 1
Number of HSP's gapped: 141
Number of HSP's successfully gapped: 9
Length of query: 66
Length of database: 10,937,602
Length adjustment: 37
Effective length of query: 29
Effective length of database: 9,296,504
Effective search space: 269598616
Effective search space used: 269598616
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: 53 (24.3 bits)