RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15589
(155 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 = 73.5 bits (181), Expect = 9e-18
Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 5/87 (5%)
Query: 49 FHQGDEGKSWYIIIQGSVDVVIYGKG----CVTSLYAGEDFGKLALVNNAPRAATIVTRE 104
QGD S YI++ GSV+V + V L G+ FG+LAL+ N PR+AT+
Sbjct: 29 IRQGDPADSLYIVLSGSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPRSATVRALT 88
Query: 105 DNCHFLRVDKDDFIRIMRDVEANTVRL 131
D L + + DF R++++ RL
Sbjct: 89 D-SELLVLPRSDFRRLLQEYPELARRL 114
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 65.0 bits (159), Expect = 1e-14
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 5/79 (6%)
Query: 49 FHQGDEGKSWYIIIQGSVDVVIYGKG----CVTSLYAGEDFGKLALVNNAPRAATIVTRE 104
F +GD S YI++ G V V + + L G+ FG+LAL+ PR+AT+V
Sbjct: 11 FREGDPADSLYIVLSGKVKVYKLDEDGREQILAFLGPGDFFGELALLGGEPRSATVVALT 70
Query: 105 DNCHFLRVDKDDFIRIMRD 123
D L + ++DF+ ++
Sbjct: 71 D-SELLVIPREDFLELLEQ 88
>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 = 59.0 bits (143), Expect = 4e-12
Identities = 26/90 (28%), Positives = 40/90 (44%), Gaps = 6/90 (6%)
Query: 49 FHQGDEGKSWYIIIQGSVDVVI---YGKGCVTSLYAGED-FGKLALVNNAPRAATIVTRE 104
QGD G S+YII+ G V+V G+ + D FG+LAL+ N+ RAA+
Sbjct: 29 IRQGDVGDSFYIIVSGEVEVYKVLEDGEEQIVGTLGPGDFFGELALLTNSRRAASAAAVA 88
Query: 105 DNCHFLRVDKDDFIRIMRDVEANTVRLKEH 134
+ + DF ++ + L E
Sbjct: 89 --LELATLLRIDFRDFLQLLPELPQLLLEL 116
>gnl|CDD|239884 cd04437, DEP_Epac, DEP (Dishevelled, Egl-10, and Pleckstrin)
domain found in Epac-like proteins. Epac (exchange
proteins directly activated by cAMP) proteins are GEFs
(guanine-nucleotide-exchange factors) for the small
GTPases, Rap1 and Rap2. They are directly regulated by
cyclic AMP, a second messenger that plays a role in the
control of diverse cellular processes, such as cell
adhesion and insulin secretion. Epac-like proteins
share a common domain architecture, containing RasGEF,
DEP and CAP-effector (cAMP binding) domains. The DEP
domain is involved in membrane localization.
Length = 125
Score = 57.4 bits (139), Expect = 2e-11
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 4 AGWVLRTLLLNDESGTLRDRKTSGGRTIARRCASGSELVDWLMTMFH 50
AG LR +L+D +RDRK R+C G+ELVDWL+
Sbjct: 1 AGRALRNAILSDAPHLIRDRKYHL--RTYRQCCVGTELVDWLLQQSP 45
>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 = 44.8 bits (106), Expect = 3e-06
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 49 FHQGDEGKSWYIIIQGSVDVVIY---GKGCVTSLYAGED-FGKLALVNNAPRAATIVTRE 104
F +G+E S YII+ G V + G+ + D FG+LAL+ PR+A+ V
Sbjct: 35 FTEGEEADSLYIILSGIVKLYANTEDGREIILGFLGPGDFFGELALLGGDPRSASAVALT 94
Query: 105 DNCHFLRVDKDDFIRIMR 122
D L + + DF+ ++
Sbjct: 95 D-VEVLEIPRKDFLELLA 111
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator Crp;
Provisional.
Length = 211
Score = 41.5 bits (98), Expect = 4e-05
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 47 TMFHQGDEGKSWYIIIQGSVDVVIY---GKGCVTS-LYAGEDFGKLAL-VNNAPRAATIV 101
T+ H G++ ++ Y I++GSV V+I GK + S L G+ G+L L R+A +
Sbjct: 30 TLIHAGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVR 89
Query: 102 TR 103
+
Sbjct: 90 AK 91
>gnl|CDD|216020 pfam00610, DEP, Domain found in Dishevelled, Egl-10, and
Pleckstrin (DEP). The DEP domain is responsible for
mediating intracellular protein targeting and
regulation of protein stability in the cell. The DEP
domain is present in a number of signaling molecules,
including Regulator of G protein Signaling (RGS)
proteins, and has been implicated in membrane
targeting. New findings in yeast, however, demonstrate
a major role for a DEP domain in mediating the
interaction of an RGS protein to the C-terminal tail of
a GPCR, thus placing RGS in close proximity with its
substrate G protein alpha subunit.
Length = 74
Score = 32.2 bits (74), Expect = 0.018
Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 19 TLRDRKTSGGRTIARRCASGSELVDWLMTMFH 50
L+DRK +T C +GSE VDWLM F
Sbjct: 3 KLKDRK-KHLKTY-PNCFTGSEAVDWLMDNFE 32
>gnl|CDD|239836 cd04371, DEP, DEP domain, named after Dishevelled, Egl-10, and
Pleckstrin, where this domain was first discovered. The
function of this domain is still not clear, but it is
believed to be important for the membrane association
of the signaling proteins in which it is present. New
studies show that the DEP domain of Sst2, a yeast RGS
protein is necessary and sufficient for receptor
interaction.
Length = 81
Score = 32.3 bits (74), Expect = 0.021
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 7 VLRTLLLNDESGTLRDRKTSGGRTIARRCASGSELVDWLMTMF 49
++R +L +D ++DRK +T C +GSELVDWL+
Sbjct: 2 LVRIMLDSDSGVPIKDRKY-HLKTY-PNCFTGSELVDWLLDNL 42
>gnl|CDD|214489 smart00049, DEP, Domain found in Dishevelled, Egl-10, and
Pleckstrin. Domain of unknown function present in
signalling proteins that contain PH, rasGEF, rhoGEF,
rhoGAP, RGS, PDZ domains. DEP domain in Drosophila
dishevelled is essential to rescue planar polarity
defects and induce JNK signalling (Cell 94, 109-118).
Length = 77
Score = 30.3 bits (69), Expect = 0.096
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 15 DESGTLRDRKTSGGRTIARRCASGSELVDWLM 46
E+G + +T C +GSELVDWLM
Sbjct: 1 PETGLKLRDRKYFLKTY-PNCFTGSELVDWLM 31
>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 = 30.6 bits (69), Expect = 0.27
Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 17/89 (19%)
Query: 42 VDWLM------------TMFHQGDEGKSWYIIIQGSVDVVIYGKGC---VTSLYAGEDFG 86
V W+M + H+G + YI++ G + I G V S GE G
Sbjct: 154 VAWMMASGTPQKLPAGTILIHEGGTVDALYILLYGEASLSISPDGPGREVGSSRRGEILG 213
Query: 87 KLALVN-NAPRAATIVTREDNCHFLRVDK 114
+ +N + P AT+ E N L +DK
Sbjct: 214 ETPFLNGSLPGTATVKAIE-NSVLLAIDK 241
>gnl|CDD|239886 cd04439, DEP_1_P-Rex, DEP (Dishevelled, Egl-10, and Pleckstrin)
domain 1 found in P-Rex-like proteins. The P-Rex family
is the guanine-nucleotide exchange factor (GEF) for the
small GTPase Rac that contains an N-terminal RhoGEF
domain, two DEP and PDZ domains. Rac-GEF activity is
stimulated by phosphatidylinositol
(3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second
messenger, and by the G beta-gamma subunits of
heterotrimeric G proteins. The DEP domains are not
involved in mediating these stimuli, but may be of
importance for basal and stimulated levels Rac-GEF
activity.
Length = 81
Score = 27.1 bits (60), Expect = 1.3
Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 12 LLNDESGTLRDRKTSGGRTIARRCASGSELVDWLMTM--FHQGDEG 55
++ + ++DR+ + +C G+E V WL+ + + +EG
Sbjct: 7 MMCKQGSLIKDRRRK--LSTFPKCFLGNEFVSWLLEIGEISKPEEG 50
>gnl|CDD|239888 cd04441, DEP_2_DEP6, DEP (Dishevelled, Egl-10, and Pleckstrin)
domain 2 found in DEP6-like proteins. DEP6 proteins
contain two DEP and a PDZ domain. Their function is
unknown.
Length = 85
Score = 27.0 bits (60), Expect = 2.0
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 12 LLNDESGTLRDRKTSGGRTIARRCASGSELVDWLM 46
L++ E+ L+ R+ G + R GSE +DWL+
Sbjct: 11 LMSTENSILQVREEEGVKY--ERTFVGSEFIDWLL 43
>gnl|CDD|239895 cd04448, DEP_PIKfyve, DEP (Dishevelled, Egl-10, and Pleckstrin)
domain found in fungal RhoGEF (GDP/GTP exchange factor)
PIKfyve-like proteins. PIKfyve contains N-terminal Fyve
finger and DEP domains, a central chaperonin-like
domain and a C-terminal PIPK (phosphatidylinositol
phosphate kinase) domain. PIKfyve-like proteins are
important phosphatidylinositol (3)-monophosphate
(PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which
plays a major role in multivesicular body (MVB) sorting
and control of retrograde traffic from the vacuole back
to the endosome and/or Golgi. PIKfyve itself has been
shown to be play a role in regulating
early-endosome-to-trans-Golgi network (TGN) retrograde
trafficking.
Length = 81
Score = 25.5 bits (56), Expect = 6.5
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 35 CASGSELVDWLMT 47
C G ELV+WL+
Sbjct: 28 CILGKELVNWLIR 40
>gnl|CDD|213979 TIGR04366, cupin_WbuC, cupin fold metalloprotein, WbuC family.
Members of this family show sequence similarity to
cupin fold proteins (see pfam07883), including
conserved His residues likely to serve as metal-binding
ligands. Many members occur in bacterial O-antigen
biosynthesis regions. Some members have acquired the
gene symbol wbuC (e.g. Jarvis, et al, 2011), but
publications using this term do not ascribe a function.
Length = 132
Score = 25.6 bits (57), Expect = 8.2
Identities = 7/20 (35%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 59 YIIIQGSVDVVIY-GKGCVT 77
+I+++G +DV+++ G VT
Sbjct: 59 FIVLEGELDVLLFDDDGEVT 78
>gnl|CDD|235038 PRK02436, xerD, site-specific tyrosine recombinase XerD-like
protein; Reviewed.
Length = 245
Score = 26.1 bits (58), Expect = 8.3
Identities = 11/46 (23%), Positives = 17/46 (36%)
Query: 110 LRVDKDDFIRIMRDVEANTVRLKEHGKDVLVLERMVNCSSHQHFFQ 155
L ++K R++ EA L+ + E S Q FF
Sbjct: 146 LTIEKAGGKRVLTLPEALLPFLEAILNQTYLFEHKGKPYSRQWFFN 191
>gnl|CDD|222619 pfam14242, DUF4342, Domain of unknown function (DUF4342). This
family of proteins is found in bacteria. Proteins in
this family are typically between 97 and 206 amino
acids in length. There is a single completely conserved
residue P that may be functionally important.
Length = 84
Score = 25.0 bits (55), Expect = 9.0
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 35 CASGSELVDWLMTMFHQGDEGKSWYIIIQ 63
SGSELV+ + + +G+ + III+
Sbjct: 12 KVSGSELVEKIKELIKKGNVRR---IIIK 37
>gnl|CDD|236490 PRK09376, rho, transcription termination factor Rho; Provisional.
Length = 416
Score = 25.9 bits (58), Expect = 10.0
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 130 RLKEHGKDVLVL 141
RL EHGKDV++L
Sbjct: 250 RLVEHGKDVVIL 261
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
0.324 0.137 0.421
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: 7,942,710
Number of extensions: 717065
Number of successful extensions: 933
Number of sequences better than 10.0: 1
Number of HSP's gapped: 926
Number of HSP's successfully gapped: 26
Length of query: 155
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 66
Effective length of database: 6,990,096
Effective search space: 461346336
Effective search space used: 461346336
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 (21.5 bits)
S2: 55 (25.1 bits)