RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13685
(72 letters)
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. 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 = 320
Score = 61.5 bits (150), Expect = 4e-13
Identities = 22/60 (36%), Positives = 32/60 (53%)
Query: 7 VISTWSDPIAGYIDNLYGPTGLVTGVQAGIIRCISNARHIKADMVPADYVVNALICCTWD 66
V +T +P G+IDN GP GL GI+R ++ + AD++P D V NAL+
Sbjct: 222 VGATLKEPFPGWIDNFNGPDGLFLAYGKGILRTMNADPNAVADIIPVDVVANALLAAAAY 281
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 54.9 bits (133), Expect = 7e-11
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 12 SDPIAGYIDNLY-GPTGLVTGVQAGIIRCISNARHIKADMVPADYVVNAL 60
+ G+I+ GP GL+ G G++ I + D+VP DYV NA+
Sbjct: 196 GESRTGWINGDDFGPRGLLGGAGLGVLPDILGDPDARLDLVPVDYVANAI 245
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 36.6 bits (85), Expect = 3e-04
Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 7 VISTWSDPIAGYIDNLYGPTGLVTGVQAGIIRC-ISNARHIKADMVPADYVVNALI 61
+ ST+ +P G+I+ L ++ G G + C +++ + D++PAD VVNA+I
Sbjct: 264 ITSTYKEPFPGWIEGLRTIDSVIVGYGKGKLTCFLADPNSV-LDVIPADMVVNAMI 318
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR family
domains have the characteristic active site tetrad and a
well-conserved NAD(P)-binding motif. This subgroup is
not well characterized, its members are annotated as
having a variety of putative functions. One
characterized member is Pseudomonas fluorescens MupV a
protein involved in the biosynthesis of Mupirocin, a
polyketide-derived antibiotic. 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 = 293
Score = 34.3 bits (79), Expect = 0.002
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 11 WSDPIAGYIDNLYGPTGLVTGVQA-GIIRCISNARHIKADMVPADYVVNALIC 62
D G I+ + G L+ + G + + + ++VP DYV +A++
Sbjct: 179 VGDSKTGRIEKIDGLYELLNLLAKLGRWLPMPGNKGARLNLVPVDYVADAIVY 231
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 33.3 bits (76), Expect = 0.005
Identities = 25/66 (37%), Positives = 32/66 (48%), Gaps = 23/66 (34%)
Query: 6 SVI-STWSDPIAGYIDN--------LYGPTGLVTGVQA---GIIRCISNARHIKADMVPA 53
SVI STW DP G+++ LY G +TG A G++ D+VPA
Sbjct: 376 SVIESTWKDPFPGWMEGNRMMDPIVLYYGKGQLTGFLADPNGVL-----------DVVPA 424
Query: 54 DYVVNA 59
D VVNA
Sbjct: 425 DMVVNA 430
>gnl|CDD|234525 TIGR04259, oxa_formateAnti, oxalate/formate antiporter. This model
represents a subgroup of the more broadly defined model
TIGR00890, which in turn belongs to the Major
Facilitator transporter family. Seed members for this
family include the known oxalate/formate antiporter of
Oxalobacter formigenes, as well as transporter subunits
co-clustered with the two genes of a system that
decarboxylates oxalate into formate. In many of these
cassettes, two subunits are found rather than one,
suggesting the antiporter is sometimes homodimeric,
sometimes heterodimeric.
Length = 405
Score = 28.6 bits (64), Expect = 0.23
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 7 VISTWSDPIAGYIDNLYGPTGLVTGVQAGIIRCISNARHIKADMVPADYVVNAL 60
V TW PI G+ + YGP +V GI+ + + AD +PA Y +
Sbjct: 49 VTETWLVPIEGWFVDKYGPRIVVMF--GGIMCGLGWVLNAYADSLPALYAAAVV 100
>gnl|CDD|176889 cd08880, RHO_alpha_C_ahdA1c-like, C-terminal catalytic domain of
the large/alpha subunit (ahdA1c) of a ring-hydroxylating
dioxygenase from Sphingomonas sp. strain P2 and related
proteins. C-terminal catalytic domain of the large
subunit (ahdA1c) of the AhdA3A4A2cA1c salicylate
1-hydroxylase complex from Sphingomonas sp. strain P2,
and related Rieske-type non-heme iron aromatic
ring-hydroxylating oxygenases (RHOs, also known as
aromatic ring hydroxylating dioxygenases). AhdA3A4A2cA1c
is one of three known isofunctional salicylate
1-hydroxylase complexes in strain P2, involved in
phenanthrene degradation, which catalyze the
monooxygenation of salicylate, the metabolite of
phenanthene degradation, to produce catechol. This
complex prefers salicylate over other substituted
salicylates; the other two salicylate 1-hydroxylases
have different substrate preferences. RHOs utilize
non-heme Fe(II) to catalyze the addition of hydroxyl
groups to the aromatic ring, an initial step in the
oxidative degradation of aromatic compounds. RHOs are
composed of either two or three protein components, and
are comprised of an electron transport chain (ETC) and
an oxygenase. The ETC transfers reducing equivalents
from the electron donor to the oxygenase component,
which in turn transfers electrons to the oxygen
molecules. The oxygenase components are oligomers,
either (alpha)n or (alpha)n(beta)n. The alpha subunits
are the catalytic components and have an N-terminal
domain, which binds a Rieske-like 2Fe-2S cluster, and a
C-terminal domain which binds the non-heme Fe(II). The
Fe(II) is co-ordinated by conserved His and Asp
residues. Other oxygenases belonging to this subgroup
include the alpha subunits of anthranilate
1,2-dioxygenase from Burkholderia cepacia DBO1, a
polycyclic aromatic hydrocarbon dioxygenase from
Cycloclasticus sp. strain A5 (PhnA dioxygenase),
salicylate-5-hydroxylase from Ralstonia sp. U2,
ortho-halobenzoate 1,2-dioxygenase from Pseudomonas
aeruginosa strain JB2, and the terephthalate
1,2-dioxygenase system from Delftia tsuruhatensis strain
T7. This subfamily belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket.
Length = 222
Score = 26.8 bits (60), Expect = 0.73
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 14/63 (22%)
Query: 21 NLYGPTGLVTG--------VQAGIIRCISNARHI----KADMVPADYVVN-ALICCTWDG 67
NL GP G V+ VQ G+ R + D+ +D++V A I W
Sbjct: 158 NLVGPAGFVSMEDGEAIEFVQRGVEG-DGGDRSVIEMGGGDVESSDHMVTEAAIRGFWKY 216
Query: 68 YNK 70
Y K
Sbjct: 217 YRK 219
>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional.
Length = 76
Score = 25.9 bits (57), Expect = 1.1
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 31 GVQAGIIRCISNARHIKADMVPADYVVNA 59
G+ IR I + + + D+ +DY V
Sbjct: 35 GIDVKQIRLIYSGKQMSDDLKLSDYKVVP 63
>gnl|CDD|238928 cd01966, Nitrogenase_NifN_1, Nitrogenase_nifN1: A subgroup of the
NifN subunit of the NifEN complex: NifN forms an
alpha2beta2 tetramer with NifE. NifN and nifE are
structurally homologous to nitrogenase MoFe protein beta
and alpha subunits respectively. NifEN participates in
the synthesis of the iron-molybdenum cofactor (FeMoco)
of the MoFe protein. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to the NifEN complex where it is further
processed to FeMoco. The nifEN bound precursor of FeMoco
has been identified as a molybdenum-free, iron- and
sulfur- containing analog of FeMoco. It has been
suggested that this nifEN bound precursor also acts as a
cofactor precursor in nitrogenase systems which require
a cofactor other than FeMoco: i.e. iron-vanadium
cofactor (FeVco) or iron only cofactor (FeFeco).
Length = 417
Score = 26.4 bits (59), Expect = 1.2
Identities = 10/43 (23%), Positives = 19/43 (44%)
Query: 15 IAGYIDNLYGPTGLVTGVQAGIIRCISNARHIKADMVPADYVV 57
IA D L + + + A I+ ++ + +PA+ VV
Sbjct: 305 IALEPDLLAALSSFLAEMGAEIVAAVATTDSPALEKLPAEEVV 347
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 26.3 bits (58), Expect = 1.5
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 23 YGPTGLVTGVQAGIIRCISNARHIKADMVP-ADYVV 57
Y GL ++ G+ R + + D P AD +V
Sbjct: 285 YSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIV 320
>gnl|CDD|185636 PTZ00457, PTZ00457, acyl-CoA dehydrogenase; Provisional.
Length = 520
Score = 25.6 bits (56), Expect = 2.5
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 38 RCISNARHIKADMVPADYVVNALICCTWDGY 68
+C +NAR + M D++ ++ +CC + Y
Sbjct: 343 KCFANARLFLSMMESRDFLYSSAVCCGVEDY 373
>gnl|CDD|217222 pfam02774, Semialdhyde_dhC, Semialdehyde dehydrogenase,
dimerisation domain. This Pfam entry contains the
following members: N-acetyl-glutamine semialdehyde
dehydrogenase (AgrC) Aspartate-semialdehyde
dehydrogenase.
Length = 167
Score = 24.6 bits (54), Expect = 5.3
Identities = 7/26 (26%), Positives = 11/26 (42%)
Query: 29 VTGVQAGIIRCISNARHIKADMVPAD 54
T V+ + R S +K + P D
Sbjct: 79 ATCVRVPVFRGHSETVTVKLKLKPID 104
>gnl|CDD|213310 cd05945, DltA, D-alanine:D-alanyl carrier protein ligase (DltA).
DltA belongs to the class I AMP-forming adenylation
domain superfamily, which also includes acetyl-CoA
synthetase, luciferase, and the adenylation domains of
non-ribosomal synthetases. It catalyzes the two-step
activation reaction of D-alanine: the formation of a
substrate-AMP molecule as an intermediate, and then the
transfer of the amino acid adenylate to teichoic acid in
the biosynthesis of lipoteichoic acid (LTA) and wall
teichoic acid (WTA) in gram-positive bacteria.
Length = 447
Score = 24.5 bits (54), Expect = 5.9
Identities = 7/8 (87%), Positives = 7/8 (87%)
Query: 19 IDNLYGPT 26
I NLYGPT
Sbjct: 243 IINLYGPT 250
>gnl|CDD|240300 PTZ00165, PTZ00165, aspartyl protease; Provisional.
Length = 482
Score = 24.3 bits (53), Expect = 6.3
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 42 NARHIKADMVPADYVV 57
N R IK DM P DYV+
Sbjct: 376 NGRKIKFDMDPEDYVI 391
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
0.322 0.138 0.450
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,664,970
Number of extensions: 266863
Number of successful extensions: 266
Number of sequences better than 10.0: 1
Number of HSP's gapped: 264
Number of HSP's successfully gapped: 17
Length of query: 72
Length of database: 10,937,602
Length adjustment: 42
Effective length of query: 30
Effective length of database: 9,074,734
Effective search space: 272242020
Effective search space used: 272242020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.1 bits)