RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13626
(127 letters)
>gnl|CDD|152640 pfam12205, GIT1_C, G protein-coupled receptor kinase-interacting
protein 1 C term. This domain family is found in
eukaryotes, and is approximately 120 amino acids in
length. The family is found in association with
pfam01412, pfam00023, pfam08518. GIT1 plays an important
role in cell adhesion, motility, cytoskeletal remodeling
and membrane trafficking. To perform this function, it
localises p21-activated kinase (PAK) and PAK-interactive
exchange factor to focal adhesions. Its activation is
regulated by interaction between its paxillin-binding C
terminal and the LD motifs of paxillin. The C terminal
folds into a four helix bundle.
Length = 123
Score = 84.9 bits (210), Expect = 2e-22
Identities = 51/118 (43%), Positives = 78/118 (66%), Gaps = 14/118 (11%)
Query: 20 MPQSEEVVRRTDQVTKRIQELAAHMRSSD--KCHSFVPHAERIRIAVSELSAIFPQNTNN 77
+P +E+V+R+T+Q+TK IQEL +R++ K SFVP +E I AV+E++A+FP+ N+
Sbjct: 8 LPSTEDVIRKTEQITKNIQEL---LRAAQEGKHESFVPCSENILTAVNEMAALFPERPNS 64
Query: 78 DLIRHALRSLNTSTVRLQAEC--AQLEGSA-------ERVRSCAYNMAKANKQLLTQF 126
+ +R++LR L +S RLQ EC A G A ++V CAY++AKA KQL+T
Sbjct: 65 ETVRNSLRLLTSSAERLQNECKKAVPPGIAVDMQLVTQQVIQCAYDIAKAAKQLVTIT 122
>gnl|CDD|193486 cd04081, CBM35_galactosidase-like, Carbohydrate Binding Module
family 35 (CBM35); appended mainly to enzymes that bind
alpha-D-galactose (CBM35-Gal), including glycoside
hydrolase (GH) families GH31 and GH43. This family
includes carbohydrate binding module family 35 (CBM35);
these are non-catalytic carbohydrate binding domains
that are appended mainly to enzymes that bind
alpha-D-galactose (CBM35-Gal), including glycoside
hydrolase (GH) families GH31 and GH43. Examples of
proteins which contain CBM35s belonging to this family
includes the CBM35 of an exo-beta-1,3-galactanase from
Phanerochaete chrysosporium 9(Pc1,3Gal43A) which is
appended to a GH43 domain, and the CBM6 of domain of
two bifunctional proteins with
beta-L-arabinopyranosidase/alpha-D-galactopyranosidase
activities from Fusarium oxysporum 12S, Foap1 and Foap2
(Fo/AP1 and Fo/AP2), that are appended to GH31 domains.
CBM35s are unique in that they display conserved
specificity through extensive sequence similarity but
divergent function through their appended catalytic
modules. They are known to bind alpha-D-galactose (Gal),
mannan (Man), xylan, glucuronic acid (GlcA), a
beta-polymer of mannose, and possibly glucans, forming
four subfamilies based on general ligand specificities
(galacto, urono, manno, and gluco configurations). Some
CBM35s bind their ligands in a calcium-dependent manner.
In contrast to most CBMs that are generally rigid
proteins, CBM35 undergoes significant conformational
change upon ligand binding. GH43 includes
beta-xylosidases and beta-xylanases, using
aryl-glycosides as substrates, while family GH31
includes alpha-glucosidases and alpha-xylosidases that
cleave a terminal carbohydrate moiety from substrates
that vary considerably in size, mostly accommodating
alpha-D-glucose and alpha-D-xylose.
Length = 123
Score = 27.6 bits (62), Expect = 0.98
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 92 VRLQAECAQLEGSAERVRSCAY 113
R +AE A L G A RV SC+
Sbjct: 1 TRYEAEAATLGGGA-RVVSCSG 21
>gnl|CDD|215553 PLN03052, PLN03052, acetate--CoA ligase; Provisional.
Length = 728
Score = 27.7 bits (62), Expect = 1.6
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 52 SFVPHAERIRIAVSELSAIFPQNTNNDLIRHALRSL 87
SF P R+ +S+ AIF Q D+I +S+
Sbjct: 266 SFAPSEIATRLKISKAKAIFTQ----DVIVRGGKSI 297
>gnl|CDD|239718 cd03749, proteasome_alpha_type_1, proteasome_alpha_type_1. The 20S
proteasome, multisubunit proteolytic complex, is the
central enzyme of nonlysosomal protein degradation in
both the cytosol and nucleus. It is composed of 28
subunits arranged as four homoheptameric rings that
stack on top of one another forming an elongated
alpha-beta-beta-alpha cylinder with a central cavity.
The proteasome alpha and beta subunits are members of
the N-terminal nucleophile (Ntn)-hydrolase superfamily.
Their N-terminal threonine residues are exposed as a
nucleophile in peptide bond hydrolysis. Mammals have 7
alpha and 7 beta proteasome subunits while archaea have
one of each.
Length = 211
Score = 26.9 bits (60), Expect = 3.3
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 71 FPQNTNNDLIRHALRSLNTST 91
F + +LI+HALR+L +
Sbjct: 174 FEDCSLEELIKHALRALRETL 194
>gnl|CDD|114903 pfam06211, BAMBI, BMP and activin membrane-bound inhibitor (BAMBI)
N-terminal domain. This family consists of several
eukaryotic BMP and activin membrane-bound inhibitor
(BAMBI) proteins. Members of the transforming growth
factor-beta (TGF-beta) superfamily, including TGF-beta,
bone morphogenetic proteins (BMPs), activins and nodals,
are vital for regulating growth and differentiation.
BAMBI is related to TGF-beta-family type I receptors but
lacks an intracellular kinase domain. BAMBI is
co-expressed with the ventralising morphogen BMP4 during
Xenopus embryogenesis and requires BMP signalling for
its expression. The protein stably associates with
TGF-beta-family receptors and inhibits BMP and activin
as well as TGF-beta signalling.
Length = 107
Score = 26.0 bits (57), Expect = 3.4
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 65 SELSAIF-----PQNTNNDLIRHALRSLNTSTVRLQAECAQLE-GSAERVRSCAYNM 115
SEL+A F PQNTN+ L L SL ST ++ G + + C +M
Sbjct: 43 SELNACFTRLLDPQNTNSPLTHGCLDSLLNSTDTCHSKSTFNHSGGSAPLECCHEDM 99
>gnl|CDD|153138 cd06350, PBP1_GPCR_family_C_like, Ligand-binding domain of
membrane-bound glutamate receptors that mediate
excitatory transmission on the cellular surface through
initial binding of glutamate and are categorized into
ionotropic glutamate receptors (iGluRs) and metabotropic
glutamate receptors (mGluRs). Ligand-binding domain of
membrane-bound glutamate receptors that mediate
excitatory transmission on the cellular surface through
initial binding of glutamate and are categorized into
ionotropic glutamate receptors (iGluRs) and metabotropic
glutamate receptors (mGluRs). The metabotropic glutamate
receptors (mGluR) are key receptors in the modulation of
excitatory synaptic transmission in the central nervous
system. The mGluRs are coupled to G proteins and are
thus distinct from the iGluRs which internally contain
ligand-gated ion channels. The mGluR structure is
divided into three regions: the extracellular region,
the seven-spanning transmembrane region and the
cytoplasmic region. The extracellular region is further
devided into the ligand-binding domain (LBD) and the
cysteine-rich domain. The LBD has sequence similarity to
the LIVBP, which is a bacterial periplasmic protein
(PBP), as well as to the extracellular region of both
iGluR and the gamma-aminobutyric acid (GABA)b receptor.
iGluRs are divided into three main subtypes based on
pharmacological profile: NMDA, AMPA, and kainate
receptors. All family C GPCRs have a large extracellular
N terminus that contain a domain with homology to
bacterial periplasmic amino acid-binding proteins.
Length = 348
Score = 26.6 bits (59), Expect = 3.7
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 52 SFVPHAERIRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVR 93
E+ I ++ P ++ + I+ L+ L +ST R
Sbjct: 179 DLEEELEKNGICIAF-VEAIPPSSTEEDIKRILKKLKSSTAR 219
>gnl|CDD|222239 pfam13581, HATPase_c_2, Histidine kinase-like ATPase domain.
Length = 125
Score = 26.1 bits (58), Expect = 4.7
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 57 AERIRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVRLQAECA 99
E + +AV E A+ TN + HA R VR++ E
Sbjct: 29 LEEVELAVEE--AL----TN--AVEHAYREDPEGPVRVRLEID 63
>gnl|CDD|240100 cd04752, Commd4, COMM_Domain containing protein 4. The COMM Domain
is found at the C-terminus of a variety of proteins;
presumably all COMM_Domain containing proteins are
located in the nucleus and the COMM domain plays a role
in protein-protein interactions. Several family members
have been shown to bind and inhibit NF-kappaB.
Length = 174
Score = 26.2 bits (58), Expect = 5.1
Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 13/76 (17%)
Query: 5 NQNNYMECFQSTTTRMPQSEEVVRRTDQV--TKRIQE-----------LAAHMRSSDKCH 51
Q+ E ++ + R+ + E V R D + + +QE + H
Sbjct: 89 KQSKLQESLRANSLRLSRLESVDWRVDYILSSSELQEVNEPLVQLRLKVRNADTGEITPH 148
Query: 52 SFVPHAERIRIAVSEL 67
F A++ R+ ++EL
Sbjct: 149 PFSVSADKFRVLLAEL 164
>gnl|CDD|173036 PRK14572, PRK14572, D-alanyl-alanine synthetase A; Provisional.
Length = 347
Score = 26.0 bits (57), Expect = 6.2
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 23 SEEVV--RRTDQVTKRIQELAAHMRSSDKCHSF 53
SEE+ R +DQ KR+QELA S C +
Sbjct: 262 SEEITPARISDQEMKRVQELAIRAHESLGCKGY 294
>gnl|CDD|224744 COG1831, COG1831, Predicted metal-dependent hydrolase (urease
superfamily) [General function prediction only].
Length = 285
Score = 25.8 bits (57), Expect = 6.3
Identities = 18/76 (23%), Positives = 24/76 (31%), Gaps = 24/76 (31%)
Query: 21 PQSEEVVRRTDQVTKRIQELAA--------HMRSSDKCH----------------SFVPH 56
P SEEV +++V + ELA H S D+ V H
Sbjct: 134 PVSEEVWEASNEVLEYAMELAKDVDCAVQLHTESLDEETYEEIAEMAKEAGIKPYRVVKH 193
Query: 57 AERIRIAVSELSAIFP 72
+ E IFP
Sbjct: 194 HAPPLVLKCEEVGIFP 209
>gnl|CDD|184515 PRK14111, PRK14111, F0F1 ATP synthase subunit gamma; Provisional.
Length = 290
Score = 25.9 bits (57), Expect = 6.5
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 8/58 (13%)
Query: 20 MPQSEEVVRR------TDQVTKRIQELAA-HMRSSDK-CHSFVPHAERIRIAVSELSA 69
MP + E+ RR T Q+T+ ++ ++A MR + + + P+A+RIR + +L+A
Sbjct: 1 MPSTREIRRRIRSVKNTAQITRAMEMVSASKMRRAQRNVLATRPYADRIRDVMGDLTA 58
>gnl|CDD|233113 TIGR00747, fabH, 3-oxoacyl-(acyl-carrier-protein) synthase III.
FabH in general initiate elongation in type II fatty
acid synthase systems found in bacteria and plants. The
two members of this subfamily from Bacillus subtilis
differ from each other, and from FabH from E. coli, in
acyl group specificity. Active site residues include
Cys112, His244 and Asn274 of E. coli FabH. Cys-112 is
the site of acyl group attachment [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 318
Score = 25.8 bits (57), Expect = 8.1
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 8/66 (12%)
Query: 27 VRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRI--AVSELSAIFPQNTNNDLIRHAL 84
VR+ V + E A + D FVPH +RI A+++ + + ++
Sbjct: 218 VRKMGDVVEETLE-ANGLDPED-IDWFVPHQANLRIIEALAKRLELDMSQVVKTVHKYG- 274
Query: 85 RSLNTS 90
NTS
Sbjct: 275 ---NTS 277
>gnl|CDD|221188 pfam11725, AvrE, Pathogenicity factor. This family is secreted by
gram-negative Gammaproteobacteria such as Pseudomonas
syringae of tomato and the fire blight plant pathogen
Erwinia amylovora, amongst others. It is an essential
pathogenicity factor of approximately 198 kDa. Its
injection into the host-plant is dependent upon the
bacterial type III or Hrp secretion system. The family is
long and carries a number of predicted functional
regions, including an ERMS or endoplasmic reticulum
membrane retention signal at both the C- and the
N-termini, a leucine-zipper motif from residues 539-560,
and a nuclear localisation signal at 1358-1361. this
conserved AvrE-family of effectors is among the few that
are required for full virulence of many phytopathogenic
pseudomonads, erwinias and pantoeas.
Length = 1771
Score = 25.9 bits (57), Expect = 8.3
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 5/64 (7%)
Query: 34 TKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNT-NNDLIRHALRSLNTSTV 92
TK + ELA + E+I+ + L+ F T ND ALRSL V
Sbjct: 1517 TKLLAELAKQTNAEYAKTP----DEKIQAQLDGLNEHFADKTVQNDDQYEALRSLKRLVV 1572
Query: 93 RLQA 96
R +A
Sbjct: 1573 RQEA 1576
>gnl|CDD|168927 PRK07374, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1170
Score = 25.5 bits (56), Expect = 9.9
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 2/48 (4%)
Query: 31 DQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNTNND 78
D K+ ++A + ++K +F HA + IA L + P NND
Sbjct: 501 DPRVKKWVDMAMRIEGTNK--TFGVHAAGVVIASDPLDELVPLQRNND 546
>gnl|CDD|223727 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and related
FAD-dependent oxidoreductases [Coenzyme metabolism /
Energy production and conversion].
Length = 387
Score = 25.4 bits (56), Expect = 10.0
Identities = 17/93 (18%), Positives = 35/93 (37%), Gaps = 4/93 (4%)
Query: 20 MPQSEEVVRRTDQVTKRIQELAA---HMRSSDKCHSFVPHAERIRIAVSELSAIFPQNTN 76
P + + R + R++ L H+ D + + + L + P++
Sbjct: 48 SPNALRALERLG-LWDRLEALGVPPLHVMVVDDGGRRLLIFDAAELGRGALGYVVPRSDL 106
Query: 77 NDLIRHALRSLNTSTVRLQAECAQLEGSAERVR 109
+ + A R+L T+R AE +E + V
Sbjct: 107 LNALLEAARALPNVTLRFGAEVEAVEQDGDGVT 139
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 0.125 0.351
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,841,505
Number of extensions: 477590
Number of successful extensions: 577
Number of sequences better than 10.0: 1
Number of HSP's gapped: 572
Number of HSP's successfully gapped: 30
Length of query: 127
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 42
Effective length of database: 7,167,512
Effective search space: 301035504
Effective search space used: 301035504
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 (21.8 bits)
S2: 53 (24.2 bits)