RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 033892
(109 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 = 108 bits (272), Expect = 2e-30
Identities = 39/81 (48%), Positives = 54/81 (66%), Gaps = 2/81 (2%)
Query: 17 KIVAVGRNYAAHAKELGNA--VPKEPVLFLKPTSSYLGNGGTIEVPHPLDSLHHEVELAV 74
KIV VGRNYA HA+E+G +P+EPV FLKP ++ +G I +P L +E ELAV
Sbjct: 61 KIVCVGRNYADHAEEMGKDRDIPEEPVFFLKPPTAVIGPNDPIPLPPGSKGLDYEGELAV 120
Query: 75 VIGQKARDVPETTAMDYVGGF 95
VIG++ +DV A+DY+ G+
Sbjct: 121 VIGKRGKDVSVEDALDYIAGY 141
>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 = 91.2 bits (227), Expect = 3e-24
Identities = 40/83 (48%), Positives = 51/83 (61%), Gaps = 4/83 (4%)
Query: 17 KIVAVGRNYAAHAKELGNAVPKE----PVLFLKPTSSYLGNGGTIEVPHPLDSLHHEVEL 72
KI+ VG NY +HAKELG+ V PV FLKP S+ +G G I +P + L +E EL
Sbjct: 1 KIIGVGLNYTSHAKELGSGVEPPDYGPPVFFLKPPSALVGPGDPIVLPRGSERLDYEAEL 60
Query: 73 AVVIGQKARDVPETTAMDYVGGF 95
AVVIG+ R V A+DYV G+
Sbjct: 61 AVVIGKDLRAVTPEEALDYVAGY 83
>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 = 89.1 bits (221), Expect = 3e-23
Identities = 36/79 (45%), Positives = 52/79 (65%)
Query: 17 KIVAVGRNYAAHAKELGNAVPKEPVLFLKPTSSYLGNGGTIEVPHPLDSLHHEVELAVVI 76
I A+G NYA HA ELG + P+EP++FLK ++ G+ G P + +H+E ELAVV+
Sbjct: 44 TIFALGLNYADHASELGFSPPEEPLVFLKGNNTLTGHKGVTYRPKDVRFMHYECELAVVV 103
Query: 77 GQKARDVPETTAMDYVGGF 95
G+ A++V AMDYV G+
Sbjct: 104 GKTAKNVKREDAMDYVLGY 122
>gnl|CDD|182650 PRK10691, PRK10691, hypothetical protein; Provisional.
Length = 219
Score = 77.8 bits (192), Expect = 4e-19
Identities = 35/80 (43%), Positives = 49/80 (61%)
Query: 16 TKIVAVGRNYAAHAKELGNAVPKEPVLFLKPTSSYLGNGGTIEVPHPLDSLHHEVELAVV 75
+K+V VG NYA H KE+G+A P+EPVLF+KP ++ + +P S+HHEVELAV+
Sbjct: 17 SKVVCVGSNYAKHIKEMGSATPEEPVLFIKPETALCDLRQPLAIPKDFGSVHHEVELAVL 76
Query: 76 IGQKARDVPETTAMDYVGGF 95
IG R E + G+
Sbjct: 77 IGATLRQATEEHVRKAIAGY 96
>gnl|CDD|185125 PRK15203, PRK15203, 4-hydroxyphenylacetate degradation bifunctional
isomerase/decarboxylase; Provisional.
Length = 429
Score = 75.5 bits (185), Expect = 2e-17
Identities = 40/95 (42%), Positives = 57/95 (60%), Gaps = 1/95 (1%)
Query: 1 MATASSAVQKLIQAGTKIVAVGRNYAAHAKELGNAVPKEPVLFLKPTSSYLGNGGTIEVP 60
+ T S GT + A+G NYA HA EL P+EP++FLK ++ G+ T P
Sbjct: 209 VTTHKSFPTPPHPHGT-LFALGLNYADHASELEFKPPEEPLVFLKAPNTLTGDNQTSVRP 267
Query: 61 HPLDSLHHEVELAVVIGQKARDVPETTAMDYVGGF 95
+ ++ +H+E EL VVIG++AR V E AMDYV G+
Sbjct: 268 NNIEYMHYEAELVVVIGKQARKVSEADAMDYVAGY 302
Score = 36.2 bits (83), Expect = 0.002
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 34 NAVPKEPVLFLKPTSSYLGNGGTIEVPHPLDSLHHEVELAVVIGQKARDVPETTAMDYVG 93
A PK V F+KP ++ + G I P + + +A+++G+ A V E A +Y+
Sbjct: 29 KAPPKTAVWFIKPRNTVIRCGEPIPFPQG-EKVLSGATVALIVGKTATKVREEDAAEYIA 87
Query: 94 GF 95
G+
Sbjct: 88 GY 89
>gnl|CDD|237193 PRK12764, PRK12764, hypothetical protein; Provisional.
Length = 500
Score = 60.2 bits (146), Expect = 5e-12
Identities = 34/87 (39%), Positives = 48/87 (55%), Gaps = 1/87 (1%)
Query: 8 VQKLIQAGTKIVAVGRNYAAHAKELGNAVPKEPVLFLKPTSSYLGNGGTIEVPHPLDSLH 67
V L+ K++AV NY + A + G P +P FLKP+SS +GGT+E P + L
Sbjct: 14 VAPLLARPGKVIAVHLNYPSRAAQRGRT-PAQPSYFLKPSSSLALSGGTVERPAGTELLA 72
Query: 68 HEVELAVVIGQKARDVPETTAMDYVGG 94
E E+A+VIG+ AR V A +V
Sbjct: 73 FEGEIALVIGRPARRVSPEDAWSHVAA 99
>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 = 54.0 bits (130), Expect = 4e-10
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 8/90 (8%)
Query: 17 KIVAVGRNYAAHAKELGNAV--------PKEPVLFLKPTSSYLGNGGTIEVPHPLDSLHH 68
+ V NY L A PK PVL++KP +++ G G I +P ++ L
Sbjct: 2 TVFGVALNYREQLDRLQEAFQQAPYKAPPKTPVLYIKPRNTHNGCGQPIPLPAGVEKLRS 61
Query: 69 EVELAVVIGQKARDVPETTAMDYVGGFIFV 98
LA+V+G+ A V E A+DYV G+ V
Sbjct: 62 GATLALVVGRTACRVREEEALDYVAGYALV 91
>gnl|CDD|112645 pfam03841, SelA, L-seryl-tRNA selenium transferase.
Length = 367
Score = 30.0 bits (68), Expect = 0.16
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 13 QAGTKIVAVGRNYAAHAKELGNAVPKEPVLFLKP-TSSYLGNGGTIEVPHP-LDSLHHEV 70
Q+G ++V VG H K+ A+ + L +K TS+Y G T EV L +L E
Sbjct: 110 QSGARLVEVGTTNRTHLKDYEQAINENTALLMKVHTSNYRIQGFTKEVSLAELVALGKEH 169
Query: 71 ELAVV 75
L V
Sbjct: 170 GLPVY 174
>gnl|CDD|236919 PRK11504, tynA, tyramine oxidase; Provisional.
Length = 647
Score = 28.7 bits (65), Expect = 0.58
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 59 VPHPLDSL-HHEVELAVVIGQKARDVPETTAMDYVG 93
V HPLD L E+E AV I + + E+T +
Sbjct: 12 VSHPLDPLTAAEIEAAVAILRAEGLLGESTRFVSIE 47
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 27.5 bits (61), Expect = 1.3
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 29 AKELGNAV-----PKEPVL-FLKPTSSYLGNGGTIEVPHPLDSLHHEVELAVVIGQKARD 82
A ++GN V P E + + S +LGN + L+ + +E + IG+ D
Sbjct: 533 ADKIGNFVKERGPPLELLSKLRQEGSEFLGNASSRAALDELEIMFKALEKSKAIGKIVFD 592
Query: 83 VPETTAMDYVGGFIF 97
+ +DY G I+
Sbjct: 593 LSLARGLDYYTGVIY 607
>gnl|CDD|217136 pfam02602, HEM4, Uroporphyrinogen-III synthase HemD. This family
consists of uroporphyrinogen-III synthase HemD
EC:4.2.1.75 also known as Hydroxymethylbilane hydrolyase
(cyclizing) from eukaryotes, bacteria and archaea. This
enzyme catalyzes the reaction: Hydroxymethylbilane <=>
uroporphyrinogen-III + H(2)O. Some members of this
family are multi-functional proteins possessing other
enzyme activities related to porphyrin biosynthesis,
such as hemD from Clostridium josui with pfam00590,
however the aligned region corresponds with the
uroporphyrinogen-III synthase EC:4.2.1.75 activity only.
Uroporphyrinogen-III synthase is the fourth enzyme in
the heme pathway. Mutant forms of the
Uroporphyrinogen-III synthase gene cause congenital
erythropoietic porphyria in humans a recessive inborn
error of metabolism also known as Gunther disease.
Length = 230
Score = 26.2 bits (58), Expect = 3.8
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 12/50 (24%)
Query: 3 TASSAVQKLIQA---------GTKIVAVGRNYAAHAKELG---NAVPKEP 40
T+ S V+ ++ K+ A+G A +ELG + V +EP
Sbjct: 174 TSPSTVRSFLELLPDEGELLKSVKVAAIGPTTAEALRELGLRVDVVAEEP 223
>gnl|CDD|235135 PRK03592, PRK03592, haloalkane dehalogenase; Provisional.
Length = 295
Score = 26.1 bits (58), Expect = 4.3
Identities = 9/15 (60%), Positives = 12/15 (80%), Gaps = 2/15 (13%)
Query: 39 EPVLFL--KPTSSYL 51
+P++FL PTSSYL
Sbjct: 28 DPIVFLHGNPTSSYL 42
>gnl|CDD|153271 cd07307, BAR, The Bin/Amphiphysin/Rvs (BAR) domain, a
dimerization module that binds membranes and detects
membrane curvature. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions
including organelle biogenesis, membrane trafficking or
remodeling, and cell division and migration. Mutations
in BAR containing proteins have been linked to diseases
and their inactivation in cells leads to altered
membrane dynamics. A BAR domain with an additional
N-terminal amphipathic helix (an N-BAR) can drive
membrane curvature. These N-BAR domains are found in
amphiphysins and endophilins, among others. BAR domains
are also frequently found alongside domains that
determine lipid specificity, such as the Pleckstrin
Homology (PH) and Phox Homology (PX) domains which are
present in beta centaurins (ACAPs and ASAPs) and
sorting nexins, respectively. A FES-CIP4 Homology (FCH)
domain together with a coiled coil region is called the
F-BAR domain and is present in Pombe/Cdc15 homology
(PCH) family proteins, which include Fes/Fes tyrosine
kinases, PACSIN or syndapin, CIP4-like proteins, and
srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM
homology Domain (IMD) is found in multi-domain
proteins, such as IRSp53 and MIM, that act as
scaffolding proteins and transducers of a variety of
signaling pathways that link membrane dynamics and the
underlying actin cytoskeleton. BAR domains form dimers
that bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions. The I-BAR domain induces membrane
protrusions in the opposite direction compared to
classical BAR and F-BAR domains, which produce membrane
invaginations. BAR domains that also serve as protein
interaction domains include those of arfaptin and
OPHN1-like proteins, among others, which bind to Rac
and Rho GAP domains, respectively.
Length = 194
Score = 25.9 bits (57), Expect = 4.7
Identities = 9/49 (18%), Positives = 17/49 (34%)
Query: 5 SSAVQKLIQAGTKIVAVGRNYAAHAKELGNAVPKEPVLFLKPTSSYLGN 53
+KL+ + ++ A + +ELG +P L G
Sbjct: 13 IKDTKKLLDSLKELPAAAEKLSEALQELGKELPDLSNTDLGEALEKFGK 61
>gnl|CDD|204184 pfam09265, Cytokin-bind, Cytokinin dehydrogenase 1, FAD and
cytokinin binding. Members of this family adopt an
alpha+beta sandwich structure with an antiparallel
beta-sheet, in a ferredoxin-like fold. They are
predominantly found in plant cytokinin dehydrogenase 1,
where they are capable of binding both FAD and cytokinin
substrates. The substrate displays a 'plug-into-socket'
binding mode that seals the catalytic site and precisely
positions the carbon atom undergoing oxidation in close
contact with the reactive locus of the flavin.
Length = 280
Score = 25.8 bits (57), Expect = 5.1
Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 7/33 (21%)
Query: 84 PETTAMDYVGGFIFVKILLLL-------FSLKD 109
P DYV GF+F+ L+ FS D
Sbjct: 28 PNGGGFDYVEGFVFLNRQGLVNNWRSSFFSPSD 60
>gnl|CDD|187579 cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1
alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like,
atypical (a) SDRs. This subgroup of extended SDR-like
proteins are atypical SDRs. They have a glycine-rich
NAD(P)-binding motif similar to the typical SDRs,
GXXGXXG, and have the YXXXK active site motif (though
not the other residues of the SDR tetrad). Members
identified include NDUFA9 (mitochondrial) and putative
nucleoside-diphosphate-sugar epimerase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif
is often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 273
Score = 25.3 bits (56), Expect = 6.8
Identities = 7/30 (23%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 8 VQKLIQAGTKIVAVGRN--YAAHAKELGNA 35
V +L + G++++ R YA +G+
Sbjct: 17 VNRLAKRGSQVIVPYRCEAYARRLLVMGDL 46
>gnl|CDD|151156 pfam10640, Pox_ATPase-GT, mRNA capping enzyme N-terminal, ATPase
and guanylyltransferase. This domain is the N-terminus
of the large subunit viral mRNA capping enzyme, and
carries both the ATPase and the guanylyltransferase
activities of the enzyme. The guanylyltransferase
enzymatic region runs from residues 242
(leucine)-273(arginine), the core of the acitve site
being the lysine residue at 260. The ATPase activity is
at the very N-terminal part of the domain.
Length = 314
Score = 25.3 bits (56), Expect = 6.8
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 57 IEVPHPLDSLHHEVEL 72
+ P P D +HHEVEL
Sbjct: 1 VPNPDPDDDVHHEVEL 16
>gnl|CDD|179395 PRK02253, PRK02253, deoxyuridine 5'-triphosphate
nucleotidohydrolase; Provisional.
Length = 167
Score = 24.9 bits (55), Expect = 7.8
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 35 AVPKEPVLFLKPTSSYLGNGGTIE 58
+P++ V F P SS L NG T+E
Sbjct: 88 NIPEDHVGFAYPRSSLLRNGCTLE 111
>gnl|CDD|180392 PRK06084, PRK06084, O-acetylhomoserine
aminocarboxypropyltransferase; Validated.
Length = 425
Score = 25.2 bits (55), Expect = 8.0
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 1 MATASSAVQKLIQAGTKIVAVGRNYAAHAKELGNAVPK 38
MA + A+Q + +AG IV+V + Y L + +P+
Sbjct: 83 MAAITYAIQTIAEAGDNIVSVAKLYGGTYNLLAHTLPR 120
>gnl|CDD|218295 pfam04858, TH1, TH1 protein. TH1 is a highly conserved but
uncharacterized metazoan protein. No homologue has been
identified in Caenorhabditis elegans. TH1 binds
specifically to A-Raf kinase.
Length = 582
Score = 25.2 bits (55), Expect = 8.9
Identities = 7/31 (22%), Positives = 9/31 (29%)
Query: 2 ATASSAVQKLIQAGTKIVAVGRNYAAHAKEL 32
+ + LI G V H K L
Sbjct: 86 QMTNLLAEWLIVTGVSPTKVQAMVENHLKTL 116
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.135 0.380
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,513,963
Number of extensions: 479304
Number of successful extensions: 498
Number of sequences better than 10.0: 1
Number of HSP's gapped: 493
Number of HSP's successfully gapped: 34
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)