RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1917
(212 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 = 79.3 bits (196), Expect = 2e-19
Identities = 32/149 (21%), Positives = 60/149 (40%), Gaps = 47/149 (31%)
Query: 62 FLKNLDTLQVKEMVESMHQAEYKADSYVITEGEAGNDLFVSAEGEFQVIKDGKILAVMGP 121
LD +++E+ +++ + + A +I +G+ + L++ G +V K
Sbjct: 1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLD-------- 52
Query: 122 GKAFGELAILYNCTRTASIRGFLTVLHFNFSVSAEGEFQVIKDGKILAVMGPGKAFGELA 181
+G Q I+ +GPG FGELA
Sbjct: 53 ---------------------------------EDGREQ------IVGFLGPGDLFGELA 73
Query: 182 ILYNCTRTASIRALTPCKVWMLDRRVFQK 210
+L N R+A++RALT ++ +L R F++
Sbjct: 74 LLGNGPRSATVRALTDSELLVLPRSDFRR 102
>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 = 67.0 bits (164), Expect = 1e-14
Identities = 28/84 (33%), Positives = 46/84 (54%), Gaps = 5/84 (5%)
Query: 62 FLKNLDTLQVKEMVESMHQAEYKADSYVITEGEAGNDLFVSAEGEFQVIKD-----GKIL 116
KNLD +++E+ +++ Y A +I +G+ G+ ++ GE +V K +I+
Sbjct: 1 LFKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIV 60
Query: 117 AVMGPGKAFGELAILYNCTRTASI 140
+GPG FGELA+L N R AS
Sbjct: 61 GTLGPGDFFGELALLTNSRRAASA 84
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 59.6 bits (145), Expect = 5e-12
Identities = 28/129 (21%), Positives = 48/129 (37%), Gaps = 47/129 (36%)
Query: 82 EYKADSYVITEGEAGNDLFVSAEGEFQVIKDGKILAVMGPGKAFGELAILYNCTRTASIR 141
+K + EG+ + L++ G+ +V K +
Sbjct: 3 SFKKGEVIFREGDPADSLYIVLSGKVKVYKLDE--------------------------- 35
Query: 142 GFLTVLHFNFSVSAEGEFQVIKDGKILAVMGPGKAFGELAILYNCTRTASIRALTPCKVW 201
+G Q ILA +GPG FGELA+L R+A++ ALT ++
Sbjct: 36 --------------DGREQ------ILAFLGPGDFFGELALLGGEPRSATVVALTDSELL 75
Query: 202 MLDRRVFQK 210
++ R F +
Sbjct: 76 VIPREDFLE 84
>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 = 50.6 bits (121), Expect = 8e-08
Identities = 30/151 (19%), Positives = 51/151 (33%), Gaps = 47/151 (31%)
Query: 60 NDFLKNLDTLQVKEMVESMHQAEYKADSYVITEGEAGNDLFVSAEGEFQVIKDGKILAVM 119
N L L + ++ + + + + TEGE + L++ G ++
Sbjct: 5 NPLLNLLPSELLELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYA-------- 56
Query: 120 GPGKAFGELAILYNCTRTASIRGFLTVLHFNFSVSAEGEFQVIKDGKILAVMGPGKAFGE 179
+ +G IL +GPG FGE
Sbjct: 57 ---------------------------------NTEDGREI------ILGFLGPGDFFGE 77
Query: 180 LAILYNCTRTASIRALTPCKVWMLDRRVFQK 210
LA+L R+AS ALT +V + R+ F +
Sbjct: 78 LALLGGDPRSASAVALTDVEVLEIPRKDFLE 108
>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 = 0.038
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 9/67 (13%)
Query: 74 MVESMHQAEYKADSYVITEGEAGNDLFVSAEGEFQV---------IKDGKILAVMGPGKA 124
MV HQ E A + +I EG+A + LF+ +G F V + LA + G+
Sbjct: 4 MVAIGHQREIAAGTTLIEEGKAADFLFILLDGTFTVTTPQPEDNPLTRAFELARLSRGEI 63
Query: 125 FGELAIL 131
GE+++L
Sbjct: 64 VGEMSLL 70
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator Crp;
Provisional.
Length = 211
Score = 32.6 bits (75), Expect = 0.086
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 164 DGK--ILAVMGPGKAFGELAIL-YNCTRTASIRALTPCKV 200
+GK IL+ + G GEL + R+A +RA T C+V
Sbjct: 57 EGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEV 96
Score = 31.1 bits (71), Expect = 0.28
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 79 HQAEYKADSYVITEGEAGNDLFVSAEGEFQVI---KDGK--ILAVMGPGKAFGELAIL-Y 132
H +Y A S +I GE L+ +G V+ ++GK IL+ + G GEL +
Sbjct: 21 HIHKYPAKSTLIHAGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEE 80
Query: 133 NCTRTASIR 141
R+A +R
Sbjct: 81 GQERSAWVR 89
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 32.5 bits (74), Expect = 0.14
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 12/73 (16%)
Query: 74 MVESMHQAEY---KADSYVITEGEAGNDLFVSAEGEFQVI----KDGKILAVMGPGKAFG 126
+V M +AEY + D VI + EA +D+++ GE ++I + +++ +G G FG
Sbjct: 393 LVTKM-KAEYIPPRED--VIMQNEAPDDVYIVVSGEVEIIDSEGEKERVVGTLGCGDIFG 449
Query: 127 ELAILYNCTRTAS 139
E+ L C R S
Sbjct: 450 EVGAL--CCRPQS 460
>gnl|CDD|178459 PLN02868, PLN02868, acyl-CoA thioesterase family protein.
Length = 413
Score = 31.2 bits (71), Expect = 0.31
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 10/76 (13%)
Query: 61 DFLKNLDTLQ------VKEMVESMHQAEYKADSYVITEGEAGNDLFVSAEGEFQVIK--- 111
+FL ++ LQ +K++ E + Y YV+ EGE G+ L+ +GE +V
Sbjct: 8 EFLGSVPLLQRLPSSSLKKIAEVVVPKRYGKGEYVVREGEPGDGLYFIWKGEAEVSGPAE 67
Query: 112 -DGKILAVMGPGKAFG 126
+ + ++ FG
Sbjct: 68 EESRPEFLLKRYDYFG 83
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 29.7 bits (68), Expect = 0.64
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 8/31 (25%)
Query: 98 DLFVSAEG--------EFQVIKDGKILAVMG 120
D+FV+A G F+ +KDG ILA G
Sbjct: 80 DIFVTATGNKDVITREHFRAMKDGAILANAG 110
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 28.2 bits (64), Expect = 3.9
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 8/31 (25%)
Query: 98 DLFVSAEG--------EFQVIKDGKILAVMG 120
D+FV+A G + +KDG ILA +G
Sbjct: 269 DIFVTATGNKDVITAEHMEAMKDGAILANIG 299
>gnl|CDD|178914 PRK00173, rph, ribonuclease PH; Reviewed.
Length = 238
Score = 27.0 bits (61), Expect = 6.3
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 12/49 (24%)
Query: 175 KAFGELAILYNC--------TRTASIR----ALTPCKVWMLDRRVFQKS 211
KA GE I +C TRTASI AL ++ R +K+
Sbjct: 105 KALGERTITIDCDVIQADGGTRTASITGAYVALADALNKLVARGKLKKN 153
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 27.2 bits (61), Expect = 6.6
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 75 VESMHQAEYKADSYVITEGEAGNDLFVSAEGEFQVIKDGKILAVMG 120
V +M +A D +V GN + E F+ +KDG ILA G
Sbjct: 255 VMTMEEAAKTGDIFVTA---TGNKDVIRKE-HFEKMKDGAILANAG 296
>gnl|CDD|212663 cd07782, FGGY_YpCarbK_like, Yersinia Pseudotuberculosis
carbohydrate kinase-like subgroup; belongs to the FGGY
family of carbohydrate kinases. This subgroup is
composed of the uncharacterized Yersinia
Pseudotuberculosis carbohydrate kinase that has been
named glyerol/xylulose kinase and similar
uncharacterized proteins from bacteria and eukaryota.
Carbohydrate kinases catalyze the ATP-dependent
phosphorylation of their carbohydrate substrate to
produce phosphorylated sugar and ADP. The presence of
Mg2+ is required for catalytic activity. This subgroup
shows high homology to characterized ribulokinases and
belongs to the FGGY family of carbohydrate kinases, the
monomers of which contain two large domains, which are
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain.
Length = 536
Score = 27.2 bits (61), Expect = 7.3
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 69 LQVKEMVESMHQAEYKADSYVITEGEAGNDLFV 101
+ ++E+M+ A +K D+ G + N LFV
Sbjct: 424 YGTRHIIEAMNAAGHKIDTLFACGGLSKNPLFV 456
>gnl|CDD|217705 pfam03739, YjgP_YjgQ, Predicted permease YjgP/YjgQ family. Members
of this family are predicted integral membrane proteins
of unknown function. They are about 350 amino acids long
and contain about 6 transmembrane regions. They are
predicted to be permeases although there is no
verification of this.
Length = 354
Score = 26.9 bits (60), Expect = 8.1
Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 2/42 (4%)
Query: 26 GESSTNGQTANDIQIQRYDKDFRSKQLIKA--AIMDNDFLKN 65
+ +G + I +D D +I A A +D+D
Sbjct: 157 DKVDPDGNRLEGVFIYDFDSDGGLTSIITAKSATLDSDTGGG 198
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
0.318 0.134 0.378
Gapped
Lambda K H
0.267 0.0864 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,343,382
Number of extensions: 950190
Number of successful extensions: 875
Number of sequences better than 10.0: 1
Number of HSP's gapped: 867
Number of HSP's successfully gapped: 28
Length of query: 212
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 119
Effective length of database: 6,812,680
Effective search space: 810708920
Effective search space used: 810708920
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 (25.5 bits)