RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4974
(345 letters)
>gnl|CDD|223669 COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta
hydrolase superfamily) [General function prediction
only].
Length = 282
Score = 73.9 bits (180), Expect = 5e-15
Identities = 46/296 (15%), Positives = 80/296 (27%), Gaps = 52/296 (17%)
Query: 76 FFSIKGCDIRFIKYGSGAQVLFFTYGVLGEIRNSFKKQLTAFDPKL--FTSIFWDPPGNV 133
+ G + + + G G L +G G ++ + I D G
Sbjct: 4 LLAADGVRLAYREAGGGGPPLVLLHGFPGSSSV-WRPVFKVLPALAARYRVIAPDLRG-- 60
Query: 134 VLYLLGKTCSGYGQSLPKGRSFVPFQYIEEDVDIAYELLKLLGVCKVSLFGWCDGGHLSF 193
GRS + D LL LG+ KV L G GG ++
Sbjct: 61 -----------------HGRSDPAGYSLSAYADDLAALLDALGLEKVVLVGHSMGGAVAL 103
Query: 194 VFSMKYPHMVHKLVI---------WGTKSFLTIDNVRVFEGMRRLSNWSPMARSEVLKAY 244
++++P V LV+ + L A + +L A
Sbjct: 104 ALALRHPDRVRGLVLIGPAPPPGLLEAALRQPAGAAPLAALADLLLGLDAAAFAALLAAL 163
Query: 245 DNDVNYITGIFNQYVDMVNL--------------------IFKSYGRNVYQELLPYVDVP 284
+ + + + L + VP
Sbjct: 164 GLLAALAAAARAGLAEALRAPLLGAAAAAFARAARADLAAALLALLDRDLRAALARITVP 223
Query: 285 VLVFHSADDVMVSTQQVQSLLNQLKF-CQYYQFSSGGHSCHIKHGQVFNEISRNFI 339
L+ H DD +V + + L L + GH H++ + F F+
Sbjct: 224 TLIIHGEDDPVVPAELARRLAAALPNDARLVVIPGAGHFPHLEAPEAFAAALLAFL 279
>gnl|CDD|221720 pfam12697, Abhydrolase_6, Alpha/beta hydrolase family. This family
contains alpha/beta hydrolase enzymes of diverse
specificity.
Length = 187
Score = 66.3 bits (162), Expect = 6e-13
Identities = 40/191 (20%), Positives = 61/191 (31%), Gaps = 37/191 (19%)
Query: 144 GYGQSLPKGRSFVPFQYIEEDVDIAYELLKLLGVCKVSLFGWCDGGHLSFVFSMKYPHMV 203
G+G S +E+D LL LG+ V L G GG ++ + + P V
Sbjct: 34 GHGDS---DGPPRTPYSLEDDAADLAALLDALGLGPVVLVGHSLGGAVALAAAARRPERV 90
Query: 204 HKLVIWGTKSFLTIDNVRVFEGMRRLSNWSPMARSEVLKAYDNDVNYITGIFNQYVDMVN 263
LV+ + L A +L+A
Sbjct: 91 AGLVLISP----------PLRDLEELLAADAAALLALLRAA------------------- 121
Query: 264 LIFKSYGRNVYQELLPYVDVPVLVFHSADDVMVSTQQVQSLLNQLKFCQYYQFSSGGHSC 323
+E L + VPVLV H DD +V + + L L + GH
Sbjct: 122 -----LLDADLREALARLTVPVLVIHGEDDPLVPPEAARRLAEALPGAELVVLPGAGHLP 176
Query: 324 HIKHGQVFNEI 334
H++H + E
Sbjct: 177 HLEHPEEVAEA 187
>gnl|CDD|201306 pfam00561, Abhydrolase_1, alpha/beta hydrolase fold. This
catalytic domain is found in a very wide range of
enzymes.
Length = 226
Score = 39.8 bits (93), Expect = 9e-04
Identities = 39/216 (18%), Positives = 65/216 (30%), Gaps = 27/216 (12%)
Query: 144 GYGQSLPKGRSFVPFQYIEEDVDIAYELLKLLGVCKVSLFGWCDGGHLSFVFSMKYPHMV 203
G+G+S + F + ++ + LL LG+ KV+L G GG ++ ++ KYP V
Sbjct: 10 GFGRS-SPPKDFADY-RFDDLAEDLEALLDALGLDKVNLVGHSMGGLIALAYAAKYPDRV 67
Query: 204 HKLVIWGTKSFLTIDNVRVFEGMRRLSNWSPMARSEVLKAYDNDVNYITGIFNQYVDMVN 263
LV+ GT + + G I V+
Sbjct: 68 KALVLVGTVHPAGLSSPLTPRGNLLGLLLDNFFNRLYDSVEALLGRAIKQFQALGRPFVS 127
Query: 264 LIFKSYGRNVYQ-------------------------ELLPYVDVPVLVFHSADDVMVST 298
K + + L +DVP L+ DD +V
Sbjct: 128 DFLKQFELSSLIRFGETLALDGLLGYALGYDLVWDRSAALKDIDVPTLIIWGDDDPLVPP 187
Query: 299 QQVQSLLNQLKFCQYYQFSSGGHSCHIKHGQVFNEI 334
+ L Q GH ++ E+
Sbjct: 188 DASEKLAALFPNAQLVVIDDAGHLAQLEKPDEVAEL 223
>gnl|CDD|211851 TIGR03611, RutD, pyrimidine utilization protein D. This protein is
observed in operons extremely similar to that
characterized in E. coli K-12 responsible for the import
and catabolism of pyrimidines, primarily uracil. This
protein is a member of the hydrolase, alpha/beta fold
family defined by pfam00067.
Length = 248
Score = 38.2 bits (89), Expect = 0.003
Identities = 14/50 (28%), Positives = 22/50 (44%)
Query: 284 PVLVFHSADDVMVSTQQVQSLLNQLKFCQYYQFSSGGHSCHIKHGQVFNE 333
PVL+ + DD++V L L Q GGH+ ++ + FN
Sbjct: 199 PVLLIAARDDMLVPYTCSLRLAAALPNAQLKLLPYGGHASNVTDPETFNR 248
>gnl|CDD|130895 TIGR01836, PHA_synth_III_C, poly(R)-hydroxyalkanoic acid synthase,
class III, PhaC subunit. This model represents the PhaC
subunit of a heterodimeric form of polyhydroxyalkanoic
acid (PHA) synthase. Excepting the PhaC of Bacillus
megaterium (which needs PhaR), all members require PhaE
(TIGR01834) for activity and are designated class III.
This enzyme builds ester polymers for carbon and energy
storage that accumulate in inclusions, and both this
enzyme and the depolymerase associate with the
inclusions. Class III enzymes polymerize
short-chain-length hydroxyalkanoates [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 350
Score = 35.5 bits (82), Expect = 0.036
Identities = 36/149 (24%), Positives = 65/149 (43%), Gaps = 34/149 (22%)
Query: 160 YIEEDVDIAYELLKLLGVCKVSLFGWCDGGHLSFVFSMKYPHMVHKLVIWGTK-SFLTID 218
YI++ VD + + + ++SL G C GG S ++ YP + LV T F T
Sbjct: 121 YIDKCVDY---ICRTSKLDQISLLGICQGGTFSLCYAALYPDKIKNLVTMVTPVDFETPG 177
Query: 219 NVRVFEGMRRLSNWSPMARSEVLKAYDND--VNYITGIFNQYVDMVNLIFKSYGRNVYQE 276
N+ LSNW+ + D D V+ + I + +++ L+ K + YQ
Sbjct: 178 NM--------LSNWA--------RHVDIDLAVDTMGNIPGELLNLTFLMLKPF-SLGYQ- 219
Query: 277 LLPYVDVPVLVFHSADDVMVSTQQVQSLL 305
YV++ D++ ++V++ L
Sbjct: 220 --KYVNLV--------DILEDERKVENFL 238
>gnl|CDD|131480 TIGR02427, protocat_pcaD, 3-oxoadipate enol-lactonase. Members of
this family are 3-oxoadipate enol-lactonase. Note that
the substrate is known as 3-oxoadipate enol-lactone,
2-oxo-2,3-dihydrofuran-5-acetate,
4,5-Dihydro-5-oxofuran-2-acetate, and
5-oxo-4,5-dihydrofuran-2-acetate. The enzyme the
catalyzes the fourth step in the protocatechuate
degradation to beta-ketoadipate and then to succinyl-CoA
and acetyl-CoA. 4-hydroxybenzoate, 3-hydroxybenzoate,
and vanillate all can be converted in one step to
protocatechuate. This enzyme also acts in catechol
degradation. In genomes that catabolize both catechol
and protocatechuate, two forms of this enzyme may be
found. All members of the seed alignment for this model
were chosen from within protocatechuate degradation
operons of at least three genes of the pathway, from
genomes with the complete pathway through
beta-ketoadipate [Energy metabolism, Other].
Length = 251
Score = 33.9 bits (78), Expect = 0.089
Identities = 12/63 (19%), Positives = 26/63 (41%)
Query: 276 ELLPYVDVPVLVFHSADDVMVSTQQVQSLLNQLKFCQYYQFSSGGHSCHIKHGQVFNEIS 335
+ L + VP L D + V+ + + + ++ + GH ++ + FN
Sbjct: 187 DRLGAIAVPTLCIAGDQDGSTPPELVREIADLVPGARFAEIRGAGHIPCVEQPEAFNAAL 246
Query: 336 RNF 338
R+F
Sbjct: 247 RDF 249
>gnl|CDD|132386 TIGR03343, biphenyl_bphD, 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
hydrolase. Members of this family are
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, or
HOPD hydrolase, the BphD protein of biphenyl
degradation. BphD acts on the product of ring
meta-cleavage by BphC. Many species carrying bphC and
bphD are capable of degrading polychlorinated biphenyls
as well as biphenyl itself.
Length = 282
Score = 33.4 bits (76), Expect = 0.16
Identities = 41/194 (21%), Positives = 69/194 (35%), Gaps = 32/194 (16%)
Query: 171 LLKLLGVCKVSLFGWCDGGHLSFVFSMKYPHMVHKLVIWGT----KSFLTIDNVRVFEGM 226
L+ L + K L G GG + F+++YP + KL++ G S + + +
Sbjct: 94 LMDALDIEKAHLVGNSMGGATALNFALEYPDRIGKLILMGPGGLGPSLFAPMPMEGIKLL 153
Query: 227 RRL-SNWSPMARSEVLKAYDNDVNYIT---------GIFNQYVDMVNLIFKSYGRNVYQE 276
+L + S ++L + D + IT I Q + N + S +
Sbjct: 154 FKLYAEPSYETLKQMLNVFLFDQSLITEELLQGRWENIQRQPEHLKNFLISS-------Q 206
Query: 277 LLPY-----------VDVPVLVFHSADDVMVSTQQVQSLLNQLKFCQYYQFSSGGHSCHI 325
P + LV DD V LL + Q + FS GH
Sbjct: 207 KAPLSTWDVTARLGEIKAKTLVTWGRDDRFVPLDHGLKLLWNMPDAQLHVFSRCGHWAQW 266
Query: 326 KHGQVFNEISRNFI 339
+H FN + +F+
Sbjct: 267 EHADAFNRLVIDFL 280
>gnl|CDD|221718 pfam12695, Abhydrolase_5, Alpha/beta hydrolase family. This family
contains a diverse range of alpha/beta hydrolase
enzymes.
Length = 145
Score = 32.0 bits (73), Expect = 0.18
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 276 ELLPYVDVPVLVFHSADDVMVSTQQVQSLLNQLKF-CQYYQFSSGGHS 322
+ L + VPVL+ H D +V ++ ++L L + GHS
Sbjct: 98 DDLAKLTVPVLIIHGTRDGVVPPEEAEALAAALPGPAELVVIEGAGHS 145
>gnl|CDD|213272 cd05904, 4CL, 4-Coumarate-CoA Ligase (4CL). 4-Coumarate:coenzyme A
ligase is a key enzyme in the phenylpropanoid metabolic
pathway for monolignol and flavonoid biosynthesis. It
catalyzes the synthesis of hydroxycinnamate-CoA
thioesters in a two-step reaction, involving the
formation of hydroxycinnamate-AMP anhydride and the
nucleophilic substitution of AMP by CoA. The
phenylpropanoid pathway is one of the most important
secondary metabolism pathways in plants and
hydroxycinnamate-CoA thioesters are the precursors of
lignin and other important phenylpropanoids.
Length = 504
Score = 33.0 bits (76), Expect = 0.20
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 3 QVNPSKRLSGGVFLCSFDFIPRTMSGKVKRKDL 35
QV P K++ VF+ D IP++ SGK+ R++L
Sbjct: 475 QVAPYKKVRKVVFV---DAIPKSPSGKILRREL 504
>gnl|CDD|224932 COG2021, MET2, Homoserine acetyltransferase [Amino acid transport
and metabolism].
Length = 368
Score = 32.3 bits (74), Expect = 0.37
Identities = 15/72 (20%), Positives = 25/72 (34%), Gaps = 2/72 (2%)
Query: 270 GRNVYQELLPYVDVPVLVFHSADDVMVSTQQVQSLLNQLKFCQYYQF--SSGGHSCHIKH 327
GR L + PVLV D + + ++L L + S GH +
Sbjct: 294 GRGDLTAALARIKAPVLVVGITSDWLFPPELQRALAEALPAAGALREIDSPYGHDAFLVE 353
Query: 328 GQVFNEISRNFI 339
+ + R F+
Sbjct: 354 SEAVGPLIRKFL 365
Score = 28.8 bits (65), Expect = 4.6
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 161 IEEDVDIAYELLKLLGVCKV-SLFGWCDGGHLSFVFSMKYPHMVHKLVIWGTKSFLTIDN 219
I + V LL LG+ K+ ++ G GG + ++++YP V + + T + L+ N
Sbjct: 129 IRDMVRAQRLLLDALGIKKLAAVVGGSMGGMQALEWAIRYPDRVRRAIPIATAARLSAQN 188
Query: 220 VRVFEGMRR 228
+ E R+
Sbjct: 189 IAFNEVQRQ 197
>gnl|CDD|235859 PRK06765, PRK06765, homoserine O-acetyltransferase; Provisional.
Length = 389
Score = 32.0 bits (73), Expect = 0.40
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 150 PKGRSFVPFQYIEEDVDIAYELLKLLGVCKV-SLFGWCDGGHLSFVFSMKYPHMVHKLV 207
P G F P I + V + EL+K LG+ ++ ++ G GG + +++ YPHMV +++
Sbjct: 133 PYGMDF-PVVTILDFVRVQKELIKSLGIARLHAVMGPSMGGMQAQEWAVHYPHMVERMI 190
>gnl|CDD|224423 COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases
[Amino acid transport and metabolism].
Length = 620
Score = 31.3 bits (71), Expect = 0.82
Identities = 31/182 (17%), Positives = 59/182 (32%), Gaps = 29/182 (15%)
Query: 131 GNVVLYLLGKTCSGYGQSLPKGRSFVPFQYIEEDVDIAYELLKLLGV---CKVSLFGWCD 187
G VL + +GYG+ ED+ A + L L + ++ + G
Sbjct: 423 GYAVLAPNYRGSTGYGREFADAIRGDWGGVDLEDLIAAVDALVKLPLVDPERIGITGGSY 482
Query: 188 GGHLSFVFSMKYPHMVHKLVIWGTKSFLTIDNVRVFEGMRRLSNWSPMARSEVLKAYDND 247
GG+++ + + K P + + G +D + F ++
Sbjct: 483 GGYMTLLAATKTPRFKAAVAVAGG-----VDWLLYFGEST--EGLRFDPEENGGGPPEDR 535
Query: 248 VNYITGIFNQYVDMVNLIFKSYGRNVYQELLPYVDVPVLVFHSADDVMVSTQQVQSLLNQ 307
Y Y D + P+L+ H +D V +Q + L++
Sbjct: 536 EKYEDRSPIFYAD-------------------NIKTPLLLIHGEEDDRVPIEQAEQLVDA 576
Query: 308 LK 309
LK
Sbjct: 577 LK 578
>gnl|CDD|221971 pfam13193, DUF4009, Domain of unknown function (DUF4009). This
is a small domain that is found C terminal to
pfam00501. It has a central beta sheet core that is
flanked by alpha helices.
Length = 43
Score = 27.8 bits (63), Expect = 0.85
Identities = 8/22 (36%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 22 IPRTMSGKVKRKDLVKKILENQ 43
+P+T SGK+ R+ L++ I +
Sbjct: 13 LPKTRSGKILRR-LLRAIALGE 33
>gnl|CDD|132100 TIGR03056, bchO_mg_che_rel, putative magnesium chelatase accessory
protein. Members of this family belong to the
alpha/beta fold family hydrolases (pfam00561). Members
are found in bacterial genomes if and only if they
encoded for anoxygenic photosynthetic systems similar to
that of Rhodobacter capsulatus and other
alpha-Proteobacteria. Members often are encoded in the
same operon as subunits of the protoporphyrin IX
magnesium chelatase, and were once designated BchO. No
literature supports a role as an actual subunit of
magnesium chelatase, but an accessory role is possible,
as suggested by placement by its probable hydrolase
activity [Energy metabolism, Photosynthesis].
Length = 278
Score = 31.0 bits (70), Expect = 0.86
Identities = 9/47 (19%), Positives = 19/47 (40%)
Query: 278 LPYVDVPVLVFHSADDVMVSTQQVQSLLNQLKFCQYYQFSSGGHSCH 324
LP + +P+ + +D V + + ++ + GGH H
Sbjct: 216 LPRITIPLHLIAGEEDKAVPPDESKRAATRVPTATLHVVPGGGHLVH 262
>gnl|CDD|223395 COG0318, CaiC, Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases
II [Lipid metabolism / Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 534
Score = 30.9 bits (70), Expect = 1.0
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 20 DFIPRTMSGKVKRKDLVKKILENQ 43
D +PRT SGK+ R+ L ++
Sbjct: 506 DELPRTASGKIDRRALREEYRAEP 529
>gnl|CDD|234315 TIGR03695, menH_SHCHC,
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate
synthase. This protein catalyzes the formation of
SHCHC, or (1 R,6
R)-2-succinyl-6-hydroxy-2,
4-cyclohexadiene-1-carboxylate, by elmination of
pyruvate from
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
carboxylate (SEPHCHC). Note that SHCHC synthase activity
previously was attributed to MenD, which in fact is
SEPHCHC synthase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Menaquinone and ubiquinone].
Length = 252
Score = 30.6 bits (70), Expect = 1.0
Identities = 12/46 (26%), Positives = 23/46 (50%)
Query: 166 DIAYELLKLLGVCKVSLFGWCDGGHLSFVFSMKYPHMVHKLVIWGT 211
+ LL LG+ L G+ GG ++ ++++YP V L++
Sbjct: 59 LLLATLLDQLGIEPFFLVGYSMGGRIALYYALQYPERVQGLILESG 104
>gnl|CDD|130799 TIGR01738, bioH, pimelyl-[acyl-carrier protein] methyl ester
esterase. This CoA-binding enzyme is required for the
production of pimeloyl-coenzyme A, the substrate of the
BioF protein early in the biosynthesis of biotin. Its
exact function is unknown, but is proposed in ref 2.
This enzyme belongs to the alpha/beta hydrolase fold
family (Pfam model pfam00561). Members of this family
are restricted to the Proteobacteria [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 245
Score = 30.6 bits (69), Expect = 1.2
Identities = 14/65 (21%), Positives = 26/65 (40%)
Query: 275 QELLPYVDVPVLVFHSADDVMVSTQQVQSLLNQLKFCQYYQFSSGGHSCHIKHGQVFNEI 334
++ L + VP L + D +V + V L + Y F+ H+ + H + F +
Sbjct: 181 RQPLQNISVPFLRLYGYLDGLVPAKVVPYLDKLAPHSELYIFAKAAHAPFLSHAEAFCAL 240
Query: 335 SRNFI 339
F
Sbjct: 241 LVAFK 245
>gnl|CDD|233393 TIGR01392, homoserO_Ac_trn, homoserine O-acetyltransferase. This
family describes homoserine-O-acetyltransferase, an
enzyme of methionine biosynthesis. This model has been
rebuilt to identify sequences more broadly, including a
number of sequences suggested to be homoserine
O-acetyltransferase based on proximity to other Met
biosynthesis genes [Amino acid biosynthesis, Aspartate
family].
Length = 351
Score = 30.4 bits (69), Expect = 1.3
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 150 PKGRSF---VPFQYIEEDVDIAYELLKLLGVCKV-SLFGWCDGGHLSFVFSMKYPHMVHK 205
P GR + P I +DV LL LG+ ++ ++ G GG + +++ YP V
Sbjct: 95 PGGRPYGSDFPLITIRDDVKAQKLLLDHLGIEQIAAVVGGSMGGMQALEWAIDYPERVRA 154
Query: 206 LVIWGTKSFLTIDNVRVFEGMRR 228
+V+ T + + + E R+
Sbjct: 155 IVVLATSARHSAWCIAFNEVQRQ 177
>gnl|CDD|180393 PRK06087, PRK06087, short chain acyl-CoA synthetase; Reviewed.
Length = 547
Score = 30.5 bits (69), Expect = 1.3
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 20 DFIPRTMSGKVKRKDLVKKILENQGSQ 46
D +PRT SGK+++ L K I+
Sbjct: 515 DKLPRTASGKIQKFLLRKDIMRRLTQD 541
>gnl|CDD|234107 TIGR03101, hydr2_PEP, exosortase A system-associated hydrolase 2.
This group of proteins are members of the alpha/beta
hydrolase superfamily. These proteins are generally
found in genomes containing the exosortase/PEP-CTERM
protein expoert system , specifically the type 1 variant
of this system described by the Genome Property
GenProp0652. When found in this context they are
invariably present in the vicinity of a second,
relatively unrelated enzyme (ortholog 1, TIGR03100) of
the same superfamily.
Length = 266
Score = 29.8 bits (67), Expect = 1.9
Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 163 EDVDIAYELLKLLGVCKVSLFGWCDGGHLSFVFSMKYPHMVHKLVIW----GTKSFLT 216
EDV AY L G V+L+G G L+ + ++LV+W K L
Sbjct: 84 EDVAAAYRWLIEQGHPPVTLWGLRLGALLALDAANPLAAKCNRLVLWQPVVSGKQQLQ 141
>gnl|CDD|213279 cd05911, Firefly_Luc_like, Firefly luciferase of light emitting
insects and 4-Coumarate-CoA Ligase (4CL). This family
contains two functionally unique groups of proteins; one
group is insect firefly luciferases and the other is
plant 4-coumarate:coenzyme A ligases. However, they
share significant sequence similarity in spite of their
functional diversity. Luciferase catalyzes the
production of light in the presence of MgATP, molecular
oxygen, and luciferin. In the first step, luciferin is
activated by acylation of its carboxylate group with
ATP, resulting in an enzyme-bound luciferyl adenylate.
In the second step, luciferyl adenylate reacts with
molecular oxygen, producing an enzyme-bound excited
state product (Luc=O*) and releasing AMP. This
excited-state product then decays to the ground state
(Luc=O), emitting a quantum of visible light.
4-coumarate:coenzyme A ligase is a key enzyme in the
phenylpropanoid metabolic pathway for monolignol and
flavonoid biosynthesis. It catalyzes the synthesis of
hydroxycinnamate-CoA thioesters in a two-step reaction,
involving the formation of hydroxycinnamate-AMP
anhydride and then the nucleophilic substitution of AMP
by CoA. The phenylpropanoid pathway is one of the most
important secondary metabolism pathways in plants and
hydroxycinnamate-CoA thioesters are the precursors of
lignin and other important phenylpropanoids.
Length = 487
Score = 29.5 bits (67), Expect = 2.8
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 3 QVNPSKRLSGGVFLCSF-DFIPRTMSGKV 30
+V K+L GGV F D IP++ SGK+
Sbjct: 461 KVAKYKQLRGGVV---FVDEIPKSPSGKI 486
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 29.7 bits (66), Expect = 3.1
Identities = 21/71 (29%), Positives = 29/71 (40%)
Query: 18 SFDFIPRTMSGKVKRKDLVKKILENQGSQKTYGLQETLLDTQLPSRTDFIHQDVFTEGFF 77
S+ FI R S + R D V L + S ++ QLP +F H +F F
Sbjct: 638 SYYFIWRLSSSVLNRADTVLTSLPSLSSSAASAVESKHHSFQLPVVPNFSHWHLFCTAFC 697
Query: 78 SIKGCDIRFIK 88
S G F+K
Sbjct: 698 SKIGSSYFFVK 708
>gnl|CDD|224561 COG1647, COG1647, Esterase/lipase [General function prediction
only].
Length = 243
Score = 28.8 bits (65), Expect = 3.4
Identities = 28/152 (18%), Positives = 54/152 (35%), Gaps = 20/152 (13%)
Query: 163 EDVDIAYELLKLLGVCKVSLFGWCDGGHLSFVFSMKYPHMVHKLVIWGT-----KSFLTI 217
EDV+ Y LK G ++++ G GG + + YP K+V + I
Sbjct: 70 EDVEDGYRDLKEAGYDEIAVVGLSMGGVFALKLAYHYP--PKKIVPMCAPVNVKSWRIII 127
Query: 218 DN-VRVFEGMRRLSNWSPMARSEVLKAYDNDVNYITGIFNQYVDMVNLIFKSYGRNVYQE 276
+ + F ++ + +K+Y + +T Q ++ +S
Sbjct: 128 EGLLEYFRNAKKYEGKDQEQIDKEMKSYKDT--PMTTTA-QLKKLIKDARRS-------- 176
Query: 277 LLPYVDVPVLVFHSADDVMVSTQQVQSLLNQL 308
L + P LV D MV + + + +
Sbjct: 177 -LDKIYSPTLVVQGRQDEMVPAESANFIYDHV 207
>gnl|CDD|213276 cd05908, A_NRPS_MycA_like, The adenylation domain of nonribosomal
peptide synthetases (NRPS) similar to mycosubtilin
synthase subunit A (MycA). The adenylation (A) domain
of NRPS recognizes a specific amino acid or hydroxy acid
and activates it as (amino)-acyl adenylate by hydrolysis
of ATP. The activated acyl moiety then forms thioester
to the enzyme-bound cofactor phosphopantetheine of a
peptidyl carrier protein domain. This family includes
NRPS similar to mycosubtilin synthase subunit A (MycA).
Mycosubtilin, which is characterized by a beta-amino
fatty acid moiety linked to the circular heptapeptide
Asn-Tyr-Asn-Gln-Pro-Ser-Asn, belongs to the iturin
family of lipopeptide antibiotics. The mycosubtilin
synthase subunit A (MycA) combines functional domains
derived from peptide synthetases, amino transferases,
and fatty acid synthases. Nonribosomal peptide
synthetases are large multifunction enzymes that
synthesize many therapeutically useful peptides. NRPS
has a distinct modular structure in which each module is
responsible for the recognition, activation, and, in
some cases, modification of a single amino acid residue
of the final peptide product. The modules can be
subdivided into domains that catalyze specific
biochemical reactions.
Length = 499
Score = 28.8 bits (65), Expect = 4.7
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 22 IPRTMSGKVKRKDLVKKILEN 42
IP+T SGK++R L ++ L
Sbjct: 477 IPKTTSGKIQRYKLAQQFLNG 497
>gnl|CDD|223506 COG0429, COG0429, Predicted hydrolase of the alpha/beta-hydrolase
fold [General function prediction only].
Length = 345
Score = 28.5 bits (64), Expect = 5.7
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 5/48 (10%)
Query: 277 LLPYVDVPVLVFHSADDVMVSTQQV---QSLLNQLKFCQYYQFSSGGH 321
LLP + P L+ ++ DD + + + Q +LN GGH
Sbjct: 269 LLPKIRKPTLIINAKDDPFMPPEVIPKLQEMLN--PNVLLQLTEHGGH 314
>gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 468
Score = 28.4 bits (64), Expect = 6.5
Identities = 13/30 (43%), Positives = 14/30 (46%)
Query: 164 DVDIAYELLKLLGVCKVSLFGWCDGGHLSF 193
D + A ELLK LG G DG LS
Sbjct: 303 DPEKAKELLKGLGYTDNGGDGEKDGEPLSL 332
>gnl|CDD|215950 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 220
Score = 27.6 bits (62), Expect = 7.4
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 8/40 (20%)
Query: 154 SFVPFQYIEE-------DVDIAYELLKLLGV-CKVSLFGW 185
+ PF Y++E DVD+A + K LGV + W
Sbjct: 8 DYPPFSYVDENGKLVGFDVDLAKAIAKRLGVKVEFVPVSW 47
>gnl|CDD|234709 PRK00275, glnD, PII uridylyl-transferase; Provisional.
Length = 895
Score = 28.5 bits (64), Expect = 7.5
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 269 YGRNVYQELLPYVDVPVLVFHSADD 293
YGR EL PY D+ +L+ + D
Sbjct: 87 YGRG---ELHPYSDIDLLILLDSAD 108
>gnl|CDD|215137 PLN02246, PLN02246, 4-coumarate--CoA ligase.
Length = 537
Score = 28.0 bits (63), Expect = 7.8
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 3 QVNPSKRLSGGVFLCSFDFIPRTMSGKVKRKDLVKKI 39
QV KR+ F+ D IP+ SGK+ RKDL K+
Sbjct: 501 QVVFYKRIHKVFFV---DSIPKAPSGKILRKDLRAKL 534
>gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated.
Length = 251
Score = 27.7 bits (62), Expect = 7.9
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 10/62 (16%)
Query: 20 DFIPRTMSGKVKRKDLVKKILENQGSQKTYGLQETLLDTQLPSRTDFIHQDVFT---EGF 76
D++PR+M K K+ + + LE Q+ + ++ + ++V EGF
Sbjct: 98 DWLPRSMREKTKKVEAAIEKLE----QR---YMRNVTPKEVAAELGMTEEEVEATMNEGF 150
Query: 77 FS 78
F+
Sbjct: 151 FA 152
>gnl|CDD|215312 PLN02574, PLN02574, 4-coumarate--CoA ligase-like.
Length = 560
Score = 27.9 bits (62), Expect = 8.6
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 3 QVNPSKRLSGGVFLCSFDFIPRTMSGKVKRKDLVKKILENQGSQK 47
QV P K++ VF+ S IP++ +GK+ R++L K+ L N S +
Sbjct: 519 QVAPYKKVRKVVFVQS---IPKSPAGKILRREL-KRSLTNSVSSR 559
>gnl|CDD|182883 PRK10985, PRK10985, putative hydrolase; Provisional.
Length = 324
Score = 27.6 bits (62), Expect = 9.2
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 277 LLPYVDVPVLVFHSADD-VMVSTQQVQSLLNQLKFCQYYQ-FSSGGH 321
LL + P L+ H+ DD M T +V L YQ GGH
Sbjct: 250 LLNQIRKPTLIIHAKDDPFM--THEVIPKPESLPPNVEYQLTEHGGH 294
>gnl|CDD|188121 TIGR01250, pro_imino_pep_2, proline-specific peptidase, Bacillus
coagulans-type subfamily. This model describes a
subfamily of the alpha/beta fold family of hydrolases.
Characterized members include prolinases (Pro-Xaa
dipeptidase, EC 3.4.13.8), prolyl aminopeptidases (EC
3.4.11.5), and a leucyl aminopeptidase.
Length = 289
Score = 27.7 bits (62), Expect = 9.6
Identities = 39/217 (17%), Positives = 72/217 (33%), Gaps = 44/217 (20%)
Query: 161 IEEDVDIAYELLKLLGVCKVSLFGWCDGGHLSFVFSMKYPHMVHKLVIWGTKSFLTIDNV 220
I+ VD E+ + LG+ K L G GG L+ +++KY + L+I +D+
Sbjct: 80 IDYFVDELEEVREKLGLDKFYLLGHSWGGMLAQEYALKYGQHLKGLIISS-----MLDSA 134
Query: 221 RVFEG-MRRLSNWSPMARSEVLKAYD-----NDVNYITGIF---NQYVDM-------VNL 264
+ + RL P +K + ++ Y + + + +
Sbjct: 135 PEYVKELNRLRKELPPEVRAAIKRCEASGDYDNPEYQEAVEVFYHHLLCRLRKWPEALKH 194
Query: 265 IFKSYGRNVYQ------ELLP--------YVD------VPVLVFHSADDVM-VSTQQVQS 303
+ NVY E D VP L+ D M +
Sbjct: 195 LKSGGNTNVYNIMQGPNEFTITGNLKDWDITDKLSEIKVPTLLTVGEFDTMTPEAAREMQ 254
Query: 304 LLNQLKFCQYYQFSSGGHSCHIKHGQVFNEISRNFIL 340
+ + F G H I+ +V+ ++ +FI
Sbjct: 255 --ELIAGSRLVVFPDGSHMTMIEDPEVYFKLLSDFIR 289
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
0.324 0.141 0.433
Gapped
Lambda K H
0.267 0.0868 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,817,661
Number of extensions: 1719687
Number of successful extensions: 1947
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1943
Number of HSP's successfully gapped: 43
Length of query: 345
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 247
Effective length of database: 6,590,910
Effective search space: 1627954770
Effective search space used: 1627954770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 59 (26.3 bits)