RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15783
(86 letters)
>gnl|CDD|224014 COG1089, Gmd, GDP-D-mannose dehydratase [Cell envelope biogenesis,
outer membrane].
Length = 345
Score = 119 bits (300), Expect = 2e-34
Identities = 44/72 (61%), Positives = 54/72 (75%)
Query: 12 AMWMMLQQDTPQDFVIATGETHSVREFVEAAFLYIGKTIVWEGTGKDEVGKEKDTGIVRV 71
AMW+MLQQ+ P D+VIATGETHSVREFVE AF +G + WEGTG DE G + TG + V
Sbjct: 234 AMWLMLQQEEPDDYVIATGETHSVREFVELAFEMVGIDLEWEGTGVDEKGVDAKTGKIIV 293
Query: 72 KVNENYFRPTEV 83
+++ YFRP EV
Sbjct: 294 EIDPRYFRPAEV 305
>gnl|CDD|233427 TIGR01472, gmd, GDP-mannose 4,6-dehydratase. Alternate name:
GDP-D-mannose dehydratase. This enzyme converts
GDP-mannose to GDP-4-dehydro-6-deoxy-D-mannose, the
first of three steps for the conversion of GDP-mannose
to GDP-fucose in animals, plants, and bacteria. In
bacteria, GDP-L-fucose acts as a precursor of surface
antigens such as the extracellular polysaccharide
colanic acid of E. coli. Excluded from this model are
members of the clade that score poorly because of highly
dervied (phylogenetically long-branch) sequences, e.g.
Aneurinibacillus thermoaerophilus Gmd, described as a
bifunctional GDP-mannose
4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase
(PUBMED:11096116) [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 343
Score = 116 bits (291), Expect = 4e-33
Identities = 48/72 (66%), Positives = 59/72 (81%)
Query: 12 AMWMMLQQDTPQDFVIATGETHSVREFVEAAFLYIGKTIVWEGTGKDEVGKEKDTGIVRV 71
AMW+MLQQD P D+VIATGETHSVREFVE +F YIGKT+ W+ G +EVG+ K+TG V V
Sbjct: 235 AMWLMLQQDKPDDYVIATGETHSVREFVEVSFEYIGKTLNWKDKGINEVGRCKETGKVHV 294
Query: 72 KVNENYFRPTEV 83
+++ YFRPTEV
Sbjct: 295 EIDPRYFRPTEV 306
>gnl|CDD|178259 PLN02653, PLN02653, GDP-mannose 4,6-dehydratase.
Length = 340
Score = 86.4 bits (214), Expect = 6e-22
Identities = 31/72 (43%), Positives = 42/72 (58%), Gaps = 17/72 (23%)
Query: 12 AMWMMLQQDTPQDFVIATGETHSVREFVEAAFLYIGKTIVWEGTGKDEVGKEKDTGIVRV 71
AMW+MLQQ+ P D+V+AT E+H+V EF+E AF Y+G KD V
Sbjct: 241 AMWLMLQQEKPDDYVVATEESHTVEEFLEEAFGYVGL------NWKDH-----------V 283
Query: 72 KVNENYFRPTEV 83
+++ YFRP EV
Sbjct: 284 EIDPRYFRPAEV 295
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have the
canonical active site triad and NAD-binding pattern,
however the active site Asn is often missing and may be
substituted with Asp. A Glu residue has been identified
as an important active site base. 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 = 80.3 bits (199), Expect = 7e-20
Identities = 35/72 (48%), Positives = 42/72 (58%), Gaps = 17/72 (23%)
Query: 12 AMWMMLQQDTPQDFVIATGETHSVREFVEAAFLYIGKTIVWEGTGKDEVGKEKDTGIVRV 71
A W++LQQ P D+VIATGETHSVREFVE AF G TG + V
Sbjct: 227 AYWLLLQQGEPDDYVIATGETHSVREFVELAFEESGL-----------------TGDIEV 269
Query: 72 KVNENYFRPTEV 83
+++ YFRPTEV
Sbjct: 270 EIDPRYFRPTEV 281
>gnl|CDD|224651 COG1737, RpiR, Transcriptional regulators [Transcription].
Length = 281
Score = 33.4 bits (77), Expect = 0.006
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 11 YAMWMMLQQDTPQDFVIA---TGETHSVREFVEAA 42
+ M L TP D VIA +G T + E E A
Sbjct: 166 HGQLMQLALLTPGDVVIAISFSGYTREIVEAAELA 200
>gnl|CDD|215299 PLN02543, PLN02543, pfkB-type carbohydrate kinase family protein.
Length = 496
Score = 28.3 bits (63), Expect = 0.45
Identities = 22/59 (37%), Positives = 27/59 (45%), Gaps = 15/59 (25%)
Query: 11 YAMWMMLQQDTPQDFVIATGETHS------VREFVEAAFLYIGKTIVWEGTGKDEVGKE 63
Y+ W MLQ D P+ F A G S VR AAF+ GK G D+ G+E
Sbjct: 154 YSQWKMLQWDPPE-FARAPGGPPSNVAISHVRLGGRAAFM--GK------VGDDDFGEE 203
>gnl|CDD|187550 cd05239, GDP_FS_SDR_e, GDP-fucose synthetase, extended (e) SDRs.
GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase)
acts in the NADP-dependent synthesis of GDP-fucose from
GDP-mannose. Two activities have been proposed for the
same active site: epimerization and reduction. Proteins
in this subgroup are extended SDRs, which have a
characteristic active site tetrad and an NADP-binding
motif, [AT]GXXGXXG, that is a close match to the
archetypical form. 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 = 300
Score = 27.9 bits (63), Expect = 0.54
Identities = 11/47 (23%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 8 LSKYAMWMMLQQDTPQDFVIATGETHSVREFVEAAFLYIGKTIVWEG 54
L++ ++++ D P + +G S+RE EA I + + ++G
Sbjct: 213 LARAIVFLLENYDEPIIVNVGSGVEISIRELAEA----IAEVVGFKG 255
>gnl|CDD|183426 PRK12309, PRK12309, transaldolase/EF-hand domain-containing
protein; Provisional.
Length = 391
Score = 26.6 bits (59), Expect = 1.5
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 6/47 (12%)
Query: 45 YIGKTIVW--EGTGKDEVGKEKDTGIVRVKVNENYFR----PTEVIG 85
++G+ + W + TG+D +D G+ V NY++ TEV+G
Sbjct: 182 FVGRILDWYKKETGRDSYPGAEDPGVQSVTQIYNYYKKFGYKTEVMG 228
>gnl|CDD|163655 cd07412, MPP_YhcR_N, Bacillus subtilis YhcR endonuclease and
related proteins, N-terminal metallophosphatase domain.
YhcR is a Bacillus subtilis sugar-nonspecific
endonuclease. It cleaves endonucleolytically to yield
nucleotide 3'-monophosphate products, similar to
Staphylococcus aureus micrococcal nuclease. YhcR appears
to be located in the cell wall, and is thought to be a
substrate for a Bacillus subtilis sortase. YhcR is the
major calcium-activated nuclease of B. subtilis. The
N-terminal metallophosphatase domain belongs to a large
superfamily of distantly related metallophosphatases
(MPPs) that includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 288
Score = 26.1 bits (58), Expect = 2.6
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 28 ATGETHSVREFVEAAFLYIGKTIVWEGTGKD 58
T + F A F Y+ + +GTG
Sbjct: 104 PTTGCQAGYPFPGANFPYLAANVYDKGTGTP 134
>gnl|CDD|189906 pfam01247, Ribosomal_L35Ae, Ribosomal protein L35Ae.
Length = 95
Score = 24.5 bits (54), Expect = 5.7
Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 14/56 (25%)
Query: 34 SVREFVEAAFLYIGKTIVWEGTGKDEVGKEK-------------DTGIVRVKVNEN 76
V +A F Y+GK + + K + K ++G+VR K N
Sbjct: 28 GVNTKEDAQF-YLGKRVAYVYKAKKKKNGSKIRVIWGKVTRPHGNSGVVRAKFRRN 82
>gnl|CDD|224776 COG1863, MnhE, Multisubunit Na+/H+ antiporter, MnhE subunit
[Inorganic ion transport and metabolism].
Length = 158
Score = 24.9 bits (55), Expect = 5.9
Identities = 5/23 (21%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 6 LNLSKYAMWMMLQQD-TPQDFVI 27
LN+ W++L +P + ++
Sbjct: 7 LNILLALFWLLLTGSFSPANLIL 29
>gnl|CDD|162081 TIGR00874, talAB, transaldolase. This family includes the majority
of known and predicted transaldolase sequences,
including E. coli TalA and TalB. It excluded two other
families. The first includes E. coli transaldolase-like
protein TalC. The second family includes the putative
transaldolases of Helicobacter pylori and Mycobacterium
tuberculosis [Energy metabolism, Pentose phosphate
pathway].
Length = 317
Score = 24.7 bits (54), Expect = 7.7
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 45 YIGKTIVW--EGTGKDEVGKEKDTGIVRVKVNENYFR----PTEVIG 85
++G+ + W TGK E E+D G+ VK NY++ PTEV+G
Sbjct: 176 FVGRILDWYKAATGKKEYSIEEDPGVASVKKIYNYYKKHGYPTEVMG 222
>gnl|CDD|224234 COG1315, COG1315, Uncharacterized conserved protein [Function
unknown].
Length = 543
Score = 24.7 bits (54), Expect = 8.7
Identities = 15/64 (23%), Positives = 22/64 (34%), Gaps = 8/64 (12%)
Query: 20 DTPQDFVIATGETHSVREFVEAAFL------YIGKTIVWEGTGKDEVGK-EKDTGI-VRV 71
D V+ +V+ VE A + ++GK IV +G G I
Sbjct: 280 DVEDGMVVKAEGNITVKGTVENANVSASGDIFVGKGIVGKGEGCIRAKGLVFAKFIENNA 339
Query: 72 KVNE 75
KV
Sbjct: 340 KVEL 343
>gnl|CDD|236311 PRK08609, PRK08609, hypothetical protein; Provisional.
Length = 570
Score = 24.5 bits (54), Expect = 9.1
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 24 DFVIATGETHSVRE 37
DF+IAT E +VRE
Sbjct: 195 DFIIATDEPEAVRE 208
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 0.135 0.397
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,392,464
Number of extensions: 354117
Number of successful extensions: 264
Number of sequences better than 10.0: 1
Number of HSP's gapped: 262
Number of HSP's successfully gapped: 16
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
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 (21.7 bits)
S2: 53 (24.1 bits)