RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5057
(87 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 = 77.4 bits (191), Expect = 3e-20
Identities = 31/84 (36%), Positives = 47/84 (55%), Gaps = 1/84 (1%)
Query: 1 MFEKPVEAGDIVIRQGDDGDFFYVIESGRYEASVE-IDGEDKLMHAYEDKGSFGELALLY 59
+ E+ AG+++IRQGD D Y++ SG E DG ++++ FGELALL
Sbjct: 17 LEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLG 76
Query: 60 NMPRAATIKATSTGSLWAMDRKTF 83
N PR+AT++A + L + R F
Sbjct: 77 NGPRSATVRALTDSELLVLPRSDF 100
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 70.4 bits (173), Expect = 9e-18
Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 3 EKPVEAGDIVIRQGDDGDFFYVIESGRYEASVEIDGEDKLMHAYEDKGS-FGELALLYNM 61
+ + G+++ R+GD D Y++ SG+ + + + + A+ G FGELALL
Sbjct: 1 LRSFKKGEVIFREGDPADSLYIVLSGKVKVYKLDEDGREQILAFLGPGDFFGELALLGGE 60
Query: 62 PRAATIKATSTGSLWAMDRKTFY 84
PR+AT+ A + L + R+ F
Sbjct: 61 PRSATVVALTDSELLVIPREDFL 83
>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 = 70.9 bits (174), Expect = 1e-17
Identities = 33/84 (39%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 1 MFEKPVEAGDIVIRQGDDGDFFYVIESGRYEASVE-IDGEDKLMHAYEDKGSFGELALLY 59
+ AG+++IRQGD GD FY+I SG E DGE++++ FGELALL
Sbjct: 17 LEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLT 76
Query: 60 NMPRAATIKATSTGSLWAMDRKTF 83
N RAA+ A + L + R F
Sbjct: 77 NSRRAASAAAVAL-ELATLLRIDF 99
>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 = 65.2 bits (159), Expect = 1e-14
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 1 MFEKPVEAGDIVIRQGDDGDFFYVIESGRYEASVE-IDGEDKLMHAYEDKGSFGELALLY 59
+ + + G+++ +G++ D Y+I SG + DG + ++ FGELALL
Sbjct: 23 LEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYANTEDGREIILGFLGPGDFFGELALLG 82
Query: 60 NMPRAATIKATSTGSLWAMDRKTF 83
PR+A+ A + + + RK F
Sbjct: 83 GDPRSASAVALTDVEVLEIPRKDF 106
>gnl|CDD|234384 TIGR03896, cyc_nuc_ocin, bacteriocin-type transport-associated
protein. Members of this protein family are
uncharacterized and contain two copies of the cyclic
nucleotide-binding domain pfam00027. Members are
restricted to select cyanobacteria but are found
regularly in association with a transport operon that,
in turn, is associated with the production of putative
bacteriocins. The models describing the transport
operon are TIGR03794, TIGR03796, and TIGR03797.
Length = 317
Score = 34.1 bits (78), Expect = 0.004
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 6 VEAGDIVIRQGDDGDFFYVIESGRYEASVEIDGEDKLMHAYE----DKGSF-GELALLYN 60
+ AG +I +G DF +++ G + + ++ L A+E +G GE++LL
Sbjct: 13 IAAGTTLIEEGKAADFLFILLDGTFTVTTPQPEDNPLTRAFELARLSRGEIVGEMSLLET 72
Query: 61 MPRAATIKATSTGSLW 76
P ATIKA S
Sbjct: 73 RPPVATIKAVP-KSRV 87
Score = 32.9 bits (75), Expect = 0.010
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 4 KPVEAGDIVIRQGDDGDFFYVIESGRYEASVEIDGEDKLMHAYEDKGSFGELALLY-NMP 62
+ + AG I+I +G D Y++ G S+ DG + + + GE L ++P
Sbjct: 164 QKLPAGTILIHEGGTVDALYILLYGEASLSISPDGPGREVGSSRRGEILGETPFLNGSLP 223
Query: 63 RAATIKATSTGSLWAMDRK 81
AT+KA L A+D++
Sbjct: 224 GTATVKAIENSVLLAIDKQ 242
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator
Crp; Provisional.
Length = 211
Score = 33.0 bits (76), Expect = 0.008
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 12 VIRQGDDGDFFYVIESGRYEASVEIDGED--KLMHAYEDKGSF-GELALL-YNMPRAATI 67
+I G+ + Y I G +V I E+ +++ +Y ++G F GEL L R+A +
Sbjct: 31 LIHAGEKAETLYYIVKG--SVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWV 88
Query: 68 KA 69
+A
Sbjct: 89 RA 90
>gnl|CDD|178459 PLN02868, PLN02868, acyl-CoA thioesterase family protein.
Length = 413
Score = 29.7 bits (67), Expect = 0.12
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 7 EAGDIVIRQGDDGDFFYVIESGRYEAS 33
G+ V+R+G+ GD Y I G E S
Sbjct: 37 GKGEYVVREGEPGDGLYFIWKGEAEVS 63
>gnl|CDD|239766 cd04100, Asp_Lys_Asn_RS_N, Asp_Lys_Asn_RS_N: N-terminal,
anticodon recognition domain of class 2b aminoacyl-tRNA
synthetases (aaRSs). This domain is a beta-barrel
domain (OB fold) involved in binding the tRNA anticodon
stem-loop. Class 2b aaRSs include the homodimeric
aspartyl-, asparaginyl-, and lysyl-tRNA synthetases
(AspRS, AsnRS, and LysRS). aaRSs catalyze the specific
attachment of amino acids (AAs) to their cognate tRNAs
during protein biosynthesis. This 2-step reaction
involves i) the activation of the AA by ATP in the
presence of magnesium ions, followed by ii) the
transfer of the activated AA to the terminal ribose of
tRNA. In the case of the class2b aaRSs, the activated
AA is attached to the 3'OH of the terminal ribose.
Eukaryotes contain 2 sets of aaRSs, both of which are
encoded by the nuclear genome. One set concerns with
cytoplasmic protein synthesis, whereas the other
exclusively with mitochondrial protein synthesis.
Included in this group are archeal and archeal-like
AspRSs which are non-discriminating and can charge both
tRNAAsp and tRNAAsn. E. coli cells have two isoforms of
LysRSs (LysS and LysU) encoded by two distinct genes,
which are differentially regulated. The cytoplasmic and
the mitochondrial isoforms of human LysRS are encoded
by a single gene. Yeast cytoplasmic and mitochondrial
LysRSs participate in mitochondrial import of
cytoplasmic tRNAlysCUU. In addition to their
housekeeping role, human LysRS may function as a
signaling molecule that activates immune cells. Tomato
LysRS may participate in a process possibly connected
to conditions of oxidative-stress conditions or heavy
metal uptake. It is known that human tRNAlys and LysRS
are specifically packaged into HIV-1 suggesting a role
for LysRS in tRNA packaging. AsnRS is immunodominant
antigen of the filarial nematode Brugia malayai and is
of interest as a target for anti-parasitic drug design.
Human AsnRS has been shown to be a pro-inflammatory
chemokine which interacts with CCR3 chemokine receptors
on T cells, immature dendritic cells and macrophages.
Length = 85
Score = 27.5 bits (62), Expect = 0.37
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 11 IVIRQGDDGDFFYVIESGRYEASVEIDGE 39
+V+ + + G+FF E R E+ V + G
Sbjct: 31 VVVNKEELGEFFEEAEKLRTESVVGVTGT 59
>gnl|CDD|181817 PRK09392, ftrB, transcriptional activator FtrB; Provisional.
Length = 236
Score = 26.9 bits (60), Expect = 1.1
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 8 AGDIVIRQGDDGDFFYVIESGRYEASVEIDGEDKLM 43
G ++I +G+ DF +V+ G E S + +
Sbjct: 37 PGTMLITEGEPADFLFVVLDGLVELSASSQDRETTL 72
>gnl|CDD|180916 PRK07276, PRK07276, DNA polymerase III subunit delta'; Validated.
Length = 290
Score = 26.5 bits (59), Expect = 2.0
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 30 YEASVEIDGEDKLMHAYEDKGSFG--ELALL 58
++ I +D+L HAY G F E+AL
Sbjct: 11 FQRFQTILEQDRLNHAYLFSGDFASFEMALF 41
>gnl|CDD|237431 PRK13570, PRK13570, anthranilate synthase component I; Provisional.
Length = 455
Score = 25.3 bits (56), Expect = 4.4
Identities = 13/36 (36%), Positives = 14/36 (38%), Gaps = 3/36 (8%)
Query: 2 FEKPVEAGDIVIRQGDDGDFFYVIESGRYEASVEID 37
F VE IR GD F V+ S R A D
Sbjct: 197 FCGMVEKAKEYIRAGD---IFQVVLSQRLSAEFTGD 229
>gnl|CDD|215508 PLN02941, PLN02941, inositol-tetrakisphosphate 1-kinase.
Length = 328
Score = 25.3 bits (56), Expect = 4.7
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 12 VIRQGDDGDFFYVI 25
+IR+ GD +YVI
Sbjct: 285 MIREHGTGDRYYVI 298
>gnl|CDD|206223 pfam14053, DUF4248, Domain of unknown function (DUF4248). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 73 and 86 amino
acids in length.
Length = 69
Score = 24.4 bits (54), Expect = 4.7
Identities = 9/21 (42%), Positives = 10/21 (47%), Gaps = 3/21 (14%)
Query: 51 SFGELALLYN---MPRAATIK 68
ELALLY P +A K
Sbjct: 7 GKSELALLYFPDLTPASAVRK 27
>gnl|CDD|236959 PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE;
Provisional.
Length = 234
Score = 24.8 bits (55), Expect = 6.8
Identities = 11/39 (28%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 6 VEAGD-IVIRQGDDGDFFYVIES-GRYEASVEIDGEDKL 42
++ GD + + GD G++ I G+ E +EI + +L
Sbjct: 30 LKEGDELRLFDGDGGEYLAEITEIGKKEVELEILEKLEL 68
>gnl|CDD|225011 COG2100, COG2100, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 414
Score = 24.7 bits (54), Expect = 6.9
Identities = 18/80 (22%), Positives = 29/80 (36%), Gaps = 10/80 (12%)
Query: 11 IVIRQGDDGDF---FYVIESGRYEASVEIDGED-KLMHAYEDKGSFGELALLYNMPRAAT 66
IV R+ DF ++ SVE+D ED L +++ +A L +
Sbjct: 14 IVWRRTLTADFERKIEEAIVRKFRVSVEVDVEDGYLAIPTDNEDIERFVAFLISNNLGGL 73
Query: 67 IKATSTGSLWAMDRKTFYCN 86
+K T R+ Y
Sbjct: 74 LKNKYTK------RRVIYII 87
>gnl|CDD|183004 PRK11161, PRK11161, fumarate/nitrate reduction transcriptional
regulator; Provisional.
Length = 235
Score = 24.7 bits (54), Expect = 7.2
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 4 KPVEAGDIVIRQGDDGDFFYVIESG 28
KP++ G + + GD+ Y I SG
Sbjct: 40 KPIQKGQTLFKAGDELKSLYAIRSG 64
>gnl|CDD|234441 TIGR04014, B12_SAM_MJ_0865, B12-binding domain/radical SAM domain
protein, MJ_0865 family. Members of this family have
both a B12 binding homology domain (pfam02310) and a
radical SAM domain (pfam04055), and occur only once per
genome. This protein occurs so far only in methanogenic
archaea. Some species with members of this family have a
related protein with similar domain architecture (see
TIGR04013) [Unknown function, Enzymes of unknown
specificity].
Length = 434
Score = 24.7 bits (54), Expect = 8.2
Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 7 EAGDIVIRQGDDGDFFYVIESGRYEASVEIDGEDK----LMHAY 46
E +V+ +D + +V G Y A + + E + ++HA
Sbjct: 353 ELARLVLELPEDENPVFVPHEGEYRALLLSEAEARAFDLMLHAE 396
>gnl|CDD|216127 pfam00800, PDT, Prephenate dehydratase. This protein is involved
in Phenylalanine biosynthesis. This protein catalyzes
the decarboxylation of prephenate to phenylpyruvate.
Length = 181
Score = 24.4 bits (54), Expect = 9.1
Identities = 5/24 (20%), Positives = 11/24 (45%)
Query: 49 KGSFGELALLYNMPRAATIKATST 72
+G+F E A L ++ + +
Sbjct: 7 EGTFSEQAALKLFGQSVELVPCPS 30
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
0.319 0.137 0.407
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: 4,454,528
Number of extensions: 359531
Number of successful extensions: 339
Number of sequences better than 10.0: 1
Number of HSP's gapped: 334
Number of HSP's successfully gapped: 22
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.3 bits)