RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9188
(104 letters)
>gnl|CDD|223257 COG0179, MhpD, 2-keto-4-pentenoate
hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase
(catechol pathway) [Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 266
Score = 117 bits (296), Expect = 4e-34
Identities = 43/81 (53%), Positives = 55/81 (67%), Gaps = 1/81 (1%)
Query: 10 AREHGLPWTVGKSFDTACPVSDFIPEH-EIKDPDDVPLWLKVNGELRQKSTTGDMLFKTG 68
E G PWT K FDT PV +I EI DP ++PL L+VNGE+RQ+ T DM+F
Sbjct: 154 MEEKGRPWTRAKGFDTFAPVGPWIVTKDEISDPQNLPLSLRVNGEVRQRGNTSDMIFSIP 213
Query: 69 DLISYISQHMTLEPYDLILTG 89
+LI+Y+S+ MTLEP D+ILTG
Sbjct: 214 ELIAYLSRFMTLEPGDVILTG 234
>gnl|CDD|216570 pfam01557, FAA_hydrolase, Fumarylacetoacetate (FAA) hydrolase
family. This family consists of fumarylacetoacetate
(FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH)
and it also includes HHDD isomerase/OPET decarboxylase
from E. coli strain W. FAA is the last enzyme in the
tyrosine catabolic pathway, it hydrolyses
fumarylacetoacetate into fumarate and acetoacetate which
then join the citric acid cycle. Mutations in FAA cause
type I tyrosinemia in humans this is an inherited
disorder mainly affecting the liver leading to liver
cirrhosis, hepatocellular carcinoma, renal tubular
damages and neurologic crises amongst other symptoms.
The enzymatic defect causes the toxic accumulation of
phenylalanine/tyrosine catabolites. The E. coli W enzyme
HHDD isomerase/OPET decarboxylase contains two copies of
this domain and functions in fourth and fifth steps of
the homoprotocatechuate pathway; here it decarboxylates
OPET to HHDD and isomerises this to OHED. The final
products of this pathway are pyruvic acid and succinic
semialdehyde. This family also includes various
hydratases and 4-oxalocrotonate decarboxylases which are
involved in the bacterial meta-cleavage pathways for
degradation of aromatic compounds. 2-hydroxypentadienoic
acid hydratase, encoded by mhpD in E. coli, is involved
in the phenylpropionic acid pathway of E. coli and
catalyzes the conversion of 2-hydroxy pentadienoate to
4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor.
OHED hydratase encoded by hpcG in E. coli is involved in
the homoprotocatechuic acid (HPC) catabolism. XylI in P.
putida is a 4-Oxalocrotonate decarboxylase.
Length = 207
Score = 103 bits (260), Expect = 2e-29
Identities = 36/80 (45%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 11 REHGLPWTVGKSFDTACPVSDFIPEH-EIKDPDDVPLWLKVNGELRQKSTTGDMLFKTGD 69
PW KSFD P+ +I E+ DP D+ L L+VNGEL Q +T DM+F +
Sbjct: 96 DRDYRPWFRAKSFDGFAPLGPWIVTPDELGDPADLELRLRVNGELVQDGSTADMIFSPAE 155
Query: 70 LISYISQHMTLEPYDLILTG 89
LI+++S+ +TLEP D+ILTG
Sbjct: 156 LIAHLSRFLTLEPGDIILTG 175
>gnl|CDD|182650 PRK10691, PRK10691, hypothetical protein; Provisional.
Length = 219
Score = 97.1 bits (242), Expect = 2e-26
Identities = 38/85 (44%), Positives = 52/85 (61%), Gaps = 1/85 (1%)
Query: 6 LQKHAREHGLPWTVGKSFDTACPVSDFIPEHEIK-DPDDVPLWLKVNGELRQKSTTGDML 64
LQ ++ G PW K+FD +CP+S FIP E DP + L L VNGE+RQ+ T DM+
Sbjct: 107 LQGKMKKAGQPWEKAKAFDNSCPISGFIPVAEFTGDPQNTTLGLSVNGEVRQQGNTADMI 166
Query: 65 FKTGDLISYISQHMTLEPYDLILTG 89
LI+Y+S+ TL D++LTG
Sbjct: 167 HPIVPLIAYMSRFFTLRAGDVVLTG 191
>gnl|CDD|131356 TIGR02303, HpaG-C-term, 4-hydroxyphenylacetate degradation
bifunctional isomerase/decarboxylase, C-terminal
subunit. This model represents one of two
subunits/domains of the bifunctional
isomerase/decarboxylase involved in
4-hydroxyphenylacetate degradation. In E. coli and some
other species this enzyme is encoded by a single
polypeptide containing both this domain and the closely
related N-terminal domain (TIGR02305). In other species
such as Pasteurella multocida these domains are found as
two separate proteins (usually as tandem genes).
Together, these domains carry out the decarboxylation of
5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to
2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent
isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Length = 245
Score = 77.9 bits (192), Expect = 5e-19
Identities = 32/70 (45%), Positives = 47/70 (67%), Gaps = 1/70 (1%)
Query: 21 KSFDTACPVSDFIPE-HEIKDPDDVPLWLKVNGELRQKSTTGDMLFKTGDLISYISQHMT 79
K+ DT P+ +I + +++DP ++ L VNGEL Q+ T DM+F +LI Y+S+ MT
Sbjct: 145 KNRDTFTPIGPWIVDKEDVEDPMNLWLRTYVNGELTQEGNTSDMIFSVAELIEYLSEFMT 204
Query: 80 LEPYDLILTG 89
LEP D+ILTG
Sbjct: 205 LEPGDVILTG 214
>gnl|CDD|185125 PRK15203, PRK15203, 4-hydroxyphenylacetate degradation bifunctional
isomerase/decarboxylase; Provisional.
Length = 429
Score = 66.6 bits (162), Expect = 3e-14
Identities = 33/70 (47%), Positives = 44/70 (62%), Gaps = 1/70 (1%)
Query: 21 KSFDTACPVSDFI-PEHEIKDPDDVPLWLKVNGELRQKSTTGDMLFKTGDLISYISQHMT 79
KS D P+ I P+ I DP ++ L VNGELRQ+ TT D++F LI+Y+S+ MT
Sbjct: 325 KSRDGLTPILSTIVPKEAIPDPHNLTLRTFVNGELRQQGTTADLIFSVPFLIAYLSEFMT 384
Query: 80 LEPYDLILTG 89
L P D+I TG
Sbjct: 385 LNPGDMIATG 394
Score = 36.6 bits (84), Expect = 8e-04
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 16 PWTVGKSFDTACPVSDFIPEHEIKDPDDVPLWLKVNGELRQKSTTGDMLFKTGDLISYIS 75
P K D CP+ + + + + D++ ++ ++NG T D+ L+S +S
Sbjct: 105 PAIKAKCRDGFCPIGETVA---LSNVDNLTIYTEINGRPADHWNTADLQRNAAQLLSALS 161
Query: 76 QHMTLEPYDLILTG 89
+ TL P D IL G
Sbjct: 162 EFATLNPGDAILLG 175
>gnl|CDD|131358 TIGR02305, HpaG-N-term, 4-hydroxyphenylacetate degradation
bifunctional isomerase/decarboxylase, N-terminal
subunit. This model represents one of two
subunits/domains of the bifunctional
isomerase/decarboxylase involved in
4-hydroxyphenylacetate degradation. In E. coli and some
other species this enzyme is encoded by a single
polypeptide containing both this domain and the closely
related C-terminal domain (TIGR02303). In other species
such as Pasteurella multocida these domains are found as
two separate proteins (usually as tandem genes).
Together, these domains carry out the decarboxylation of
5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to
2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent
isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).
Length = 205
Score = 62.4 bits (152), Expect = 3e-13
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 20 GKSFDTACPVSDFIPEHEIKDPDDVPLWLKVNGELRQKSTTGDMLFKTGDLISYISQHMT 79
K D CP+ +P I +PD++ ++ +NG+ Q + T +++ LIS +S+ MT
Sbjct: 108 AKCRDGFCPIGPEVPLSAIGNPDELTIYTYINGKPAQSNNTSNLVRSAAQLISELSEFMT 167
Query: 80 LEPYDLILTGKAG 92
L P D++L G
Sbjct: 168 LNPGDVLLLGTPE 180
>gnl|CDD|237193 PRK12764, PRK12764, hypothetical protein; Provisional.
Length = 500
Score = 58.2 bits (141), Expect = 2e-11
Identities = 23/46 (50%), Positives = 31/46 (67%), Gaps = 2/46 (4%)
Query: 46 LWLK--VNGELRQKSTTGDMLFKTGDLISYISQHMTLEPYDLILTG 89
L ++ VNGEL Q TT D+LF L++ +SQ +TLE D+ILTG
Sbjct: 146 LRVRTWVNGELVQDDTTEDLLFPFAQLVADLSQLLTLEEGDVILTG 191
>gnl|CDD|128421 smart00111, C4, C-terminal tandem repeated domain in type 4
procollagens. Duplicated domain in C-terminus of type 4
collagens. Mutations in alpha-5 collagen IV are
associated with X-linked Alport syndrome.
Length = 114
Score = 27.4 bits (61), Expect = 0.78
Identities = 11/30 (36%), Positives = 12/30 (40%)
Query: 46 LWLKVNGELRQKSTTGDMLFKTGDLISYIS 75
WL Q + M K GDL YIS
Sbjct: 77 FWLSTIEPSDQFTAPRPMTPKAGDLRPYIS 106
>gnl|CDD|236045 PRK07534, PRK07534, methionine synthase I; Validated.
Length = 336
Score = 27.8 bits (62), Expect = 1.0
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 10 AREHGLPWTVGKSFDTA 26
A+ G+PW SFDTA
Sbjct: 166 AKLAGMPWCGTMSFDTA 182
>gnl|CDD|237521 PRK13820, PRK13820, argininosuccinate synthase; Provisional.
Length = 394
Score = 27.6 bits (62), Expect = 1.2
Identities = 17/59 (28%), Positives = 22/59 (37%), Gaps = 22/59 (37%)
Query: 7 QKHAREHGLPWTVGK----SFDTAC------------PVSDFIPEHEI----KDPDDVP 45
++A+E G+P VGK S D P F P EI P+D P
Sbjct: 153 IEYAKEKGIPVPVGKEKPWSIDENLWSRSIEGGKLEDP--AFEPPEEIYAWTVSPEDAP 209
>gnl|CDD|153380 cd07368, PhnC_Bs_like, PhnC is a Class III Extradiol ring-cleavage
dioxygenase involved in the polycyclic aromatic
hydrocarbon (PAH) catabolic pathway. This subfamily is
composed of Burkholderia sp. PhnC and similar poteins.
PhnC is one of nine protein products encoded by the phn
locus. These proteins are involved in the polycyclic
aromatic hydrocarbon (PAH) catabolic pathway. PhnC is a
member of the class III extradiol dioxygenase family, a
group os enzymes which use a non-heme Fe(II) to cleave
aromatic rings between a hydroxylated carbon and an
adjacent non-hydroxylated carbon. LigAB-like enzymes are
usually composed of two subunits, designated A and B,
which form a tetramer composed of two copies of each
subunit. This model represents the catalytic subunit, B.
Length = 277
Score = 27.5 bits (61), Expect = 1.3
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 5 FLQKHAREHGLPWTVGKSFDTACPVSDFIPEHEIKDP 41
+ +H E+G+ W V +SF + IP H P
Sbjct: 100 HIMQHGLEYGIDWAVARSFTVDHAAT--IPIHLAVRP 134
>gnl|CDD|213520 TIGR00276, TIGR00276, epoxyqueuosine reductase. This model was
rebuilt to exclude archaeal homologs, now that there is
new information that bacterial members are
epoxyqueuosine reductase, QueG, involved in queuosine
biosynthesis for tRNA maturation [Protein synthesis,
tRNA and rRNA base modification].
Length = 337
Score = 27.1 bits (61), Expect = 1.6
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 3/42 (7%)
Query: 16 PWTVGKSFDTACPVSDFIPEHEIKDPDDVPLWLKVNGELRQK 57
PW DF P HE+ P + L+ E ++
Sbjct: 242 PWNKFADATHE---PDFQPRHELDAPSLIELFAWDEAEFLER 280
>gnl|CDD|232849 TIGR00160, MGSA, methylglyoxal synthase. Methylglyoxal synthase
(MGS) generates methylglyoxal (MG), a toxic metabolite
(that may also be a regulatory metabolite and) that is
detoxified, prinicipally, through a pathway involving
glutathione and glyoxylase I. Totemeyer, et al.
(MUID:98149311) propose that, during a loss of control
over carbon flux, with accumulation of phosphorylated
sugars and depletion of phosphate, as might happen
during a rapid shift to a richer medium, MGS aids the
cell by converting some dihydroxyacetone phosphate
(DHAP) to MG and phosphate. This is therefore an
alternative to triosephosphate isomerase and the
remainder of the glycolytic pathway for the disposal of
DHAP during the stress of a sudden increase in
available sugars [Energy metabolism, Other].
Length = 143
Score = 26.3 bits (58), Expect = 2.2
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 66 KTGDLISYISQHMT-LEPYDLILTGKAGFIL 95
K DL++++ QH + L +DL TG G ++
Sbjct: 13 KKQDLVNFVQQHKSLLSRHDLYATGTTGELI 43
>gnl|CDD|99827 cd05784, DNA_polB_II_exo, DEDDy 3'-5' exonuclease domain of
Escherichia coli DNA polymerase II and similar
bacterial family-B DNA polymerases. The 3'-5'
exonuclease domain of Escherichia coli DNA polymerase
II (Pol II) and similar bacterial proteins. Pol II is a
family-B DNA polymerase. Family-B DNA polymerases
contain an N-terminal DEDDy DnaQ-like exonuclease
domain in the same polypeptide chain as the polymerase
domain, similar to family-A DNA polymerases. This
exonuclease domain contains three sequence motifs
termed ExoI, ExoII and ExoIII, with a specific YX(3)D
pattern at ExoIII. These motifs are clustered around
the active site and are involved in metal binding and
catalysis. The exonuclease domain has a fundamental
role in the proofreading activity of polII. It contains
a beta hairpin structure that plays an important role
in active site switching in the event of a nucleotide
misincorporation. Pol II is involved in a variety of
cellular activities, such as the repair of DNA damaged
by UV irradiation or oxidation. It plays a pivotal role
in replication-restart, a process that bypasses DNA
damage in an error-free manner. Pol II is also involved
in lagging strand synthesis.
Length = 193
Score = 26.4 bits (59), Expect = 2.5
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 3 FLFLQKHAREHGLPWTVG 20
LQ+ A HGLP +G
Sbjct: 80 LRLLQRRAEAHGLPLRLG 97
>gnl|CDD|193307 pfam12832, MFS_1_like, MFS_1 like family. In fungal members this
domain is found at the C-terminus of putative
transporter proteins.
Length = 77
Score = 25.3 bits (56), Expect = 3.4
Identities = 7/31 (22%), Positives = 12/31 (38%)
Query: 67 TGDLISYISQHMTLEPYDLILTGKAGFILMF 97
G L Y+ ++ ++ L G IL
Sbjct: 16 NGCLYPYLGLYLESLGFNYSLIGLLSAILPA 46
>gnl|CDD|235595 PRK05762, PRK05762, DNA polymerase II; Reviewed.
Length = 786
Score = 26.4 bits (59), Expect = 3.6
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 3 FLFLQKHAREHGLPWTVG 20
LQ+ A +G+P +G
Sbjct: 232 LRLLQERAERYGIPLRLG 249
>gnl|CDD|240318 PTZ00224, PTZ00224, protein phosphatase 2C; Provisional.
Length = 381
Score = 25.9 bits (57), Expect = 4.9
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 49 KVNGELRQKSTTGDMLFKTGDLISYISQ---------HMTLEPYDLIL 87
+V+G+L GD FK Y+ Q H+T + D I+
Sbjct: 166 RVDGDLAVSRAFGDRSFKVKGTGDYLEQKVIAVPDVTHLTCQSNDFII 213
>gnl|CDD|236158 PRK08132, PRK08132, FAD-dependent oxidoreductase; Provisional.
Length = 547
Score = 25.6 bits (57), Expect = 5.4
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 12 EHGLPWTVGKSF 23
+ G+ W VGK F
Sbjct: 86 DKGVSWNVGKVF 97
>gnl|CDD|168170 PRK05677, PRK05677, long-chain-fatty-acid--CoA ligase; Validated.
Length = 562
Score = 25.5 bits (56), Expect = 6.9
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 59 TTGDMLFKTGDLISYISQHMTLEPYDLI 86
T G++ +G +++ QH L+P D I
Sbjct: 51 TYGELYKLSGAFAAWLQQHTDLKPGDRI 78
>gnl|CDD|178047 PLN02427, PLN02427, UDP-apiose/xylose synthase.
Length = 386
Score = 25.2 bits (55), Expect = 7.1
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 12 EHGLPWTVGKSFDTACPVSDFIP 34
E+GL +T+ + F+ P DFIP
Sbjct: 199 ENGLEFTIVRPFNWIGPRMDFIP 221
>gnl|CDD|235723 PRK06170, PRK06170, amidase; Provisional.
Length = 490
Score = 25.4 bits (56), Expect = 7.9
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 13 HGLPWTVGKSFDTA 26
G+P TV +SF+ A
Sbjct: 77 LGIPVTVKESFNVA 90
>gnl|CDD|224716 COG1803, MgsA, Methylglyoxal synthase [Carbohydrate transport and
metabolism].
Length = 142
Score = 24.6 bits (54), Expect = 8.8
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 66 KTGDLISYISQHM-TLEPYDLILTGKAGFILM 96
K DL++++ H L +DL TG G ++
Sbjct: 15 KKDDLVNFVQAHKELLSRHDLYATGTTGGLIQ 46
>gnl|CDD|153436 cd07967, OBF_DNA_ligase_III, The Oligonucleotide/oligosaccharide
binding (OB)-fold domain of ATP-dependent DNA ligase
III is a DNA-binding module that is part of the
catalytic core unit. ATP-dependent polynucleotide
ligases catalyze phosphodiester bond formation using
nicked nucleic acid substrates with the high energy
nucleotide of ATP as a cofactor in a three step
reaction mechanism. DNA ligases play a vital role in
the diverse processes of DNA replication, recombination
and repair. ATP-dependent ligases are present in many
organisms such as viruses, bacteriohages, eukarya,
archaea and bacteria. There are three classes of
ATP-dependent DNA ligases in eukaryotic cells (I, III
and IV). DNA ligase III is not found in lower
eukaryotes and is present both in the nucleus and
mitochondria. It has several isoforms; two splice
forms, III-alpha and III-beta, differ in their
carboxy-terminal sequences. DNA ligase III-beta is
believed to play a role in homologous recombination
during meiotic prophase. DNA ligase III-alpha interacts
with X-ray Cross Complementing factor 1 (XRCC1) and
functions in single nucleotide Base Excision Repair
(BER). The mitochondrial form of DNA ligase III
originates from the nucleolus and is involved in the
mitochondrial DNA repair pathway. This isoform is
expressed by a second start site on the DNA ligase III
gene. DNA ligases have a highly modular architecture
consisting of a unique arrangement of two or more
discrete domains. The adenylation and C-terminal
oligouncleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common
to most members of the ATP-dependent DNA ligase family.
The catalytic core unit contains six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases. The OB-fold
domain contacts the nicked DNA substrate and is
required for the ATP-dependent DNA ligase
nucleotidylation step. The RxDK motif (motif VI), which
is essential for ATP hydrolysis, is located in the
OB-fold domain.
Length = 139
Score = 24.6 bits (54), Expect = 9.2
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 39 KDPDDVPLWLKVN 51
KDP VP WLK N
Sbjct: 67 KDPSKVPSWLKCN 79
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.140 0.438
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,484,142
Number of extensions: 459600
Number of successful extensions: 481
Number of sequences better than 10.0: 1
Number of HSP's gapped: 478
Number of HSP's successfully gapped: 31
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.3 bits)