RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7218
(93 letters)
>gnl|CDD|205516 pfam13336, AcetylCoA_hyd_C, Acetyl-CoA hydrolase/transferase
C-terminal domain. This family contains several enzymes
which take part in pathways involving acetyl-CoA.
Acetyl-CoA hydrolase EC:3.1.2.1 catalyzes the formation
of acetate from acetyl-CoA, CoA transferase (CAT1)
EC:2.8.3.- produces succinyl-CoA, and acetate-CoA
transferase EC:2.8.3.8 utilises acyl-CoA and acetate to
form acetyl-CoA.
Length = 152
Score = 94.4 bits (236), Expect = 2e-26
Identities = 30/49 (61%), Positives = 36/49 (73%)
Query: 33 GAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEK 81
GA V T R V YVVTE+GIA L GK+LR+RA ALI+IA PD R+ L +
Sbjct: 104 GAHVTTPRHDVDYVVTEYGIADLRGKSLRERARALISIAHPDFRDELLE 152
>gnl|CDD|223504 COG0427, ACH1, Acetyl-CoA hydrolase [Energy production and
conversion].
Length = 501
Score = 64.7 bits (158), Expect = 8e-14
Identities = 25/50 (50%), Positives = 32/50 (64%)
Query: 34 AGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEKAA 83
+ V TR V VVTE+GIA L G + R+RA A+I A PD+R LE+ A
Sbjct: 416 SHVDHTRHDVDVVVTEYGIADLRGLSPRERAAAIIECAHPDYRPWLEEYA 465
>gnl|CDD|188463 TIGR03948, butyr_acet_CoA, butyryl-CoA:acetate CoA-transferase.
This enzyme represents one of at least two mechanisms
for reclaiming CoA from butyryl-CoA at the end of
butyrate biosynthesis (an important process performed by
some colonic bacteria), namely transfer of CoA to
acetate. An alternate mechanism transfers the butyrate
onto inorganic phosphate, after which butyrate kinase
transfers the phosphate onto ADP, creating ATP [Energy
metabolism, Fermentation].
Length = 445
Score = 58.3 bits (141), Expect = 1e-11
Identities = 27/51 (52%), Positives = 34/51 (66%)
Query: 33 GAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEKAA 83
G+ V TRA+ HYVVTE+G L G + Q+A ALI+IA PD R+ L K A
Sbjct: 384 GSIVTDTRANTHYVVTEYGKVNLKGLSTWQKAEALISIAHPDFRDELIKEA 434
>gnl|CDD|234217 TIGR03458, YgfH_subfam, succinate CoA transferase. This family of
CoA transferases includes enzymes catalyzing at least
two related but distinct activities. The E. coli YgfH
protein has been characterized as a
propionyl-CoA:succinate CoA transferase where it appears
to be involved in a pathway for the decarboxylation of
succinate to propionate. The Clostridium kluyveri CAT1
protein has been characterized as a acetyl-CoA:succinate
CoA transferase and is believed to be involved in
anaerobic succinate degradation. The
propionate:succinate transferase activity has been
reported in the propionic acid fermentation of
propionibacterium species where it is distinct from the
coupled activities of distinct nucleotide-triphosphate
dependent succinate and propionate/acetate CoA
transferases (as inferred from activity in the absence
of NTPs). The family represented by this model includes
a member from Propionibacterium acnes KPA171202 which is
likely to be responsible for this activity. A closely
related clade not included in this family are the Ach1p
proteins of fungi which are acetyl-CoA hydrolases. This
name has been applied to many of the proteins modeled by
This model, possibly erroneously.
Length = 485
Score = 42.6 bits (101), Expect = 4e-06
Identities = 21/45 (46%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 43 VHYVVTEHGIAFLFGKTLRQRAHALI-NIAPPDHREALEKAAFER 86
V +VTE G+A L G + R+RA A+I N A PD+R+ L +ER
Sbjct: 415 VMVIVTEQGLADLRGLSPRERARAIIDNCAHPDYRDLLR-DYYER 458
>gnl|CDD|218121 pfam04512, Baculo_PEP_N, Baculovirus polyhedron envelope protein,
PEP, N terminus. Polyhedra are large crystalline
occlusion bodies containing nucleopolyhedrovirus
virions, and surrounded by an electron-dense structure
called the polyhedron envelope or polyhedron calyx. The
polyhedron envelope (associated) protein PEP is thought
to be an integral part of the polyhedron envelope. PEP
is concentrated at the surface of polyhedra, and is
thought to be important for the proper formation of the
periphery of polyhedra. It is thought that PEP may
stabilise polyhedra and protect them from fusion or
aggregation.
Length = 100
Score = 28.0 bits (63), Expect = 0.38
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 45 YVVTEHGIAFLFGKTLRQRAHALINI 70
VT G+ L +T +RA AL I
Sbjct: 59 LFVTALGVGLLCSRTQSERADALATI 84
>gnl|CDD|182907 PRK11023, PRK11023, outer membrane lipoprotein; Provisional.
Length = 191
Score = 28.1 bits (63), Expect = 0.48
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 46 VVTEHGIAFLFGKTLRQRAHALINIA 71
V TE+G FL G ++ A A +IA
Sbjct: 149 VTTENGEVFLLGLVTQREAKAAADIA 174
>gnl|CDD|224414 COG1497, COG1497, Predicted transcriptional regulator
[Transcription].
Length = 260
Score = 26.9 bits (60), Expect = 1.6
Identities = 11/60 (18%), Positives = 23/60 (38%)
Query: 29 RQLLGAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEKAAFERLK 88
++L+ G++ Y +T+ G +L + R + D+ A E +K
Sbjct: 47 KELVKEGLIEKEGRGEYEITKKGAEWLLEQLSDLRRFSEEVELVLDYVMVWTAIAKEDIK 106
>gnl|CDD|182874 PRK10972, PRK10972, Z-ring-associated protein; Provisional.
Length = 109
Score = 26.0 bits (57), Expect = 2.5
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 7/31 (22%)
Query: 55 LFGKTLRQRAHALINIAPPDHREALEKAAFE 85
+FG++LR +N PP+ R+AL +AA +
Sbjct: 10 IFGRSLR------VN-CPPEQRDALNQAAED 33
>gnl|CDD|241174 cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM1 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function
in RNA packaging, stabilization of RNA secondary
structure, or other macromolecular interactions. GRSF-1
contains three potential RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 79
Score = 25.2 bits (55), Expect = 3.0
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 49 EHGIAFLFGKTLRQRAHALINIAPPDHREALEKAAFERLKVM 90
E+G+ FL + + R ALI + + E ++KA + M
Sbjct: 31 ENGVHFLLNRDGKPRGDALIEL---ESEEDVQKALEQHRHYM 69
>gnl|CDD|198371 cd07803, FGGY_D-XK, D-xylulose kinases; a subgroup of the FGGY
family of carbohydrate kinases. This subfamily is
predominantly composed of bacterial D-xylulose kinases
(XK, also known as xylulokinase; EC 2.7.1.17), which
catalyze the rate-limiting step in the ATP-dependent
phosphorylation of D-xylulose to produce D-xylulose
5-phosphate (X5P) and ADP. Some uncharacterized
sequences are also included in this subfamily. The
prototypical member of this subfamily is Escherichia
coli xylulokinase (EcXK), which exists as a dimer. Each
monomer consists of two large domains separated by an
open cleft that forms an active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. XKs do not have any known allosteric
regulators, and they may have weak but significant
activity in the absence of substrate. The presence of
Mg2+ or Mn2+ is required for catalytic activity. Members
of this subfamily belong to the FGGY family of
carbohydrate kinases.
Length = 482
Score = 25.8 bits (57), Expect = 4.0
Identities = 18/74 (24%), Positives = 26/74 (35%), Gaps = 14/74 (18%)
Query: 9 PLCFFPFQVLFQASDSGRPDRQL----LGAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRA 64
L F P+ + D G + TR H+ V E G+AF +LR
Sbjct: 332 GLLFLPY---LNGERTPYNDPNARGAFFGLTLSHTRGHLARAVLE-GVAF----SLRDCL 383
Query: 65 HAL--INIAPPDHR 76
L + AP +
Sbjct: 384 EVLHGMGTAPQRIK 397
>gnl|CDD|107388 cd06393, PBP1_iGluR_Kainate_GluR5_7, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR5-7 subunits of Kainate receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR5-7 subunits of Kainate
receptor. While this N-terminal domain belongs to the
periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. There are five types of
kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2,
which are structurally similar to AMPA and NMDA subunits
of ionotropic glutamate receptors. KA1 and KA2 subunits
can only form functional receptors with one of the
GluR5-7 subunits. Moreover, GluR5-7 can also form
functional homomeric receptor channels activated by
kainate and glutamate when expressed in heterologous
systems. Kainate receptors are involved in excitatory
neurotransmission by activating postsynaptic receptors
and in inhibitory neurotransmission by modulating
release of the inhibitory neurotransmitter GABA through
a presynaptic mechanism. Kainate receptors are closely
related to AMAP receptors. In contrast of AMPA
receptors, kainate receptors play only a minor role in
signaling at synapses and their function is not well
defined.
Length = 384
Score = 25.8 bits (56), Expect = 4.2
Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 15/87 (17%)
Query: 15 FQVLFQASDSGRPD--RQLLGAGVVTTRAHVHYVVTEHGIAFLFGKTLRQRAHA------ 66
F+++F S +Q + G++T H + + L+ L ++
Sbjct: 194 FRIIFDCSHQMAAQILKQAMAMGMMTEYYHFIFTTLD-----LYALDLEPYRYSGVNLTG 248
Query: 67 --LINIAPPDHREALEKAAFERLKVMP 91
++N+ P +EK + ERL+ P
Sbjct: 249 FRILNVDNPHVSSIVEKWSMERLQAAP 275
>gnl|CDD|220674 pfam10282, Lactonase, Lactonase, 7-bladed beta-propeller. This
entry contains bacterial 6-phosphogluconolactonases
(6PGL)YbhE-type (EC:3.1.1.31) which hydrolyse
6-phosphogluconolactone to 6-phosphogluconate. The entry
also contains the fungal muconate lactonising enzyme
carboxy-cis,cis-muconate cyclase (EC:5.5.1.5) and
muconate cycloisomerase (EC:5.5.1.1), which convert
cis,cis-muconates to muconolactones and vice versa as
part of the microbial beta-ketoadipate pathway.
Structures of proteins in this family have revealed a
7-bladed beta-propeller fold.
Length = 344
Score = 25.6 bits (57), Expect = 4.6
Identities = 9/33 (27%), Positives = 11/33 (33%), Gaps = 8/33 (24%)
Query: 16 QVLFQASDSGRPDRQLLGAGVVTTRAHVHYVVT 48
QV+ P+RQ H H VV
Sbjct: 126 QVVQHEGSGPNPERQ--------EGPHAHSVVL 150
>gnl|CDD|219308 pfam07146, DUF1389, Protein of unknown function (DUF1389). This
family consists of several hypothetical bacterial
proteins which seem to be specific to Chlamydia
pneumoniae. Members of this family are typically around
400 residues in length. The function of this family is
unknown.
Length = 311
Score = 25.4 bits (56), Expect = 4.9
Identities = 13/55 (23%), Positives = 20/55 (36%), Gaps = 11/55 (20%)
Query: 43 VHYVVTEHGIAFLFGKTLRQRAHALINIA--------PPDHREALEKAAFERLKV 89
+ V + + + LR L NI+ P RE LE +RL+
Sbjct: 53 IFDFVVKQNLTI---QELRLLIDGLRNISSSKSLNNLSPKLREKLEDFGIDRLQS 104
>gnl|CDD|225379 COG2823, OsmY, Predicted periplasmic or secreted lipoprotein
[General function prediction only].
Length = 196
Score = 25.4 bits (56), Expect = 5.3
Identities = 7/23 (30%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 46 VVTEHGIAFLFG--KTLRQRAHA 66
V TE+G +L G + + A
Sbjct: 153 VETENGEVYLSGLVDSQEEAERA 175
>gnl|CDD|225593 COG3051, CitF, Citrate lyase, alpha subunit [Energy production and
conversion].
Length = 513
Score = 25.1 bits (55), Expect = 6.5
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 14/47 (29%)
Query: 36 VVTTRAHVHYVVTEHGIAFLFGKTLRQRAHALINIAPPDHREALEKA 82
V+T + V +VT+HGIA +N A PD E L +A
Sbjct: 431 VITPGSSVDVLVTDHGIA--------------VNPARPDLAERLSEA 463
>gnl|CDD|184638 PRK14345, PRK14345, lipoate-protein ligase B; Provisional.
Length = 234
Score = 24.9 bits (55), Expect = 7.0
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 22 SDSGRPDRQLLGAGVVTTRAHVHYVVTEHGIAF 54
+D GRPDR++ G+ +R VT HG A
Sbjct: 138 ADGGRPDRKIAAIGIRVSRG-----VTMHGFAL 165
>gnl|CDD|233274 TIGR01110, mdcA, malonate decarboxylase, alpha subunit. This model
describes malonate decarboxylase alpha subunit, from
both the water-soluble form as found in Klebsiella
pneumoniae and the form couple to sodium ion pumping in
Malonomonas rubra. Malonate decarboxylase Na+ pump is
the paradigm of the family of Na+ transport
decarboxylases. Essentially, it couples the energy
derived from decarboxylation of a carboxylic acid
substrate to move Na+ ion across the bilayer. Functional
malonate decarboylase is a multi subunit protein. The
alpha subunit enzymatically performs the transfer of
malonate (substrate) to an acyl carrier protein subunit
for subsequent decarboxylation, hence the name:
acetyl-S-acyl carrier protein:malonate carrier
protein-SH transferase [Transport and binding proteins,
Cations and iron carrying compounds, Energy metabolism,
Other].
Length = 543
Score = 25.2 bits (55), Expect = 7.3
Identities = 12/30 (40%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 43 VHYVVTEHGIAFLF-GKTLRQRAHALINIA 71
V ++VTE GIA+L+ ++L +R A+ +A
Sbjct: 448 VTHIVTEEGIAYLYKCRSLEERMQAIRGVA 477
>gnl|CDD|218689 pfam05681, Fumerase, Fumarate hydratase (Fumerase). This family
consists of several bacterial fumarate hydratase
proteins FumA and FumB. Fumarase, or fumarate hydratase
(EC 4.2.1.2), is a component of the citric acid cycle.
In facultative anaerobes such as Escherichia coli,
fumarase also engages in the reductive pathway from
oxaloacetate to succinate during anaerobic growth.
Three fumarases, FumA, FumB, and FumC, have been
reported in E. coli. fumA and fumB genes are homologous
and encode products of identical sizes which form
thermolabile dimers of Mr 120,000. FumA and FumB are
class I enzymes and are members of the iron-dependent
hydrolases, which include aconitase and malate
hydratase. The active FumA contains a 4Fe-4S centre,
and it can be inactivated upon oxidation to give a
3Fe-4S centre.
Length = 271
Score = 24.7 bits (55), Expect = 8.1
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 64 AHALINIA---PPDHREALEKAA 83
A A+I + PPD AL++A
Sbjct: 6 AEAIIEASTYLPPDVLAALKRAL 28
>gnl|CDD|181078 PRK07678, PRK07678, aminotransferase; Validated.
Length = 451
Score = 25.0 bits (55), Expect = 8.1
Identities = 7/16 (43%), Positives = 12/16 (75%)
Query: 76 REALEKAAFERLKVMP 91
R+ L +AA+E+LK +
Sbjct: 65 RKELAEAAYEQLKTLS 80
>gnl|CDD|224732 COG1819, COG1819, Glycosyl transferases, related to
UDP-glucuronosyltransferase [Carbohydrate transport and
metabolism / Signal transduction mechanisms].
Length = 406
Score = 24.7 bits (54), Expect = 8.7
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 57 GKTLRQRAHALINIAPPDHREALEKA 82
GK LR+R H ++ + +E +E A
Sbjct: 22 GKELRRRGHEVVFASTGKFKEFVEAA 47
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
0.329 0.139 0.432
Gapped
Lambda K H
0.267 0.0667 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,846,288
Number of extensions: 409956
Number of successful extensions: 546
Number of sequences better than 10.0: 1
Number of HSP's gapped: 546
Number of HSP's successfully gapped: 29
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.3 bits)