RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 048011
(104 letters)
>gnl|CDD|233145 TIGR00836, amt, ammonium transporter. The Ammonium Transporter
(Amt) Family (TC 2.A.49) All functionally characterized
members of the Amt family are ammonia or ammonium uptake
transporters. Some, but not others, also transport
methylammonium. The mechanism of energy coupling, if
any, to methyl-NH2 or NH3 uptake by the AmtB protein of
E. coli is not entirely clear. NH4+ uniport driven by
the pmf, energy independent NH3 facilitation, and
NH4+/K+ antiport have been proposed as possible
transport mechanisms. In Corynebacterium glutamicum and
Arabidopsis thaliana, uptake via the Amt1 homologues of
AmtB has been reported to be driven by the pmf
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 403
Score = 41.9 bits (99), Expect = 1e-05
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 26 GLSVVEPWAAMVC-LYFAPWVLIGLNILAIKLNFDDPLEGTRLHGGSGFIGS 76
G VV PW A++ L + ++ L KL DDPL+ +HG G G
Sbjct: 273 GCGVVTPWGAIIIGLVAGVLCYLAVSKLKKKLKIDDPLDAFAVHGVGGIWGL 324
>gnl|CDD|216185 pfam00909, Ammonium_transp, Ammonium Transporter Family.
Length = 399
Score = 40.4 bits (95), Expect = 4e-05
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 28 SVVEPWAAMVC-LYFAPWVLIGLNILAIKLNFDDPLEGTRLHGGSGFIGS 76
VV PW A++ L ++G L KL DDPL+ +HG G G
Sbjct: 270 GVVTPWGALIIGLIAGVVSVLGYKKLKEKLGIDDPLDVFPVHGVGGIWGG 319
>gnl|CDD|177791 PLN00200, PLN00200, argininosuccinate synthase; Provisional.
Length = 404
Score = 27.8 bits (62), Expect = 1.0
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 82 SVIVGWVRETMGPLLVCF 99
SVI+ W+RE G +VCF
Sbjct: 19 SVILKWLRENYGCEVVCF 36
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. 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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 = 304
Score = 27.2 bits (61), Expect = 1.7
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 69 GGSGFIGSQVTEL 81
GG+GFIGS + E
Sbjct: 6 GGAGFIGSHLVER 18
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. 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. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. 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 = 316
Score = 25.3 bits (56), Expect = 6.4
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 69 GGSGFIGSQVTELSVIVGW 87
G GFIGS +TE + G
Sbjct: 6 GADGFIGSHLTERLLREGH 24
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 25.3 bits (55), Expect = 7.2
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 69 GGSGFIGSQVTE 80
GG+GFIGS + E
Sbjct: 7 GGAGFIGSHLVE 18
>gnl|CDD|225489 COG2938, COG2938, Uncharacterized conserved protein [Function
unknown].
Length = 94
Score = 24.5 bits (54), Expect = 7.3
Identities = 5/14 (35%), Positives = 7/14 (50%)
Query: 9 NLRCLKWGAWRGCR 22
L+W + RG R
Sbjct: 14 RKARLRWRSRRGMR 27
>gnl|CDD|223083 COG0004, AmtB, Ammonia permease [Inorganic ion transport and
metabolism].
Length = 409
Score = 25.2 bits (56), Expect = 7.7
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 29 VVEPWAAMVC-LYFAPWVLIGLNILAIKLNFDDPLEGTRLHGGSGFIGS 76
V PW A++ L + +L KL DD L+ +HG G +G+
Sbjct: 277 FVSPWGALIIGLIAGVICYFAVKLLKKKLGVDDALDVFGVHGVGGIVGA 325
>gnl|CDD|236013 PRK07409, PRK07409, threonine synthase; Validated.
Length = 353
Score = 25.2 bits (56), Expect = 8.1
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 45 VLIGLNILAIKLNFDDPLEGTR 66
V+ G I+ I NFDD LE R
Sbjct: 122 VMYGAEIIQIDGNFDDALEIVR 143
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
0.329 0.146 0.502
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,351,365
Number of extensions: 446195
Number of successful extensions: 532
Number of sequences better than 10.0: 1
Number of HSP's gapped: 529
Number of HSP's successfully gapped: 25
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.1 bits)