RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12155
(78 letters)
>gnl|CDD|217255 pfam02862, DDHD, DDHD domain. The DDHD domain is 180 residues
long and contains four conserved residues that may form
a metal binding site. The domain is named after these
four residues. This pattern of conservation of metal
binding residues is often seen in phosphoesterase
domains. This domain is found in retinal degeneration B
proteins, as well as a family of probable
phospholipases. It has been shown that this domain is
found in a longer C terminal region that binds to PYK2
tyrosine kinase. These proteins have been called
N-terminal domain-interacting receptor (Nir1, Nir2 and
Nir3). This suggests that this region is involved in
functionally important interactions in other members of
this family.
Length = 219
Score = 117 bits (294), Expect = 8e-35
Identities = 35/87 (40%), Positives = 48/87 (55%), Gaps = 10/87 (11%)
Query: 2 FFAFGSPVGMFVNVRGIDVLG----------EEFEFPTCPKFYNIFHPFDPVAYRIEPLI 51
FFA GSP+G+F+ +RG ++ + P C YNIFHP DPVAYR+EPL+
Sbjct: 8 FFAVGSPLGLFLLLRGTNLGARSLSYVAGEDGTYGCPACKNLYNIFHPTDPVAYRLEPLV 67
Query: 52 VPAMEHVRPVQVPHHKGRKRMHLGRKH 78
P +++PV +PH K K L
Sbjct: 68 DPEYANLKPVLIPHAKKSKLGALELLE 94
>gnl|CDD|224428 COG1511, COG1511, Predicted membrane protein [Function unknown].
Length = 780
Score = 37.1 bits (86), Expect = 3e-04
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 14/57 (24%)
Query: 3 FAFGSPVGMFVNVRG---------IDVL-----GEEFEFPTCPKFYNIFHPFDPVAY 45
AF + + V++ G + VL G F P F+ I HP P+ Y
Sbjct: 666 VAFMIIIYLLVSLFGNPGKFIAIVLLVLQIAGSGGTFPIQLSPSFFQILHPALPLTY 722
>gnl|CDD|234099 TIGR03062, pip_yhgE_Cterm, YhgE/Pip C-terminal domain. This family
contains the C-terminal domain of a family of multiple
membrane-spanning proteins of Gram-positive bacteria.
One member was shown to be a host protein essential for
phage infection, so many members of this family are
called "phage infection protein". A separate model,
TIGR03061, represents the conserved N-terminal domain.
The domains are separated by regions highly variable in
both length and sequence, often containing extended
heptad repeats as described in model TIGR03057.
Length = 208
Score = 29.1 bits (66), Expect = 0.16
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 2/24 (8%)
Query: 27 FP--TCPKFYNIFHPFDPVAYRIE 48
FP P F+ HPF P+ Y +
Sbjct: 144 FPIELLPAFFQAIHPFLPMTYSVN 167
>gnl|CDD|153359 cd07675, F-BAR_FNBP1L, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Formin Binding Protein
1-Like. F-BAR domains are dimerization modules that
bind and bend membranes and are found in proteins
involved in membrane dynamics and actin reorganization.
FormiN Binding Protein 1-Like (FNBP1L), also known as
Toca-1 (Transducer of Cdc42-dependent actin assembly),
forms a complex with neural Wiskott-Aldrich syndrome
protein (N-WASP). The FNBP1L/N-WASP complex induces the
formation of filopodia and endocytic vesicles. FNBP1L is
required for Cdc42-induced actin assembly and is
essential for autophagy of intracellular pathogens. It
contains an N-terminal F-BAR domain, a central
Cdc42-binding HR1 domain, and a C-terminal SH3 domain.
F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 252
Score = 27.3 bits (60), Expect = 0.75
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 23 EEFEFPTCPKFYNIFHPFDPVAYRIEPLIVPAMEHVRPVQVPHH----KGRKRMHL--GR 76
EE F +C FYNI + + A + E ++ M H ++ + KG ++MHL GR
Sbjct: 58 EEPRFTSCLSFYNILNELNDYAGQRE-VVAEEMGHRVYGELMRYSHDLKGERKMHLQEGR 116
Query: 77 K 77
K
Sbjct: 117 K 117
>gnl|CDD|225279 COG2421, COG2421, Predicted acetamidase/formamidase [Energy
production and conversion].
Length = 305
Score = 26.5 bits (59), Expect = 1.3
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 5/54 (9%)
Query: 3 FAFGSPVGMFVNVRGIDVLGEEFEFPTCPKF-----YNIFHPFDPVAYRIEPLI 51
P G G VLG++FE P ++ IF F V ++P I
Sbjct: 83 IKPSPPWGYTAVFPGFGVLGDKFEKPALRRWKIEGAKVIFAKFPGVRIPLQPFI 136
>gnl|CDD|234235 TIGR03503, TIGR03503, TIGR03503 family protein. This set of
conserved hypothetical protein has a phylogenetic range
that closely matches that of TIGR03501, a putative
C-terminal protein targeting signal.
Length = 374
Score = 26.2 bits (58), Expect = 2.1
Identities = 8/53 (15%), Positives = 16/53 (30%)
Query: 12 FVNVRGIDVLGEEFEFPTCPKFYNIFHPFDPVAYRIEPLIVPAMEHVRPVQVP 64
V G + G E + +N+ P + E A++ +
Sbjct: 283 KGTVFGTTITGRELQLTLPEFSFNVEEPPEAEPSAEEAATEEALKAKAEQEQA 335
>gnl|CDD|185753 cd09214, GH64-like, glycosyl hydrolase 64 family. This family is
represented by the laminaripentaose-producing,
beta-1,3-glucanase (LPHase) of Streptomyces matensis and
related bacterial and ascomycete proteins. LPHase is a
member of glycoside hydrolase family 64 (GH64), it is an
inverting enzyme involved in the cleavage of long-chain
polysaccharide beta-1,3-glucans, into specific
pentasaccharide oligomers. LPHase is a two-domain
crescent fold structure: one domain is composed of 10
beta-strands, eight coming from the N-terminus of the
protein and two from the C-terminal region, and the
protein has a second inserted domain; this cd includes
both domains. This protein has an electronegative,
substrate-binding cleft, and conserved Glu and Asp
residues involved in the cleavage of the
beta-1,3-glucan, laminarin, a plant and fungal cell wall
component. Among bacteria, many beta-1,3-glucanases are
implicated in fungal cell wall degradation. Also
included in this family is GluB , the beta-1,3-glucanase
B from Lysobacter enzymogenes Strain N4-7. Recombinant
GluB demonstrated higher relative activity toward the
branched-chain beta-1,3 glucan substrate zymosan A than
toward linear beta-1,3 glucan substrates. Sometimes
these two domains are found associated with other
domains such as in the Catenulispora acidiphila DSM
44928 carbohydrate binding family 6 protein in which
they are positioned N-terminal of a carbohydrate binding
module, family 6 (CBM_6) domain. In the
Cellulosimicrobium cellulans, glucan
endo-1,3-beta-glucosidase, they are positioned
N-terminal of a RICIN, carbohydrate-binding domain, and
in the Salinispora tropica CNB-440, coagulation factor
5/8 C-terminal domain (FA58C) protein, they are
positioned C-terminal of two FA58C domains which are
proposed to function as cell surface-attached,
carbohydrate-binding domain. This FA58C-containing
protein has an internal peptide deletion (of approx. 44
residues) in the LPHase domain II.
Length = 319
Score = 25.8 bits (57), Expect = 2.3
Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 8/42 (19%)
Query: 1 MFFAFGSPVGMFVNVRGIDVLGEEFEFPTCPKFYNIFHPFDP 42
++ +FG+P+ + G D+ G P N P DP
Sbjct: 84 IYISFGNPLYIKAFQDGGDMPG-----YAGPDLNN---PTDP 117
>gnl|CDD|223754 COG0682, Lgt, Prolipoprotein diacylglyceryltransferase [Cell
envelope biogenesis, outer membrane].
Length = 287
Score = 24.9 bits (55), Expect = 4.4
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 31 PKFYNIFHPFDPVAYRIEPLIV 52
P Y IF P DPVA+ I PL +
Sbjct: 2 PLSYLIFPPIDPVAFSIGPLAI 23
>gnl|CDD|236426 PRK09243, PRK09243, nicotinate phosphoribosyltransferase;
Validated.
Length = 464
Score = 25.1 bits (56), Expect = 4.4
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 19 DVLGEEFEFPTCPKFYNIFHPFDP------VAYRIEPLIVPAMEHVRPVQ 62
DV+ E P +FHP + EPL+VP ME+ + V
Sbjct: 377 DVITLADEEEEEP--LKMFHPVHTYKSKTVKNFDAEPLLVPVMENGKRVY 424
>gnl|CDD|187652 cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like
proteins (5beta-POR), atypical (a) SDRs. 5beta-POR
catalyzes the reduction of progesterone to
5beta-pregnane-3,20-dione in Digitalis plants. This
subgroup of atypical-extended SDRs, shares the structure
of an extended SDR, but has a different glycine-rich
nucleotide binding motif (GXXGXXG) and lacks the YXXXK
active site motif of classical and extended SDRs.
Tyr-179 and Lys 147 are present in the active site, but
not in the usual SDR configuration. Given these
differences, it has been proposed that this subfamily
represents a new SDR class. Other atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 308
Score = 24.9 bits (55), Expect = 5.0
Identities = 6/20 (30%), Positives = 7/20 (35%)
Query: 21 LGEEFEFPTCPKFYNIFHPF 40
LG FP P +N
Sbjct: 202 LGAPLRFPGSPAAWNALSDA 221
>gnl|CDD|214534 smart00138, MeTrc, Methyltransferase, chemotaxis proteins.
Methylates methyl-accepting chemotaxis proteins to form
gamma-glutamyl methyl ester residues.
Length = 264
Score = 24.2 bits (53), Expect = 8.0
Identities = 7/31 (22%), Positives = 17/31 (54%)
Query: 33 FYNIFHPFDPVAYRIEPLIVPAMEHVRPVQV 63
F+ F+ + ++ PL++ + H R V++
Sbjct: 73 FFRESKHFEALEEKVLPLLIASRRHGRRVRI 103
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
0.331 0.149 0.496
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: 4,285,661
Number of extensions: 343553
Number of successful extensions: 353
Number of sequences better than 10.0: 1
Number of HSP's gapped: 352
Number of HSP's successfully gapped: 14
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.2 bits)