RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 023972
(274 letters)
>gnl|CDD|178528 PLN02940, PLN02940, riboflavin kinase.
Length = 382
Score = 532 bits (1372), Expect = 0.0
Identities = 226/267 (84%), Positives = 246/267 (92%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
MALASNS RA IE+KIS GW ESFSVIVG DEV GKPSPDIFLEAAKRLN+EPS+ L
Sbjct: 112 MALASNSPRANIEAKISCHQGWKESFSVIVGGDEVEKGKPSPDIFLEAAKRLNVEPSNCL 171
Query: 61 VIEDSVIGVVAGKAAGMEVVAVPSLPKQTHRYTAADEVINSLLDLRPEKWGLPPFQDWIE 120
VIEDS+ GV+AGKAAGMEV+AVPS+PKQTH Y++ADEVINSLLDL+PEKWGLPPF DWIE
Sbjct: 172 VIEDSLPGVMAGKAAGMEVIAVPSIPKQTHLYSSADEVINSLLDLQPEKWGLPPFNDWIE 231
Query: 121 GTLPSEPWYIGGPVVKGLGRGSKVLGIPTANLSTEGYSDVLSEHPSGVYFGWAGLSTRGV 180
GTLP EPW+IGGPV+KG GRGSKVLGIPTANLSTE YSDVLSEHPSGVYFGWAGLSTRGV
Sbjct: 232 GTLPIEPWHIGGPVIKGFGRGSKVLGIPTANLSTENYSDVLSEHPSGVYFGWAGLSTRGV 291
Query: 181 YKMVMSIGWNPYFDNAEKTIEPWLLHEFDEDFYDEELHLVIVGYIRPEANFPSLETLIAK 240
YKMVMSIGWNPYF+N EKTIEPWLLH+F EDFY EEL LVIVGYIRPEANFPSLE+LIAK
Sbjct: 292 YKMVMSIGWNPYFNNTEKTIEPWLLHDFGEDFYGEELRLVIVGYIRPEANFPSLESLIAK 351
Query: 241 IHEDRKVAERALDLPLYSKYRDDPYLK 267
IHEDR++AE+ALDLPLY+KY+DDPYL
Sbjct: 352 IHEDRRIAEKALDLPLYAKYKDDPYLT 378
>gnl|CDD|190069 pfam01687, Flavokinase, Riboflavin kinase. This family represents
the C-terminal region of the bifunctional riboflavin
biosynthesis protein known as RibC in Bacillus subtilis.
The RibC protein from Bacillus subtilis has both
flavokinase and flavin adenine dinucleotide synthetase
(FAD-synthetase) activities. RibC plays an essential
role in the flavin metabolism. This domain is thought to
have kinase activity.
Length = 125
Score = 138 bits (351), Expect = 1e-41
Identities = 51/126 (40%), Positives = 70/126 (55%), Gaps = 6/126 (4%)
Query: 127 PWYIGGPVVKGLGRGSKVLGIPTANLSTEGYSDVLSEHPSGVYFGWAGLSTRGVYKMVMS 186
P+ I G VV G GRG LG PTANLS + +GVY + + VY V +
Sbjct: 5 PYSISGTVVHGKGRGRT-LGFPTANLSLPKDKLL---PKNGVYAVRVKIDGK-VYPGVAN 59
Query: 187 IGWNPYFDNAEKTIEPWLLHEFDEDFYDEELHLVIVGYIRPEANFPSLETLIAKIHEDRK 246
IG+NP F + TIE +L +FD D Y EE+ + + ++RPE F SLE L A+I +D +
Sbjct: 60 IGYNPTFGGKKPTIEVHIL-DFDGDLYGEEIRVEFLKFLRPEKKFDSLEELKAQIKKDIE 118
Query: 247 VAERAL 252
A + L
Sbjct: 119 QARKIL 124
>gnl|CDD|214901 smart00904, Flavokinase, Riboflavin kinase. Riboflavin is
converted into catalytically active cofactors (FAD and
FMN) by the actions of riboflavin kinase, which converts
it into FMN, and FAD synthetase, which adenylates FMN to
FAD. Eukaryotes usually have two separate enzymes, while
most prokaryotes have a single bifunctional protein that
can carry out both catalyses, although exceptions occur
in both cases. While eukaryotic monofunctional
riboflavin kinase is orthologous to the bifunctional
prokaryotic enzyme. the monofunctional FAD synthetase
differs from its prokaryotic counterpart, and is instead
related to the PAPS-reductase family. The bacterial FAD
synthetase that is part of the bifunctional enzyme has
remote similarity to nucleotidyl transferases and,
hence, it may be involved in the adenylylation reaction
of FAD synthetases. This entry represents riboflavin
kinase, which occurs as part of a bifunctional enzyme or
a stand-alone enzyme.
Length = 124
Score = 134 bits (340), Expect = 6e-40
Identities = 43/127 (33%), Positives = 62/127 (48%), Gaps = 7/127 (5%)
Query: 127 PWYIGGPVVKGLGRGSKVLGIPTANLSTEGYSDVLSEHPSGVYFGWAGLSTRGVYKMVMS 186
P+ I G VV G RG LG PTANL + + +GVY + +Y V +
Sbjct: 5 PYSISGRVVHGDKRGRT-LGFPTANLPLDDRLLLP---KNGVYAVRVRV-DGKIYPGVAN 59
Query: 187 IGWNPYFDNAEKTIEPWLLHEFDEDFYDEELHLVIVGYIRPEANFPSLETLIAKIHEDRK 246
IG P F ++++E +L F D Y EE+ + + +IR E F SL+ L A+I D +
Sbjct: 60 IGTRPTFGG-DRSVEVHILD-FSGDLYGEEIEVEFLKFIRDEQKFDSLDELKAQISRDIE 117
Query: 247 VAERALD 253
A L
Sbjct: 118 EAREYLA 124
>gnl|CDD|178407 PLN02811, PLN02811, hydrolase.
Length = 220
Score = 116 bits (292), Expect = 1e-31
Identities = 60/127 (47%), Positives = 79/127 (62%), Gaps = 15/127 (11%)
Query: 1 MALASNSHRATIESKISYQHGWNESFS----VIVGSD-EVRTGKPSPDIFLEAAKRL--- 52
+A+A+ SH+ + K +HG E FS V+ G D EV+ GKP+PDIFL AA+R
Sbjct: 97 IAIATGSHKRHFDLKTQ-RHG--ELFSLMHHVVTGDDPEVKQGKPAPDIFLAAARRFEDG 153
Query: 53 NMEPSSSLVIEDSVIGVVAGKAAGMEVVAVP--SLPKQTHRYTAADEVINSLLDLRPEKW 110
++P LV ED+ GV A K AGM VV VP L K + AD+V++SLLD +PE+W
Sbjct: 154 PVDPGKVLVFEDAPSGVEAAKNAGMSVVMVPDPRLDKSYCK--GADQVLSSLLDFKPEEW 211
Query: 111 GLPPFQD 117
GLPPF D
Sbjct: 212 GLPPFPD 218
>gnl|CDD|223274 COG0196, RibF, FAD synthase [Coenzyme metabolism].
Length = 304
Score = 110 bits (278), Expect = 1e-28
Identities = 44/128 (34%), Positives = 63/128 (49%), Gaps = 10/128 (7%)
Query: 127 PWYIGGPVVKGLGRGSKVLGIPTANLSTEGYSDVLSEHPSGVYFGWAGLSTRGVYKMVMS 186
P+ I G VV G G LG PTAN+ + GVY L GVY V +
Sbjct: 185 PYSIEGKVVHGQKLGRT-LGFPTANIYLKDNVLP----AFGVYAVRVKL-DGGVYPGVAN 238
Query: 187 IGWNPYFDNAEKTIEPWLLHEFDEDFYDEELHLVIVGYIRPEANFPSLETLIAKIHEDRK 246
+G+ P D +E+++E +L F+ D Y E + + + +IR E F SL+ L +I +D
Sbjct: 239 VGYRPTVDGSERSLEVHILD-FNGDLYGERVKVRFLKFIRDEKKFDSLDELKEQIEKD-- 295
Query: 247 VAERALDL 254
ERA L
Sbjct: 296 -IERARKL 302
>gnl|CDD|223710 COG0637, COG0637, Predicted phosphatase/phosphohexomutase [General
function prediction only].
Length = 221
Score = 97.1 bits (242), Expect = 3e-24
Identities = 43/108 (39%), Positives = 65/108 (60%), Gaps = 1/108 (0%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
+A+AS+S R E ++ + G + F VIV +D+V GKP+PDI+L AA+RL ++P +
Sbjct: 105 LAVASSSPRRAAE-RVLARLGLLDYFDVIVTADDVARGKPAPDIYLLAAERLGVDPEECV 163
Query: 61 VIEDSVIGVVAGKAAGMEVVAVPSLPKQTHRYTAADEVINSLLDLRPE 108
V+EDS G+ A KAAGM VV VP+ + H +++L E
Sbjct: 164 VVEDSPAGIQAAKAAGMRVVGVPAGHDRPHLDPLDAHGADTVLLDLAE 211
>gnl|CDD|235536 PRK05627, PRK05627, bifunctional riboflavin kinase/FMN
adenylyltransferase; Reviewed.
Length = 305
Score = 91.4 bits (228), Expect = 1e-21
Identities = 41/124 (33%), Positives = 56/124 (45%), Gaps = 9/124 (7%)
Query: 130 IGGPVVKGLGRGSKVLGIPTANLSTEGYSDVLSEHP-SGVYFGWAGLSTRGVYKMVMSIG 188
I G VV G G LG PTANL P GVY + + Y V +IG
Sbjct: 188 ISGRVVHGQKLGRT-LGFPTANLPLPDRV-----LPADGVYAVRVKVDGK-PYPGVANIG 240
Query: 189 WNPYFDNAEKTIEPWLLHEFDEDFYDEELHLVIVGYIRPEANFPSLETLIAKIHEDRKVA 248
P D + +E LL +F+ D Y E + + + +R E F SL+ L A+I +D + A
Sbjct: 241 TRPTVDGGRQLLEVHLL-DFNGDLYGEHITVEFLKKLRDEQKFDSLDELKAQIAKDIETA 299
Query: 249 ERAL 252
L
Sbjct: 300 RAFL 303
>gnl|CDD|213673 TIGR02009, PGMB-YQAB-SF, beta-phosphoglucomutase family hydrolase.
This subfamily model groups together three clades: the
characterized beta-phosphoglucomutases (including those
from E.coli, B.subtilus and L.lactis, TIGR01990), a
clade of putative bPGM's from mycobacteria and a clade
including the uncharacterized E.coli and H.influenzae
yqaB genes which may prove to be beta-mutases of a
related 1-phosphosugar. All of these are members of the
larger Haloacid dehalogenase (HAD) subfamily IA and
include the "variant 3" glu-asp version of the third
conserved HAD domain (TIGR01509).
Length = 185
Score = 77.8 bits (192), Expect = 2e-17
Identities = 35/82 (42%), Positives = 49/82 (59%), Gaps = 5/82 (6%)
Query: 2 ALASNSHRA-TIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
L S+S A I +K+ G + F IV + EV+ GKP P+ FL AA+ L + P+ +
Sbjct: 108 GLGSSSKNAPRILAKL----GLRDYFDAIVDASEVKNGKPHPETFLLAAELLGVPPNECI 163
Query: 61 VIEDSVIGVVAGKAAGMEVVAV 82
V ED++ GV A +AAGM VAV
Sbjct: 164 VFEDALAGVQAARAAGMFAVAV 185
>gnl|CDD|213672 TIGR01990, bPGM, beta-phosphoglucomutase. This model represents
the beta-phosphoglucomutase enzyme which catalyzes the
interconverison of beta-D-glucose-1-phosphate and
beta-D-glucose-6-phosphate. The 6-phosphate is capable
of non-enzymatic anomerization (alpha <-> beta) while
the 1-phosphate is not. A separate enzyme is responsible
for the isomerization of the alpha anomers.
Beta-D-glucose-1-phosphate results from the
phosphorylysis of maltose (2.4.1.8), trehalose
(2.4.1.64) or trehalose-6-phosphate (2.4.1.216).
Alternatively, these reactions can be run in the
synthetic direction to create the disaccharides. All
sequenced genomes which contain a member of this family
also appear to contain at least one putative maltose or
trehalose phosphorylase. Three species, Lactococcus,
Enterococcus and Neisseria appear to contain a pair of
paralogous beta-PGM's. Beta-phosphoglucomutase is a
member of the haloacid dehalogenase superfamily of
hydrolase enzymes. These enzymes are characterized by a
series of three catalytic motifs positioned within an
alpha-beta (Rossman) fold. beta-PGM contains an inserted
alpha helical domain in between the first and second
conserved motifs and thus is a member of subfamily IA of
the superfamily. The third catalytic motif comes in
three variants, the third of which, containing a
conserved DD or ED, is the only one found here as well
as in several other related enzymes (TIGR01509). The
enzyme from L. lactis has been extensively characterized
including a remarkable crystal structure which traps the
pentacoordinate transition state [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 185
Score = 73.9 bits (182), Expect = 5e-16
Identities = 37/82 (45%), Positives = 47/82 (57%), Gaps = 5/82 (6%)
Query: 2 ALASNSHRA-TIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
ALAS S A TI K+ + F IV E++ GKP P+IFL AA+ L + PS +
Sbjct: 107 ALASASKNAPTILEKL----ELIDYFDAIVDPAELKKGKPDPEIFLAAAEGLGVSPSECI 162
Query: 61 VIEDSVIGVVAGKAAGMEVVAV 82
IED+ G+ A KAAGM V V
Sbjct: 163 GIEDAQAGIEAIKAAGMFAVGV 184
>gnl|CDD|233443 TIGR01509, HAD-SF-IA-v3, haloacid dehalogenase superfamily,
subfamily IA, variant 3 with third motif having DD or
ED. This model represents part of one structural
subfamily of the Haloacid Dehalogenase (HAD) superfamily
of aspartate-nucleophile hydrolases. The superfamily is
defined by the presence of three short catalytic motifs.
The subfamilies are defined based on the location and
the observed or predicted fold of a so-called "capping
domain", or the absence of such a domain. Subfamily I
consists of sequences in which the capping domain is
found in between the first and second catalytic motifs.
Subfamily II consists of sequences in which the capping
domain is found between the second and third motifs.
Subfamily III sequences have no capping domain in either
of these positions.The Subfamily IA and IB capping
domains are predicted by PSI-PRED to consist of an alpha
helical bundle. Subfamily I encompasses such a wide
region of sequence space (the sequences are highly
divergent) that representing it with a single model is
impossible, resulting in an overly broad description
which allows in many unrelated sequences. Subfamily IA
and IB are separated based on an aparrent phylogenetic
bifurcation. Subfamily IA is still too broad to model,
but cannot be further subdivided into large chunks based
on phylogenetic trees. Of the three motifs defining the
HAD superfamily, the third has three variant forms : (1)
hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s
where _s_ refers to a small amino acid and _h_ to a
hydrophobic one. All three of these variants are found
in subfamily IA. Individual models were made based on
seeds exhibiting only one of the variants each. Variant
3 (this model) is found in the enzymes
beta-phosphoglucomutase (TIGR01990) and
deoxyglucose-6-phosphatase, while many other enzymes of
subfamily IA exhibit this variant as well as variant 1
(TIGR01549). These three variant models were created
withthe knowledge that there will be overlap among them
- this is by design and serves the purpose of
eliminating the overlap with models of more distantly
relatedHAD subfamilies caused by an overly broad single
model [Unknown function, Enzymes of unknown
specificity].
Length = 177
Score = 72.1 bits (177), Expect = 2e-15
Identities = 35/82 (42%), Positives = 50/82 (60%), Gaps = 2/82 (2%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
+AL +NS RA + + G F V++ S +V GKP PDI+L+A K+L ++PS L
Sbjct: 98 LALLTNSPRADAKLVLE--LGLRALFDVVIDSSDVGLGKPDPDIYLQALKKLGLKPSECL 155
Query: 61 VIEDSVIGVVAGKAAGMEVVAV 82
++DS G+ A KAAGM V V
Sbjct: 156 FVDDSPAGIDAAKAAGMHTVLV 177
>gnl|CDD|232818 TIGR00083, ribF, riboflavin kinase/FMN adenylyltransferase.
multifunctional enzyme: riboflavin kinase (EC 2.7.1.26)
(flavokinase) / FMN adenylyltransferase (EC 2.7.7.2)
(FAD pyrophosphorylase) (FAD synthetase) [Biosynthesis
of cofactors, prosthetic groups, and carriers,
Riboflavin, FMN, and FAD].
Length = 288
Score = 74.0 bits (182), Expect = 2e-15
Identities = 41/127 (32%), Positives = 60/127 (47%), Gaps = 6/127 (4%)
Query: 126 EPWYIGGPVVKGLGRGSKVLGIPTANLSTEGYSDVLSEHPSGVYFGWAGLSTRGVYKMVM 185
P++I G V+ G G LG PTAN+ + L G Y L+ Y V
Sbjct: 167 RPYFICGTVIHGQKLGRT-LGFPTANIKLKNQVLPL---KGGYYVVVVLLNGE-PYPGVG 221
Query: 186 SIGWNPYFDNAEKTIEPWLLHEFDEDFYDEELHLVIVGYIRPEANFPSLETLIAKIHEDR 245
+IG P F + IE LL +F + Y +E+ + +V IRPE F SL+ L +I +D
Sbjct: 222 NIGNRPTFIGQQLVIEVHLL-DFSGELYGQEIKVTLVKKIRPEQKFSSLDELKNQIQQDI 280
Query: 246 KVAERAL 252
A++
Sbjct: 281 LQAKKWF 287
>gnl|CDD|236770 PRK10826, PRK10826, 2-deoxyglucose-6-phosphatase; Provisional.
Length = 222
Score = 71.9 bits (177), Expect = 5e-15
Identities = 32/108 (29%), Positives = 58/108 (53%), Gaps = 4/108 (3%)
Query: 3 LASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVI 62
LAS S +E + + F + ++++ KP P+++L A +L ++P + + +
Sbjct: 113 LASASPLHMLE-AVLTMFDLRDYFDALASAEKLPYSKPHPEVYLNCAAKLGVDPLTCVAL 171
Query: 63 EDSVIGVVAGKAAGMEVVAVPSLPKQTH--RYTAADEVINSLLDLRPE 108
EDS G++A KAA M + VP+ P+Q + R+ AD + SL +L
Sbjct: 172 EDSFNGMIAAKAARMRSIVVPA-PEQQNDPRWALADVKLESLTELTAA 218
>gnl|CDD|215416 PLN02779, PLN02779, haloacid dehalogenase-like hydrolase family
protein.
Length = 286
Score = 70.5 bits (173), Expect = 4e-14
Identities = 35/89 (39%), Positives = 50/89 (56%), Gaps = 1/89 (1%)
Query: 24 ESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVVAVP 83
+ V G D+V KP PDI+ AA+ L ++PS +V+EDSVIG+ A KAAGM +
Sbjct: 188 QGLDVFAG-DDVPKKKPDPDIYNLAAETLGVDPSRCVVVEDSVIGLQAAKAAGMRCIVTK 246
Query: 84 SLPKQTHRYTAADEVINSLLDLRPEKWGL 112
S ++ AD V + L D+ E + L
Sbjct: 247 SSYTADEDFSGADAVFDCLGDVPLEDFDL 275
>gnl|CDD|182679 PRK10725, PRK10725, fructose-1-P/6-phosphogluconate phosphatase;
Provisional.
Length = 188
Score = 65.5 bits (160), Expect = 6e-13
Identities = 31/86 (36%), Positives = 50/86 (58%), Gaps = 3/86 (3%)
Query: 1 MALASNSHRATIESKISYQH-GWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSS 59
MA+ + S A E+ + H G F +V +D+V+ KP+PD FL A+ + ++P+
Sbjct: 105 MAVGTGSESAIAEALL--AHLGLRRYFDAVVAADDVQHHKPAPDTFLRCAQLMGVQPTQC 162
Query: 60 LVIEDSVIGVVAGKAAGMEVVAVPSL 85
+V ED+ G+ A +AAGM+ V V L
Sbjct: 163 VVFEDADFGIQAARAAGMDAVDVRLL 188
>gnl|CDD|223943 COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General
function prediction only].
Length = 229
Score = 64.9 bits (158), Expect = 2e-12
Identities = 32/107 (29%), Positives = 53/107 (49%), Gaps = 3/107 (2%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
+ + +N R E K+ Q G + F + S++V KP P+IF A ++L + P +L
Sbjct: 117 LGILTNGARPHQERKLR-QLGLLDYFDAVFISEDVGVAKPDPEIFEYALEKLGVPPEEAL 175
Query: 61 VIEDSVIGVVAG-KAAGMEVVAVPSLPKQT-HRYTAADEVINSLLDL 105
+ DS+ + G +A GM+ V + K A D I+SL +L
Sbjct: 176 FVGDSLENDILGARALGMKTVWINRGGKPLPDALEAPDYEISSLAEL 222
>gnl|CDD|222115 pfam13419, HAD_2, Haloacid dehalogenase-like hydrolase.
Length = 176
Score = 63.1 bits (154), Expect = 3e-12
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
+ + SN R +E + G + F + SD+V KP P+ + +RL + P L
Sbjct: 96 LVILSNGSREAVERLLEK-LGLLDLFDAVFTSDDVGARKPDPEAYERVLERLGLPPEEIL 154
Query: 61 VIEDSVIGVVAGKAAGMEVVAV 82
I+DS + A +AAG++ V V
Sbjct: 155 FIDDSPEDLEAARAAGIKTVHV 176
>gnl|CDD|215497 PLN02919, PLN02919, haloacid dehalogenase-like hydrolase family
protein.
Length = 1057
Score = 66.0 bits (161), Expect = 3e-12
Identities = 33/82 (40%), Positives = 50/82 (60%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
+A+AS++ R +++ ++ F IV +D KP+PDIFL AAK L + S +
Sbjct: 180 VAVASSADRIKVDANLAAAGLPLSMFDAIVSADAFENLKPAPDIFLAAAKILGVPTSECV 239
Query: 61 VIEDSVIGVVAGKAAGMEVVAV 82
VIED++ GV A +AAGM +AV
Sbjct: 240 VIEDALAGVQAARAAGMRCIAV 261
>gnl|CDD|237310 PRK13222, PRK13222, phosphoglycolate phosphatase; Provisional.
Length = 226
Score = 64.1 bits (157), Expect = 3e-12
Identities = 29/98 (29%), Positives = 43/98 (43%), Gaps = 14/98 (14%)
Query: 19 QHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGME 78
G + FSV++G D + KP P L A ++L ++P L + DS + A +AAG
Sbjct: 129 ALGIADYFSVVIGGDSLPNKKPDPAPLLLACEKLGLDPEEMLFVGDSRNDIQAARAAGCP 188
Query: 79 VVAVPSLPKQTHRYT--------AADEVINSLLDLRPE 108
V V T+ Y D VI+ +L P
Sbjct: 189 SVGV------TYGYNYGEPIALSEPDVVIDHFAELLPL 220
>gnl|CDD|183215 PRK11587, PRK11587, putative phosphatase; Provisional.
Length = 218
Score = 63.5 bits (155), Expect = 5e-12
Identities = 33/82 (40%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 28 VIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVVAVPSLPK 87
V V ++ V+ GKP PD +L A+ L + P +V+ED+ GV++G AAG V+AV + P
Sbjct: 127 VFVTAERVKRGKPEPDAYLLGAQLLGLAPQECVVVEDAPAGVLSGLAAGCHVIAV-NAPA 185
Query: 88 QTHRYTAADEVINSLLDLRPEK 109
T R D V++SL L K
Sbjct: 186 DTPRLDEVDLVLHSLEQLTVTK 207
>gnl|CDD|223620 COG0546, Gph, Predicted phosphatases [General function prediction
only].
Length = 220
Score = 62.5 bits (152), Expect = 1e-11
Identities = 33/113 (29%), Positives = 55/113 (48%), Gaps = 11/113 (9%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
+ + +N ++ + G + F VIVG D+V KP P+ L ++L ++P +L
Sbjct: 108 LGIVTNKPERELD-ILLKALGLADYFDVIVGGDDVPPPKPDPEPLLLLLEKLGLDPEEAL 166
Query: 61 VIEDSVIGVVAGKAAGMEVVAV------PSLPKQTHRYTAADEVINSLLDLRP 107
++ DS+ ++A KAAG+ V V Q AD VI+SL +L
Sbjct: 167 MVGDSLNDILAAKAAGVPAVGVTWGYNSREELAQAG----ADVVIDSLAELLA 215
>gnl|CDD|222003 pfam13242, Hydrolase_like, HAD-hyrolase-like.
Length = 74
Score = 58.1 bits (141), Expect = 2e-11
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 14/77 (18%)
Query: 38 GKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVVAVPSLPKQTHRYTA--- 94
GKP+P + A +RL ++P ++I DS ++A +AAG+ + V T TA
Sbjct: 3 GKPNPGMLRAALERLGVDPEECVMIGDSDTDILAARAAGIRTILVL-----TGVTTAEDL 57
Query: 95 ------ADEVINSLLDL 105
D V++SL DL
Sbjct: 58 ERAPGRPDYVVDSLADL 74
>gnl|CDD|119389 cd01427, HAD_like, Haloacid dehalogenase-like hydrolases. The
haloacid dehalogenase-like (HAD) superfamily includes
L-2-haloacid dehalogenase, epoxide hydrolase,
phosphoserine phosphatase, phosphomannomutase,
phosphoglycolate phosphatase, P-type ATPase, and many
others, all of which use a nucleophilic aspartate in
their phosphoryl transfer reaction. All members possess
a highly conserved alpha/beta core domain, and many also
possess a small cap domain, the fold and function of
which is variable. Members of this superfamily are
sometimes referred to as belonging to the DDDD
superfamily of phosphohydrolases.
Length = 139
Score = 57.0 bits (138), Expect = 2e-10
Identities = 28/98 (28%), Positives = 45/98 (45%), Gaps = 17/98 (17%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEV----------------RTGKPSPDI 44
+ALA+N R + + + G ++ F ++ S+ GKP+PD
Sbjct: 43 LALATNKSRREVLELLE-ELGLDDYFDPVITSNGAAIYYPKEGLFLGGGPFDIGKPNPDK 101
Query: 45 FLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVVAV 82
L A K L ++P L++ DS+ + KAAG VAV
Sbjct: 102 LLAALKLLGVDPEEVLMVGDSLNDIEMAKAAGGLGVAV 139
>gnl|CDD|215313 PLN02575, PLN02575, haloacid dehalogenase-like hydrolase.
Length = 381
Score = 59.5 bits (144), Expect = 4e-10
Identities = 41/105 (39%), Positives = 56/105 (53%), Gaps = 2/105 (1%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
MAL S R T+E+ I G FSVIV +++V GKP P++F+ AA+ LN P +
Sbjct: 235 MALVSTRPRKTLENAIG-SIGIRGFFSVIVAAEDVYRGKPDPEMFIYAAQLLNFIPERCI 293
Query: 61 VIEDSVIGVVAGKAAGMEVVAVPSLPKQTHRYTAADEVINSLLDL 105
V +S V A A M+ VAV S + AAD V+ L +L
Sbjct: 294 VFGNSNQTVEAAHDARMKCVAVAS-KHPIYELGAADLVVRRLDEL 337
>gnl|CDD|216069 pfam00702, Hydrolase, haloacid dehalogenase-like hydrolase. This
family is structurally different from the alpha/beta
hydrolase family (pfam00561). This family includes
L-2-haloacid dehalogenase, epoxide hydrolases and
phosphatases. The structure of the family consists of
two domains. One is an inserted four helix bundle, which
is the least well conserved region of the alignment,
between residues 16 and 96 of Pseudomonas sp.
(S)-2-haloacid dehalogenase 1. The rest of the fold is
composed of the core alpha/beta domain. Those members
with the characteristic DxD triad at the N-terminus are
probably phosphatidylglycerolphosphate (PGP)
phosphatases involved in cardiolipin biosynthesis in the
mitochondria.
Length = 187
Score = 56.1 bits (135), Expect = 1e-09
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRT---GKPSPDIFLEAAKRLNMEPS 57
+A+ + +R T + F +V +D GKP P IF A + L ++P
Sbjct: 113 LAILTGDNRLTANAIARLLG----LFDALVSADLYGLVGVGKPDPKIFELALEELGVKPE 168
Query: 58 SSLVIEDSVIGVVAGKAAG 76
L++ D V + A KAAG
Sbjct: 169 EVLMVGDGVNDIPAAKAAG 187
>gnl|CDD|130516 TIGR01449, PGP_bact, 2-phosphoglycolate phosphatase, prokaryotic.
PGP is an essential enzyme in the glycolate salvage
pathway in higher organisms (photorespiration in
plants). Phosphoglycolate results from the oxidase
activity of RubisCO in the Calvin cycle when
concentrations of carbon dioxide are low relative to
oxygen. In Ralstonia (Alcaligenes) eutropha and
Rhodobacter sphaeroides, the PGP gene (CbbZ) is located
on an operon along with other Calvin cycle enzymes
including RubisCO. The only other pertinent experimental
evidence concerns the gene from E. coli. The in vitro
activity of the Ralstonia and Escherichia enzymes was
determined with crude cell extracts of strains
containing PGP on expression plasmids and compared to
controls. In E. coli, however, there does not appear to
be a functional Calvin cycle (RubisCO is absent),
although the E. coli PGP gene (gph) is on the same
operon (dam) with ribulose-5-phosphate-3-epimerase
(rpe), a gene in the pentose-phosphate pathway (along
with other, unrelated genes). The E. coli enzyme is not
expressed under normal laboratory conditions; the
pathway to which it belongs has not been determined. In
fact, the possibility exists, although unlikely, that
the E. coli enzyme and others within this equivalog have
as their physiological substrate another, closely
related molecule. The other seed chosen for this model,
from Xylella fastidiosa has no experimental evidence,
but is a plant pathogen and thus may obtain
phosphoglycolate from its host. This model has been
restricted to encompass only proteobacteria as no
related PGP has been verified outside of this clade.
Sequences from Aquifex aeolicus and Treponema pallidum
fall between the trusted and noise cutoffs. Just below
the noise cutoff is a gene which is part of the operon
for the biosynthesis of the blue pigment, indigoidine,
from Erwinia (Pectobacterium) chrysanthemi, a plant
pathogen. It does not seem likely, considering the
proposed biosynthetic mechanism, that the
dephosphorylation of phosphoglycolate or a closely
related compound is required. Possibly, this gene is
fortuitously located in this operon, or has an indirect
relationship to the necessity for the biosynthesis of
this compound. Sequences from 11 species have been
annotated as PGP or putative PGP but fall below the
noise cutoff. None of these have experimental
validation. This enzyme is a member of the Haloacid
Dehalogenase (HAD) superfamily of aspartate-nucleophile
hydrolase enzymes (pfam00702) [Energy metabolism,
Sugars].
Length = 213
Score = 55.2 bits (133), Expect = 4e-09
Identities = 23/62 (37%), Positives = 35/62 (56%)
Query: 21 GWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVV 80
G + FSV++G D + KP PD L AA+RL + P + + DS + + A +AAG V
Sbjct: 123 GLAKYFSVLIGGDSLAQRKPHPDPLLLAAERLGVAPQQMVYVGDSRVDIQAARAAGCPSV 182
Query: 81 AV 82
+
Sbjct: 183 LL 184
>gnl|CDD|215413 PLN02770, PLN02770, haloacid dehalogenase-like hydrolase family
protein.
Length = 248
Score = 53.7 bits (129), Expect = 1e-08
Identities = 30/81 (37%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 2 ALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLV 61
A +N+ R E IS G ++ F ++ E KP PD +L+A + L + + V
Sbjct: 128 AAVTNAPRENAELMISLL-GLSDFFQAVIIGSECEHAKPHPDPYLKALEVLKVSKDHTFV 186
Query: 62 IEDSVIGVVAGKAAGMEVVAV 82
EDSV G+ AG AAGM VV +
Sbjct: 187 FEDSVSGIKAGVAAGMPVVGL 207
>gnl|CDD|130521 TIGR01454, AHBA_synth_RP, 3-amino-5-hydroxybenoic acid synthesis
related protein. The enzymes in this equivalog are all
located in the operons for the biosynthesis of
3-amino-5-hydroxybenoic acid (AHBA), which is a
precursor of several antibiotics including ansatrienin ,
naphthomycin , rifamycin and mitomycin. The role that
this enzyme plays in this biosynthesis has not been
elucidated. This enzyme is a member of the Haloacid
dehalogenase superfamily (pfam00702) of
aspartate-nucleophile hydrolases. This enzyme is closely
related to phosphoglycolate phosphatase (TIGR01449), but
it is unclear what purpose a PGPase or PGPase-like
activity would serve in these biosyntheses. This model
is limited to the Gram positive Actinobacteria. The most
closely related enzyme below the noise cutoff is IndB
which is involved in the biosynthesis of Indigoidine in
Pectobacterium (Erwinia) chrysanthemi, a gamma
proteobacter. This enzyme is similarly related to PGP.
In this case, too it is unclear what role would be be
played by a PGPase activity.
Length = 205
Score = 50.3 bits (120), Expect = 2e-07
Identities = 23/61 (37%), Positives = 37/61 (60%)
Query: 21 GWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVV 80
G F ++GSDEV KP+PDI EA + L++ P ++++ D+V + + +AAG V
Sbjct: 113 GLLPLFDHVIGSDEVPRPKPAPDIVREALRLLDVPPEDAVMVGDAVTDLASARAAGTATV 172
Query: 81 A 81
A
Sbjct: 173 A 173
>gnl|CDD|215644 PLN03243, PLN03243, haloacid dehalogenase-like hydrolase;
Provisional.
Length = 260
Score = 50.0 bits (119), Expect = 3e-07
Identities = 35/105 (33%), Positives = 53/105 (50%), Gaps = 2/105 (1%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
+A+AS R +E I G FSV++ +++V GKP P++F+ AA+RL P +
Sbjct: 128 IAVASTRPRRYLERAIE-AVGMEGFFSVVLAAEDVYRGKPDPEMFMYAAERLGFIPERCI 186
Query: 61 VIEDSVIGVVAGKAAGMEVVAVPSLPKQTHRYTAADEVINSLLDL 105
V +S V A M+ VAV + +A D V+ L DL
Sbjct: 187 VFGNSNSSVEAAHDGCMKCVAVAG-KHPVYELSAGDLVVRRLDDL 230
>gnl|CDD|237311 PRK13226, PRK13226, phosphoglycolate phosphatase; Provisional.
Length = 229
Score = 48.7 bits (116), Expect = 6e-07
Identities = 22/64 (34%), Positives = 36/64 (56%)
Query: 19 QHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGME 78
Q GW + +V++G D + KP P L AA+R+ + P+ + + D ++A +AAGM
Sbjct: 131 QLGWEQRCAVLIGGDTLAERKPHPLPLLVAAERIGVAPTDCVYVGDDERDILAARAAGMP 190
Query: 79 VVAV 82
VA
Sbjct: 191 SVAA 194
>gnl|CDD|237336 PRK13288, PRK13288, pyrophosphatase PpaX; Provisional.
Length = 214
Score = 47.7 bits (114), Expect = 1e-06
Identities = 21/62 (33%), Positives = 36/62 (58%)
Query: 21 GWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVV 80
G +E F V++ D+V KP P+ L+A + L +P +L++ D+ ++AGK AG +
Sbjct: 120 GLDEFFDVVITLDDVEHAKPDPEPVLKALELLGAKPEEALMVGDNHHDILAGKNAGTKTA 179
Query: 81 AV 82
V
Sbjct: 180 GV 181
>gnl|CDD|129317 TIGR00213, GmhB_yaeD, D,D-heptose 1,7-bisphosphate phosphatase.
This family of proteins formerly designated yaeD
resembles the histidinol phosphatase domain of the
bifunctional protein HisB. The member from E. coli has
been characterized as D,D-heptose 1,7-bisphosphate
phosphatase, GmhB, involved in inner core LPS assembly
(PMID:11751812) [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 176
Score = 45.7 bits (108), Expect = 5e-06
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 39 KPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAA--GMEVVAVPSLPKQTHRYTAAD 96
KP P + L+A K L+++ + S ++ D + + AG AA V+ P AD
Sbjct: 106 KPKPGMLLQARKELHIDMAQSYMVGDKLEDMQAGVAAKVKTNVLVRTGKPITPEAENIAD 165
Query: 97 EVINSLLDL 105
V+NSL DL
Sbjct: 166 WVLNSLADL 174
>gnl|CDD|162787 TIGR02253, CTE7, HAD superfamily (subfamily IA) hydrolase,
TIGR02253. This family of sequences from archaea and
metazoans includes the human uncharacterized protein
CTE7. Pyrococcus species appear to have three different
forms of this enzyme, so it is unclear whether all
members of this family have the same function. This
family is a member of the haloacid dehalogenase (HAD)
superfamily of hydrolases which are characterized by
three conserved sequence motifs. By virtue of an alpha
helical domain in-between the first and second conserved
motif, this family is a member of subfamily IA
(TIGR01549).
Length = 221
Score = 45.9 bits (109), Expect = 5e-06
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 4/84 (4%)
Query: 26 FSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVI-GVVAGKAAGMEVVAVPS 84
F ++ S+E KP P IF A KRL ++P ++++ D + + K GM+ V +
Sbjct: 137 FDAVITSEEEGVEKPHPKIFYAALKRLGVKPEEAVMVGDRLDKDIKGAKNLGMKTVWINQ 196
Query: 85 LPKQTHR---YTAADEVINSLLDL 105
Y D I+SL +L
Sbjct: 197 GKSSKMEDDVYPYPDYEISSLREL 220
>gnl|CDD|233512 TIGR01656, Histidinol-ppas, histidinol-phosphate phosphatase family
domain. This domain is found in authentic
histidinol-phosphate phosphatases which are sometimes
found as stand-alone entities and sometimes as fusions
with imidazoleglycerol-phosphate dehydratase
(TIGR01261). Additionally, a family of proteins
including YaeD from E. coli (TIGR00213) and various
other proteins are closely related but may not have the
same substrate specificity. This domain is a member of
the haloacid-dehalogenase (HAD) superfamily of
aspartate-nucleophile hydrolases. This superfamily is
distinguished by the presence of three motifs: an
N-terminal motif containing the nucleophilic aspartate,
a central motif containing an conserved serine or
threonine, and a C-terminal motif containing a conserved
lysine (or arginine) and conserved aspartates. More
specifically, the domian modelled here is a member of
subfamily III of the HAD-superfamily by virtue of
lacking a "capping" domain in either of the two common
positions, between motifs 1 and 2, or between motifs 2
and 3.
Length = 147
Score = 42.4 bits (100), Expect = 3e-05
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 39 KPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVVAVPS 84
KP P + LEA KRL ++ S SLV+ D + + A + AG+ V +
Sbjct: 101 KPKPGLILEALKRLGVDASRSLVVGDRLRDLQAARNAGLAAVLLVD 146
>gnl|CDD|233463 TIGR01549, HAD-SF-IA-v1, haloacid dehalogenase superfamily,
subfamily IA, variant 1 with third motif having Dx(3-4)D
or Dx(3-4)E. This model represents part of one
structural subfamily of the Haloacid Dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases. The
superfamily is defined by the presence of three short
catalytic motifs. The subfamilies are defined based on
the location and the observed or predicted fold of a
so-called "capping domain", or the absence of such a
domain. Subfamily I consists of sequences in which the
capping domain is found in between the first and second
catalytic motifs. Subfamily II consists of sequences in
which the capping domain is found between the second and
third motifs. Subfamily III sequences have no capping
domain in either of these positions.The Subfamily IA and
IB capping domains are predicted by PSI-PRED to consist
of an alpha helical bundle. Subfamily I encompasses such
a wide region of sequence space (the sequences are
highly divergent) that modelling it with a single
representation is impossible, resulting in an overly
broad description which allows in many unrelated
sequences. Subfamily IA and IB are separated based on an
aparrent phylogenetic bifurcation. Subfamily IA is still
too broad to model, but cannot be further subdivided
into large chunks based on phylogenetic trees. Of the
three motifs defining the HAD superfamily, the third has
three variant forms : (1) hhhhsDxxx(x)(D/E), (2)
hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to
a small amino acid and _h_ to a hydrophobic one. All
three of these variants are found in subfamily IA.
Individual models were made based on seeds exhibiting
only one of the variants each. Variant 1 (this model) is
found in the enzymes phosphoglycolate phosphatase
(TIGR01449) and enolase-phosphatase. These three variant
models (see also TIGR01493 and TIGR01509) were created
withthe knowledge that there will be overlap among them
- this is by design and serves the purpose of
eliminating the overlap with models of more distantly
relatedHAD subfamilies caused by an overly broad single
model [Unknown function, Enzymes of unknown
specificity].
Length = 162
Score = 42.0 bits (99), Expect = 6e-05
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSL 60
+ + SN + + HG + F +I+GSDE+ + KP P+IFL A + L + P L
Sbjct: 90 LGIISNGSLRAQKLLLRK-HGLGDYFELILGSDEIGS-KPEPEIFLAALESLGVPP-EVL 146
Query: 61 VIEDSVIGVVAGKAAG 76
+ D++ + + AG
Sbjct: 147 HVGDNLSDIKGARNAG 162
>gnl|CDD|223319 COG0241, HisB, Histidinol phosphatase and related phosphatases
[Amino acid transport and metabolism].
Length = 181
Score = 41.5 bits (98), Expect = 1e-04
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 39 KPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGME-VVAVPSLPKQTHRYTAADE 97
KP P + L A K N++ S S V+ D + + A + AG++ V+ + + T A
Sbjct: 105 KPKPGMLLSALKEYNIDLSRSYVVGDRLTDLQAAENAGIKGVLVLTGIGVTTDGAGRAKW 164
Query: 98 VINSLLDL 105
V +SL +
Sbjct: 165 VFDSLAEF 172
>gnl|CDD|182552 PRK10563, PRK10563, 6-phosphogluconate phosphatase; Provisional.
Length = 221
Score = 41.6 bits (98), Expect = 2e-04
Identities = 16/41 (39%), Positives = 26/41 (63%)
Query: 39 KPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEV 79
KP P + AA+ +N+ + ++++DS G +G AAGMEV
Sbjct: 142 KPDPALMFHAAEAMNVNVENCILVDDSSAGAQSGIAAGMEV 182
>gnl|CDD|171912 PRK13223, PRK13223, phosphoglycolate phosphatase; Provisional.
Length = 272
Score = 41.0 bits (96), Expect = 3e-04
Identities = 31/86 (36%), Positives = 41/86 (47%), Gaps = 6/86 (6%)
Query: 26 FSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVVAVPSL 85
F I+G D + KP P L K + PS SL + DS V+A KAAG++ VA+
Sbjct: 144 FRWIIGGDTLPQKKPDPAALLFVMKMAGVPPSQSLFVGDSRSDVLAAKAAGVQCVALSY- 202
Query: 86 PKQTHRYTAADE----VINSLLDLRP 107
H A+E VI+ L L P
Sbjct: 203 -GYNHGRPIAEESPALVIDDLRALLP 227
>gnl|CDD|162372 TIGR01458, HAD-SF-IIA-hyp3, HAD-superfamily subfamily IIA
hydrolase, TIGR01458. This hypothetical equivalog is a
member of the IIA subfamily (TIGR01460) of the haloacid
dehalogenase superfamily of aspartate-nucleophile
hydrolases. One sequence (GP|10716807) has been
annotated as a "phospholysine phosphohistidine inorganic
pyrophosphatase," probably in reference to studies on
similarly described (but unsequenced) enzymes from
bovine and rat tissues. However, the supporting
information for this annotation has never been published
[Unknown function, Enzymes of unknown specificity].
Length = 257
Score = 40.6 bits (95), Expect = 3e-04
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 38 GKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAG-KAAGMEVVAVPSLPKQTHRYTAAD 96
GKPS FLEA + EP +++I D V G + GM + V +T +Y +D
Sbjct: 178 GKPSKTFFLEALRATGCEPEEAVMIGDDCRDDVGGAQDCGMRGIQV-----RTGKYRPSD 232
Query: 97 E 97
E
Sbjct: 233 E 233
>gnl|CDD|223720 COG0647, NagD, Predicted sugar phosphatases of the HAD superfamily
[Carbohydrate transport and metabolism].
Length = 269
Score = 39.9 bits (94), Expect = 6e-04
Identities = 16/46 (34%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 38 GKPSPDIFLEAAKRLNMEPSSSLVIEDSVIG-VVAGKAAGMEVVAV 82
GKPSP I+ A ++L ++ S L++ D + ++ KAAG++ + V
Sbjct: 189 GKPSPAIYEAALEKLGLDRSEVLMVGDRLDTDILGAKAAGLDTLLV 234
>gnl|CDD|188140 TIGR01422, phosphonatase, phosphonoacetaldehyde hydrolase. This
enzyme catalyzes the cleavage of the carbon phosphorous
bond of a phosphonate. The mechanism depends on the
substrate having a carbonyl one carbon away from the
cleavage position. This enzyme is a member of the
Haloacid Dehalogenase (HAD) superfamily of
aspartate-nucleophile hydrolases (pfam00702), and
contains a modified version of the conserved catalytic
motifs of that superfamily: the first motif is usually
DxDx(T/V), here it is DxAxT, and in the third motif the
normal conserved lysine is instead an arginine.
Additionally, the enzyme contains a unique conserved
catalytic lysine (B. cereus pos. 53) which is involved
in the binding and activation of the substrate through
the formation of a Schiff base. The substrate of this
enzyme is the product of 2-aminoethylphosphonate (AEP)
transaminase, phosphonoacetaldehyde. This degradation
pathway for AEP may be related to its toxic properties
which are utilized by microorganisms as a chemical
warfare agent [Central intermediary metabolism, Other].
Length = 253
Score = 40.0 bits (94), Expect = 6e-04
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 30 VGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLV-IEDSVIGVVAGKAAGMEVVAV 82
V +D+V G+P+P + L+ A L + +++V + D+V + G+ AGM V V
Sbjct: 147 VTADDVPAGRPAPWMALKNATELGVYDPAAVVKVGDTVPDIEEGRNAGMWTVGV 200
>gnl|CDD|236354 PRK08942, PRK08942, D,D-heptose 1,7-bisphosphate phosphatase;
Validated.
Length = 181
Score = 39.4 bits (93), Expect = 7e-04
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 39 KPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAG 76
KP P + L A+RLN++ + S ++ DS+ + A AAG
Sbjct: 103 KPKPGMLLSIAERLNIDLAGSPMVGDSLRDLQAAAAAG 140
>gnl|CDD|200170 TIGR02252, DREG-2, REG-2-like, HAD superfamily (subfamily IA)
hydrolase. This family of proteins includes
uncharacterized sequences from eukaryotes, cyanobacteria
and Leptospira as well as the DREG-2 protein from
Drosophila melanogaster which has been identified as a
rhythmically (diurnally) regulated gene. This family is
a member of the Haloacid Dehalogenase (HAD) superfamily
of aspartate-nucleophile hydrolases. The superfamily is
defined by the presence of three short catalytic motifs.
The subfamilies are defined based on the location and
the observed or predicted fold of a so-called 'capping
domain', or the absence of such a domain. This family is
a member of subfamily 1A in which the cap domain
consists of a predicted alpha helical bundle found in
between the first and second catalytic motifs. A
distinctive feature of this family is a conserved tandem
pair of tryptophan residues in the cap domain. The most
divergent sequences included within the scope of this
model are from plants and have "FW" at this position
instead. Most likely, these sequences, like the vast
majority of HAD sequences, represent phosphatase
enzymes.
Length = 203
Score = 38.8 bits (91), Expect = 0.001
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 26 FSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVI-GVVAGKAAGM 77
F +V S EV KP P IF EA +R + P +L I DS+ +AAG
Sbjct: 147 FDFVVTSYEVGAEKPDPKIFQEALERAGISPEEALHIGDSLRNDYQGARAAGW 199
>gnl|CDD|233675 TIGR01993, Pyr-5-nucltdase, pyrimidine 5'-nucleotidase. This
family of proteins includes the SDT1/SSM1 gene from
yeast which has been shown to code for a pyrimidine
(UMP/CMP) 5'nucleotidase. The family spans plants, fungi
and a small number of bacteria. These enzymes are
members of the haloacid dehalogenase (HAD) superfamily
of hydrolases, specifically the IA subfamily (variant 3,
TIGR01509).
Length = 183
Score = 37.7 bits (88), Expect = 0.002
Identities = 16/44 (36%), Positives = 26/44 (59%)
Query: 39 KPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVVAV 82
KPSP + +A + ++P ++ +DS + AGKA GM+ V V
Sbjct: 140 KPSPQAYEKALREAGVDPERAIFFDDSARNIAAGKALGMKTVLV 183
>gnl|CDD|184075 PRK13478, PRK13478, phosphonoacetaldehyde hydrolase; Provisional.
Length = 267
Score = 38.3 bits (90), Expect = 0.002
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 28 VIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLV-IEDSVIGVVAGKAAGMEVVAV 82
+V +D+V G+P P + L+ A L + ++ V ++D+V G+ G AGM V V
Sbjct: 147 HVVTTDDVPAGRPYPWMALKNAIELGVYDVAACVKVDDTVPGIEEGLNAGMWTVGV 202
>gnl|CDD|182828 PRK10907, PRK10907, intramembrane serine protease GlpG;
Provisional.
Length = 276
Score = 36.1 bits (84), Expect = 0.013
Identities = 25/63 (39%), Positives = 33/63 (52%), Gaps = 10/63 (15%)
Query: 128 WYIGGPVVKGLGRGSK-VLGIPTANLSTEGYSDVLSEHPSGVYFGWAGLSTRGVYKMVMS 186
WY+GG V K LG G V+ + +A LS G+ + SG +FG GLS GV +M
Sbjct: 159 WYLGGAVEKRLGSGKLIVITLISALLS--GW---VQSKFSGPWFG--GLS--GVVYALMG 209
Query: 187 IGW 189
W
Sbjct: 210 YVW 212
>gnl|CDD|225090 COG2179, COG2179, Predicted hydrolase of the HAD superfamily
[General function prediction only].
Length = 175
Score = 32.7 bits (75), Expect = 0.098
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 36 RTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVI-GVVAGKAAGMEVVAVPSLP 86
R KP F A K +N+ P +++ D + V+ G AGM + V L
Sbjct: 90 RAKKPFGRAFRRALKEMNLPPEEVVMVGDQLFTDVLGGNRAGMRTILVEPLV 141
>gnl|CDD|234176 TIGR03351, PhnX-like, phosphonatase-like hydrolase. This clade of
sequences are the closest homologs to the PhnX enzyme,
phosphonoacetaldehyde (Pald) hydrolase (phosphonatase,
TIGR01422). This phosphonatase-like enzyme and PhnX
itself are members of the haloacid dehalogenase (HAD)
superfamily (pfam00702) having a a number of distinctive
features that set them apart from typical HAD enzymes.
The typical HAD N-terminal motif DxDx(T/V) here is DxAGT
and the usual conserved lysine prior to the C-terminal
motif is instead an arginine. Also distinctive of
phosphonatase, and particular to its bi-catalytic
mechanism is a conserved lysine in the variable "cap"
domain. This lysine forms a Schiff base with the
aldehyde of phosphonoacetaldehyde, providing, through
the resulting positive charge, a polarization of the C-P
bond necesary for cleavage as well as a route to the
initial product of cleavage, an ene-amine. The
conservation of these elements in this
phosphonatase-like enzyme suggests that the substrate is
also, like Pald, a 2-oxo-ethylphosphonate. Despite this,
the genomic context of members of this family are quite
distinct from PhnX, which is almost invariably
associated with the 2-aminoethylphosphonate transaminase
PhnW (TIGR02326), the source of the substrate Pald.
Members of this clade are never associated with PhnW,
but rather associate with families of FAD-dependent
oxidoreductases related to deaminating amino acid
oxidases (pfam01266) as well as zinc-dependent
dehydrogenases (pfam00107). Notably, family members from
Arthrobacter aurescens TC1 and Nocardia farcinica IFM
10152 are adjacent to the PhnCDE ABC cassette
phosphonates transporter (GenProp0236) typically found
in association with the phosphonates C-P lyase system
(GenProp0232). These observations suggest two
possibilities. First, the substrate for this enzyme
family is also Pald, the non-association with PhnW not
withstanding. Alternatively, the substrate is something
very closely related such as
hydroxyphosphonoacetaldehyde (Hpald). Hpald could come
from oxidative deamination of
1-hydroxy-2-aminoethylphosphonate (HAEP) by the
associated oxidase. HAEP would not be a substrate for
PhnW due to its high specificity for AEP. HAEP has been
shown to be a constituent of the sphingophosphonolipid
of Bacteriovorax stolpii, and presumably has other
natural sources. If Hpald is the substrate, the product
would be glycoaldehyde (hydroxyacetaldehyde), and the
associated alcohol dehydrogenase may serve to convert
this to glycol.
Length = 220
Score = 32.1 bits (73), Expect = 0.21
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 2 ALASNSHRATIESKISYQHGW--NESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSS 59
AL + R T E ++ + GW + +V +V G+P+PD+ L A + ++ S
Sbjct: 107 ALTTGFDRDTAE-RLLEKLGWTVGDDVDAVVCPSDVAAGRPAPDLILRAMELTGVQDVQS 165
Query: 60 -LVIEDSVIGVVAGKAAGMEVVA 81
V D+ + AG AG V
Sbjct: 166 VAVAGDTPNDLEAGINAGAGAVV 188
>gnl|CDD|233517 TIGR01662, HAD-SF-IIIA, HAD-superfamily hydrolase, subfamily IIIA.
This subfamily falls within the Haloacid Dehalogenase
(HAD) superfamily of aspartate-nucleophile hydrolases.
The Class III subfamilies are characterized by the lack
of any domains located between either between the first
and second conserved catalytic motifs (as in the Class I
subfamilies, TIGR01493, TIGR01509, TIGR01488 and
TIGR01494) or between the second and third conserved
catalytic motifs (as in the Class II subfamilies,
TIGR01460 and TIGR01484) of the superfamily domain. The
IIIA subfamily contains five major clades:
histidinol-phosphatase (TIGR01261) and
histidinol-phosphatase-related protein (TIGR00213) which
together form a subfamily (TIGR01656), DNA
3'-phosphatase (TIGR01663, TIGR01664), YqeG (TIGR01668)
and YrbI (TIGR01670). In the case of histidinol
phosphatase and PNK-3'-phosphatase, this model
represents a domain of a bifunctional system. In the
histidinol phosphatase HisB, a C-terminal domain is an
imidazoleglycerol-phosphate dehydratase which catalyzes
a related step in histidine biosynthesis. In
PNK-3'-phosphatase, N- and C-terminal domains constitute
the polynucleotide kinase and DNA-binding components of
the enzyme [Unknown function, Enzymes of unknown
specificity].
Length = 132
Score = 31.2 bits (71), Expect = 0.26
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 39 KPSPDIFLEAAKRLN-MEPSSSLVIEDSVI-GVVAGKAAGMEVVAVP 83
KP P +FLEA KR N ++P S+ + D + + A K AG+ + V
Sbjct: 85 KPKPGMFLEALKRFNEIDPEESVYVGDQDLTDLQAAKRAGLAFILVA 131
>gnl|CDD|130524 TIGR01457, HAD-SF-IIA-hyp2, HAD-superfamily subfamily IIA
hydrolase, TIGR01457. This hypothetical equivalog is a
member of the Class IIA subfamily of the haloacid
dehalogenase superfamily of aspartate-nucleophile
hydrolases. The sequences modelled by this equivalog are
all gram positive (low-GC) bacteria. Sequences found in
This model are annotated variously as related to NagD or
4-nitrophenyl phosphatase, and this hypothetical
equivalog, of all of those within the Class IIA
subfamily, is most closely related to the E. coli NagD
enzyme and the PGP_euk equivalog (TIGR01452). However,
there is presently no evidence that this hypothetical
equivalog has the same function of either those [Unknown
function, Enzymes of unknown specificity].
Length = 249
Score = 31.4 bits (71), Expect = 0.36
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 27 SVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDS-VIGVVAGKAAGMEVVAV 82
+V G V GKP I +A + L + +L++ D+ ++AG AG++ + V
Sbjct: 166 TVSTGVKPVFIGKPESIIMEQAMRVLGTDVEETLMVGDNYATDIMAGINAGIDTLLV 222
>gnl|CDD|233462 TIGR01548, HAD-SF-IA-hyp1, haloacid dehalogenase superfamily,
subfamily IA hydrolase, TIGR01548. This model
represents a small and phylogenetically curious clade of
sequences. Sequences are found from Halobacterium (an
archaeon), Nostoc and Synechococcus (cyanobacteria) and
Phytophthora (a stramenophile eukaryote). These appear
to be members of the haloacid dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases by
general homology and the conservation of all of the
recognized catalytic motifs. The variable domain is
found in between motifs 1 and 2, indicating membership
in subfamily I and phylogeny and prediction of the alpha
helical nature of the variable domain (by PSI-PRED)
indicate membership in subfamily IA. All but the
Halobacterium sequence currently found are annotated as
"Imidazoleglycerol-phosphate dehydratase", however, the
source of the annotation could not be traced and
significant homology could not be found between any of
these sequences and known IGPD's.
Length = 197
Score = 31.4 bits (71), Expect = 0.37
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 19 QHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAA 75
HG F V + ++ KP+P+ + AAK L +E + ++ D+V ++ G+ A
Sbjct: 142 THGLEILFPVQIWMEDC-PPKPNPEPLILAAKALGVEACHAAMVGDTVDDIITGRKA 197
>gnl|CDD|180686 PRK06769, PRK06769, hypothetical protein; Validated.
Length = 173
Score = 30.9 bits (70), Expect = 0.41
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 39 KPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVVAV 82
KPS + L+AA++ ++ + VI D +VA + V
Sbjct: 93 KPSTGMLLQAAEKHGLDLTQCAVIGDRWTDIVAAAKVNATTILV 136
>gnl|CDD|215296 PLN02540, PLN02540, methylenetetrahydrofolate reductase.
Length = 565
Score = 31.6 bits (72), Expect = 0.51
Identities = 25/105 (23%), Positives = 39/105 (37%), Gaps = 32/105 (30%)
Query: 88 QTHRYTAADEVINSLLDLRPEKWGLPP---------FQDWIEGTLPSEPWYIGGPVVKGL 138
Q R A D+ L+ E WG+P F + G L S PW + GL
Sbjct: 352 QFMRPRARDK------KLQAE-WGVPLKSVEDVYEVFAKYCLGKLKSSPW----SELDGL 400
Query: 139 GRGSKVLGIPTANLSTEGY---------SDVLSEHPSGVYFGWAG 174
+K++ ++ +G+ + S+ PS GW G
Sbjct: 401 QPETKIINEQLVKINRKGFLTINSQPAVNGEKSDSPS---VGWGG 442
>gnl|CDD|233420 TIGR01452, PGP_euk, phosphoglycolate/pyridoxal phosphate
phosphatase family. PGP is an essential enzyme in the
glycolate salvage pathway in higher organisms
(photorespiration in plants). Phosphoglycolate results
from the oxidase activity of RubisCO in the Calvin cycle
when concentrations of carbon dioxide are low relative
to oxygen. In mammals, PGP is found in many tissues,
notably in red blood cells where P-glycolate is and
important activator of the hydrolysis of
2,3-bisphosphoglycerate, a major modifier of the oxygen
affinity of hemoglobin. Pyridoxal phosphate (PLP,
Vitamin B6) phosphatase is involved in the degradation
of PLP in mammals and is widely distributed in human
tissues including erythrocyes. The enzymes described
here are members of the Haloacid dehalogenase
superfamily of hydrolase enzymes (pfam00702). Unlike the
bacterial PGP equivalog (TIGR01449), which is a member
of class (subfamily) I, these enzymes are members of
class (subfamily) II. These two families have almost
certainly arisen from convergent evolution (although
these two ancestors may themselves have diverged from a
more distant HAD superfamily progenitor). The primary
seed sequence for this model comes from Chlamydomonas
reinhardtii, a photosynthetic alga. The enzyme has been
purified and characterized and these data are fully
consistent with the assignment of function as a PGPase
involved in photorespiration. The second seed, from Homo
sapiens chromosome 22 has been characterized as a
pyridoxal phosphatase. Biochemical characterization of
partially purified PGP's from various tissues including
red blood cells have been performed while one gene for
PGP has been localized to chromosome 16p13.3. The
sequence used here maps to chromosome 22. There is
indeed a related gene on chromosome 16 (and it is
expressed, since EST's are found) which shows 46%
identity and 59% positives by BLAST2 (E=1e-66). The
chromosome 16 gene is not in evidence in nraa but
translated from the genomic sequence would score 372.4
(E=7.9e-113) versus This model, well above trusted. The
third seed, from C. elegans, is only supported by
sequence similarity. This model is limited to eukaryotic
species including S. pombe and S. cerevisiae, although
several archaea score between the trusted and noise
cutoffs. This model is closely related to a family of
bacterial sequences including the E. coli NagD and B.
subtilus AraL genes which are characterized by the
ability to hydrolyze para-nitrophenylphosphate (pNPPases
or NPPases). The chlamydomonas PGPase d.
Length = 279
Score = 30.6 bits (69), Expect = 0.68
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 31 GSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSV-IGVVAGKAAGMEVVAVPSLPKQT 89
G + GKPSP +F + +++P+ +L++ D + ++ G GM V V S
Sbjct: 194 GRQPLVVGKPSPYMFECITENFSIDPARTLMVGDRLETDILFGHRCGMTTVLVLS---GV 250
Query: 90 HRYTAADEVINS 101
R A E + +
Sbjct: 251 SRLEEAQEYLAA 262
>gnl|CDD|233422 TIGR01460, HAD-SF-IIA, Haloacid Dehalogenase Superfamily Class
(subfamily) IIA. This model represents one structural
subclass of the Haloacid Dehalogenase (HAD) superfamily
of aspartate-nucleophile hydrolases. The superfamily is
defined by the presence of three short catalytic motifs.
The classes are defined based on the location and the
observed or predicted fold of a so-called "capping
domain", or the absence of such a domain. Class I
consists of sequences in which the capping domain is
found in between the first and second catalytic motifs.
Class II consists of sequences in which the capping
domain is found between the second and third motifs.
Class III sequences have no capping domain in iether of
these positions. The Class IIA capping domain is
predicted by PSI-PRED to consist of a mixed alpha-beta
fold with the basic pattern:
Helix-Helix-Helix-Sheet-Helix-Loop-Sheet-Helix-Sheet-
Helix. Presently, this subfamily encompasses a single
equivalog model (TIGR01452) for the eukaryotic
phosphoglycolate phosphatase, as well as four
hypothetical equivalogs covering closely related
sequences (TIGR01456 and TIGR01458 in eukaryotes,
TIGR01457 in gram positive bacteria and TIGR01459 in
gram negative bacteria). The Escherishia coli NagD gene
and the Bacillus subtilus AraL gene are members of this
subfamily but are not members of the any of the
presently defined equivalogs within it. NagD is part of
the NAG operon responsible for N-acetylglucosamine
metabolism. The function of this gene is unknown. Genes
from several organisms have been annotated as NagD, or
NagD-like. However, without data on the presence of
other members of this pathway, (such as in the case of
Yersinia pestis) these assignments should not be given
great weight. The AraL gene is similar: it is part of
the L-arabinose operon, but the function is unknown. A
gene from Halobacterium has been annotated as AraL, but
no other Ara operon genes have been annotated. Many of
the genes in this subfamily have been annotated as
"pNPPase" "4-nitrophenyl phosphatase" or "NPPase". These
all refer to the same activity versus a common lab test
compound used to determine phosphatase activity. There
is no evidence that this activity is physiologically
relevant [Unknown function, Enzymes of unknown
specificity].
Length = 236
Score = 30.4 bits (69), Expect = 0.72
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 31 GSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVI--EDSVIGVVAGKAAGMEVVAV 82
G + GKPSP I+ A L P V+ ++ ++ K AG + + V
Sbjct: 180 GREPTVVGKPSPAIYRAALNLLQARPERRDVMVGDNLRTDILGAKNAGFDTLLV 233
>gnl|CDD|233800 TIGR02247, HAD-1A3-hyp, epoxide hydrolase N-terminal domain-like
phosphatase. This model represents a small clade of
sequences including C. elegans and mammalian sequences
as well as a small number of bacteria. In eukaryotes,
this domain exists as an N-terminal fusion to the
soluble epoxide hydrolase enzyme and has recently been
shown to be an active phosphatase, although the nature
of the biological substrate is unclear. These appear to
be members of the haloacid dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases by
general homology and the conservation of all of the
recognized catalytic motifs (although the first motif is
unusual in the replacement of the more common aspartate
with glycine...). The variable domain is found in
between motifs 1 and 2, indicating membership in
subfamily I and phylogeny and prediction of the alpha
helical nature of the variable domain (by PSI-PRED)
indicate membership in subfamily IA.
Length = 211
Score = 30.2 bits (68), Expect = 0.84
Identities = 15/65 (23%), Positives = 26/65 (40%)
Query: 26 FSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVVAVPSL 85
F +V S KP P I+ +RL + P + ++D + A G+ + V
Sbjct: 139 FDAVVESCLEGLRKPDPRIYQLMLERLGVAPEECVFLDDLGSNLKPAAALGITTIKVSDE 198
Query: 86 PKQTH 90
+ H
Sbjct: 199 EQAIH 203
>gnl|CDD|233519 TIGR01668, YqeG_hyp_ppase, HAD superfamily (subfamily IIIA)
phosphatase, TIGR01668. This family of hypothetical
proteins is a member of the IIIA subfamily of the
haloacid dehalogenase (HAD) superfamily of hydrolases.
All characterized members of this subfamily (TIGR01662)
and most characterized members of the HAD superfamily
are phosphatases. HAD superfamily phosphatases contain
active site residues in several conserved catalytic
motifs, all of which are found conserved here. This
family consists of sequences from fungi, plants,
cyanobacteria, gram-positive bacteria and Deinococcus.
There is presently no characterization of any sequence
in this family.
Length = 170
Score = 29.7 bits (67), Expect = 1.2
Identities = 18/97 (18%), Positives = 29/97 (29%), Gaps = 20/97 (20%)
Query: 39 KPSPDIFLEAAKRLNMEPSSSLVIEDSVI-GVVAGKAAGMEVVAVPSLPKQTHRYTAADE 97
KP F A + + V+ D + V+ G G + V L
Sbjct: 91 KPPGCAFRRAHPEMGLTSEQVAVVGDRLFTDVMGGNRNGSYTILVEPLV----------- 139
Query: 98 VINSLLDLRPEKWGLPPFQDWIEGTLPSEPWYIGGPV 134
P++W + +E T+ GGP
Sbjct: 140 --------HPDQWFIKRIWRRVERTVLKFLVSRGGPA 168
>gnl|CDD|130495 TIGR01428, HAD_type_II, 2-haloalkanoic acid dehalogenase, type II.
Catalyzes the hydrolytic dehalogenation of small
L-2-haloalkanoic acids to yield the corresponding
D-2-hydroxyalkanoic acids. Belongs to the Haloacid
Dehalogenase (HAD) superfamily of aspartate-nucleophile
hydrolases (pfam00702), class (subfamily) I. Note that
the Type I HAD enzymes have not yet been fully
characterized, but clearly utilize a substantially
different catalytic mechanism and are thus unlikely to
be related.
Length = 198
Score = 29.6 bits (67), Expect = 1.2
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 5 SNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIED 64
SN A ++S + + G ++ F ++ +D VR KP+P ++ A + L + P L +
Sbjct: 115 SNGSPAMLKSLVKHA-GLDDPFDAVLSADAVRAYKPAPQVYQLALEALGVPPDEVLFVAS 173
Query: 65 SVIGVVAGKAAGMEVVAV 82
+ + K G + V
Sbjct: 174 NPWDLGGAKKFGFKTAWV 191
>gnl|CDD|219943 pfam08631, SPO22, Meiosis protein SPO22/ZIP4 like. SPO22/ZIP4 in
yeast is a meiosis specific protein involved in
sporulation. It has been shown to regulate crossover
distribution by promoting synaptonemal complex
formation.
Length = 280
Score = 29.7 bits (67), Expect = 1.4
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 200 IEPWLLHEFDEDFYDEELHLVIVGYIRPEANFPSLETLIAKIHE-DRKVAERALDLPLYS 258
+E E+ Y++ L +I E+NF + I K+ + A + LD L++
Sbjct: 128 LEILKKRPGPEEEYEDVLMRMIKSVDVTESNFELAISHINKLSDKAPASAAKCLDYLLFN 187
Query: 259 K 259
+
Sbjct: 188 R 188
>gnl|CDD|182466 PRK10444, PRK10444, UMP phosphatase; Provisional.
Length = 248
Score = 29.4 bits (66), Expect = 1.6
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 29 IVGSDEVRTGKPSPDIFLEAAKRLNMEPSSSLVIEDSV-IGVVAGKAAGMEVVAVPS 84
I G GKPSP I A ++ ++++ D++ ++AG AG+E + V S
Sbjct: 164 ISGRKPFYVGKPSPWIIRAALNKMQAHSEETVIVGDNLRTDILAGFQAGLETILVLS 220
>gnl|CDD|233980 TIGR02712, urea_carbox, urea carboxylase. Members of this family are
ATP-dependent urea carboxylase, including characterized
members from Oleomonas sagaranensis (alpha class
Proteobacterium) and yeasts such as Saccharomyces
cerevisiae. The allophanate hydrolase domain of the yeast
enzyme is not included in this model and is represented
by an adjacent gene in Oleomonas sagaranensis. The fusion
of urea carboxylase and allophanate hydrolase is
designated urea amidolyase. The enzyme from Oleomonas
sagaranensis was shown to be highly active on acetamide
and formamide as well as urea [Central intermediary
metabolism, Nitrogen metabolism].
Length = 1201
Score = 28.8 bits (65), Expect = 3.5
Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 189 WNPYFDNAEKTIEPWLLHEFDE-DFY---DEEL 217
WN Y PWLL FD+ FY +EEL
Sbjct: 1019 WNRYRLGGAFQDGPWLLRFFDQIRFYPVSEEEL 1051
>gnl|CDD|224221 COG1302, COG1302, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 131
Score = 27.6 bits (62), Expect = 4.1
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 54 MEPSSSLVIEDSVIGVVAGKAAGMEVVAVPSLP 86
E + I D VI V+AG AA EV V +
Sbjct: 6 NEELGKIEISDEVIAVIAGIAA-EEVEGVVGMA 37
>gnl|CDD|162788 TIGR02254, YjjG/YfnB, HAD superfamily (subfamily IA) hydrolase,
TIGR02254. This family consists of uncharacterized
proteobacterial and gram positive bacterial sequences
including YjjG from E. coli and YfnB from B. subtilis.
This family is a member of the haloacid dehalogenase
(HAD) superfamily of hydrolases which are characterized
by three conserved sequence motifs. By virtue of an
alpha helical domain in-between the first and second
conserved motif, this family is a member of subfamily IA
(TIGR01549). Most likely, these enzymes are
phosphatases.
Length = 224
Score = 28.2 bits (63), Expect = 4.2
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 1 MALASNSHRATIESKISYQHGWNESFSVIVGSDEVRTGKPSPDIFLEAAKRL-NMEPSSS 59
+ + +N R T ++ + G F I S++ KP +IF A +R+
Sbjct: 115 LYIVTNGVRETQYKRLR-KSGLFPFFDDIFVSEDAGIQKPDKEIFNYALERMPKFSKEEV 173
Query: 60 LVIEDSVIG-VVAGKAAGMEVV 80
L+I DS+ + G+ AG++
Sbjct: 174 LMIGDSLTADIKGGQNAGLDTC 195
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 28.3 bits (63), Expect = 5.1
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 110 WGLPPFQDWIEGTLPSEPWYIGGPVVKGLGRGSKVLGIPTANLSTEG 156
+ ++I+ P GGP+V G +V+GI TA ++ G
Sbjct: 176 GSAGGYVNFIQTDAAINPGNSGGPLVNIDG---EVVGINTAIIAPSG 219
>gnl|CDD|236761 PRK10795, PRK10795, penicillin-binding protein 2; Provisional.
Length = 634
Score = 28.2 bits (63), Expect = 5.5
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 103 LDLRPEKWGLPPFQDWIEGTLPSEPWYIGGPVVKGLGRG 141
+DL E+ G P ++W + +PWY G + G+G+G
Sbjct: 420 IDLAEERSGNMPTREWKQKRF-KKPWYQGDTIPVGIGQG 457
>gnl|CDD|132589 TIGR03550, F420_cofG, 7,8-didemethyl-8-hydroxy-5-deazariboflavin
synthase, CofG subunit. This model represents either a
subunit or a domain, depending on whether or not the
genes are fused, of a bifunctional protein that
completes the synthesis of
7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is
the chromophore of coenzyme F(420), involved in
methanogenesis in methanogenic archaea but found in
certain other lineages as well. The chromophore also
occurs as a cofactor in DNA photolyases in Cyanobacteria
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 322
Score = 28.0 bits (63), Expect = 5.6
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 224 YIRPEANFPSLETLIAKIHEDRKV--AERALDLPLYSKYRDDPYLK 267
++ PEA +P ++ L A+ E+ ER LP+Y +Y + +L
Sbjct: 273 HVNPEAPWPEIDEL-ARATEEAGFTLKER---LPVYPEYVREGWLS 314
>gnl|CDD|232841 TIGR00131, gal_kin, galactokinase. Galactokinase is a member of
the GHMP kinases (Galactokinase, Homoserine kinase,
Mevalonate kinase, Phosphomevalonate kinase) and shares
with them an amino-terminal domain probably related to
ATP binding.The galactokinases found by This model are
divided into two sets. Prokaryotic forms are generally
shorter. The eukaryotic forms are longer because of
additional central regions and in some cases are known
to be bifunctional, with regulatory activities that are
independent of galactokinase activity [Energy
metabolism, Sugars].
Length = 386
Score = 27.9 bits (62), Expect = 5.8
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 244 DRKVAERALDLPLYSKYRDD 263
D K AER+LDLPL D
Sbjct: 69 DNKFAERSLDLPLDGSEVSD 88
>gnl|CDD|218986 pfam06317, Arena_RNA_pol, Arenavirus RNA polymerase. This family
consists of several Arenavirus RNA polymerase proteins
(EC:2.7.7.48).
Length = 2206
Score = 28.0 bits (63), Expect = 6.8
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 246 KVAERALDLPLYSKYRDDPYLKITSS 271
+++R L YS Y DP+L +
Sbjct: 1432 AISKRTNSLIRYSGYPIDPFLLVEEQ 1457
>gnl|CDD|217724 pfam03780, Asp23, Asp23 family. The alkaline shock protein Asp23
was identified as an alkaline shock protein that was
expressed in a sigmaB-dependent manner in
Staphylococcus aureus.
Length = 108
Score = 26.3 bits (59), Expect = 7.2
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 59 SLVIEDSVIGVVAGKAAGMEV 79
+ I D VI +AG AA EV
Sbjct: 4 EITISDEVIAKIAGIAA-REV 23
>gnl|CDD|180485 PRK06245, cofG, FO synthase subunit 1; Reviewed.
Length = 336
Score = 27.6 bits (62), Expect = 7.7
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 224 YIRPEANFPSLETLIAKIHEDRKVA--ERALDLPLYSKYRDDPYL 266
Y+ PE +P +E L +I E+ ER LP+Y KY + +L
Sbjct: 277 YVNPEYPWPDIEEL-REILEEAGWPLKER---LPVYPKYIKEGWL 317
>gnl|CDD|179716 PRK04025, PRK04025, S-adenosylmethionine decarboxylase proenzyme;
Validated.
Length = 139
Score = 26.7 bits (59), Expect = 7.8
Identities = 18/39 (46%), Positives = 24/39 (61%), Gaps = 5/39 (12%)
Query: 43 DIFLEAAKRLNMEPSSSLVIEDSVIGVVAGKAAGMEVVA 81
+IFLEAAKR NME +S + S GV +G+ +VA
Sbjct: 28 EIFLEAAKRGNMEVKASYFFKFSPTGV-----SGVVIVA 61
>gnl|CDD|218143 pfam04551, GcpE, GcpE protein. In a variety of organisms,
including plants and several eubacteria, isoprenoids are
synthesised by the mevalonate-independent
2-C-methyl-D-erythritol 4-phosphate (MEP) pathway.
Although different enzymes of this pathway have been
described, the terminal biosynthetic steps of the MEP
pathway have not been fully elucidated. GcpE gene of
Escherichia coli is involved in this pathway.
Length = 345
Score = 27.5 bits (62), Expect = 9.1
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 222 VGYIRPEANFPSLETLIAKIHEDRKVAERALDLPLYSKYRDDP 264
+ I+ ++ P L+A IH D ++A A++ + K R +P
Sbjct: 61 LKEIKKQSPIP----LVADIHFDYRLALEAIEAGV-DKIRINP 98
>gnl|CDD|225193 COG2311, COG2311, Predicted membrane protein [Function unknown].
Length = 394
Score = 27.3 bits (61), Expect = 9.5
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 140 RGSKVLGIPTANLSTEGYSDVLSEHPSGVYFGWAGL 175
RG +LGI N+S GY +P + L
Sbjct: 20 RGFALLGILLVNISAFGYPGAAYLNPW--SGWLSPL 53
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
0.315 0.135 0.408
Gapped
Lambda K H
0.267 0.0872 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,482,116
Number of extensions: 1419955
Number of successful extensions: 1071
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1050
Number of HSP's successfully gapped: 77
Length of query: 274
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 179
Effective length of database: 6,723,972
Effective search space: 1203590988
Effective search space used: 1203590988
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: 42 (22.0 bits)
S2: 58 (25.9 bits)