RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14390
(64 letters)
>gnl|CDD|133454 cd05312, NAD_bind_1_malic_enz, NAD(P) binding domain of malic
enzyme (ME), subgroup 1. Malic enzyme (ME), a member
of the amino acid dehydrogenase (DH)-like domain
family, catalyzes the oxidative decarboxylation of
L-malate to pyruvate in the presence of cations
(typically Mg++ or Mn++) with the concomitant
reduction of cofactor NAD+ or NADP+. ME has been found
in all organisms, and plays important roles in diverse
metabolic pathways such as photosynthesis and
lipogenesis. This enzyme generally forms homotetramers.
The conversion of malate to pyruvate by ME typically
involves oxidation of malate to produce oxaloacetate,
followed by decarboxylation of oxaloacetate to produce
pyruvate and CO2. This subfamily consists of
eukaryotic and bacterial ME. Amino acid DH-like
NAD(P)-binding domains are members of the Rossmann fold
superfamily and include glutamate, leucine, and
phenylalanine DHs, methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+
as a cofactor. The NAD(P)-binding Rossmann fold
superfamily includes a wide variety of protein families
including NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 279
Score = 43.7 bits (104), Expect = 7e-07
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 1 MQTEGSTVQEARDRIWMMDIDGLLAKGR 28
M EG + +EAR +IW++D GLL K R
Sbjct: 48 MVREGLSEEEARKKIWLVDSKGLLTKDR 75
>gnl|CDD|237414 PRK13529, PRK13529, malate dehydrogenase; Provisional.
Length = 563
Score = 42.8 bits (102), Expect = 1e-06
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 1 MQTEGSTVQEARDRIWMMDIDGLLAKGR 28
M EG + +EAR R +M+D GLL
Sbjct: 318 MVREGLSEEEARKRFFMVDRQGLLTDDM 345
>gnl|CDD|133442 cd00762, NAD_bind_malic_enz, NAD(P) binding domain of malic
enzyme. Malic enzyme (ME), a member of the amino acid
dehydrogenase (DH)-like domain family, catalyzes the
oxidative decarboxylation of L-malate to pyruvate in
the presence of cations (typically Mg++ or Mn++) with
the concomitant reduction of cofactor NAD+ or NADP+.
ME has been found in all organisms and plays important
roles in diverse metabolic pathways such as
photosynthesis and lipogenesis. This enzyme generally
forms homotetramers. The conversion of malate to
pyruvate by ME typically involves oxidation of malate
to produce oxaloacetate, followed by decarboxylation of
oxaloacetate to produce pyruvate and CO2. Amino acid
DH-like NAD(P)-binding domains are members of the
Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+
as a cofactor. The NAD(P)-binding Rossmann fold
superfamily includes a wide variety of protein families
including NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 254
Score = 41.4 bits (97), Expect = 4e-06
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 1 MQTEGSTVQEARDRIWMMDIDGLLAKGRVE 30
EG + +EA RIW +D GLL K R E
Sbjct: 48 XVKEGISKEEACKRIWXVDRKGLLVKNRKE 77
>gnl|CDD|217809 pfam03949, Malic_M, Malic enzyme, NAD binding domain.
Length = 255
Score = 40.6 bits (96), Expect = 6e-06
Identities = 15/28 (53%), Positives = 19/28 (67%)
Query: 1 MQTEGSTVQEARDRIWMMDIDGLLAKGR 28
M EG + +EAR IWM+D GLL +GR
Sbjct: 48 MVREGLSEEEARKNIWMVDRKGLLTEGR 75
>gnl|CDD|215594 PLN03129, PLN03129, NADP-dependent malic enzyme; Provisional.
Length = 581
Score = 37.6 bits (88), Expect = 1e-04
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 1 MQTEGSTVQEARDRIWMMDIDGLLAKGRVE 30
+ G + +EAR RIW++D GL+ K R +
Sbjct: 345 SRQTGISEEEARKRIWLVDSKGLVTKSRKD 374
>gnl|CDD|132436 TIGR03395, sphingomy, sphingomyelin phosphodiesterase. Members of
this family are bacterial proteins that act as
sphingomyelin phosphodiesterase (EC 3.1.4.12), also
called sphingomyelinase. Some members of this family
have been shown to act as hemolysins [Cellular
processes, Pathogenesis].
Length = 283
Score = 31.4 bits (71), Expect = 0.015
Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 9 QEARDRIWMMDI---DGLLAKGRVEVVRGNGKYYSLIQELNLNRPAY 52
E +D I +I + +L G + V +G+ +Y+ + + LN++ P Y
Sbjct: 163 NEIQDFIDSKNIPKDETVLIGGDLNVNKGSNEYHDMFKTLNVSEPRY 209
>gnl|CDD|214912 smart00919, Malic_M, Malic enzyme, NAD binding domain. Malic
enzymes (malate oxidoreductases) catalyse the oxidative
decarboxylation of malate to form pyruvate.
Length = 231
Score = 30.8 bits (71), Expect = 0.024
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 12 RDRIWMMDIDGLLAKGR 28
R IW++D GLL KGR
Sbjct: 51 RKNIWLVDSKGLLTKGR 67
>gnl|CDD|183799 PRK12862, PRK12862, malic enzyme; Reviewed.
Length = 763
Score = 30.2 bits (69), Expect = 0.041
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 12 RDRIWMMDIDGLLAKGRVE 30
R+ IW+ DI G++ +GR E
Sbjct: 219 RENIWVTDIKGVVYEGRTE 237
>gnl|CDD|240357 PTZ00317, PTZ00317, NADP-dependent malic enzyme; Provisional.
Length = 559
Score = 29.2 bits (66), Expect = 0.087
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 1 MQTEGSTVQEARDRIWMMDIDGLLAKGR 28
G T +EA +++D GL+ R
Sbjct: 320 AAEYGVTREEALKSFYLVDSKGLVTTTR 347
>gnl|CDD|133028 cd04185, GT_2_like_b, Subfamily of Glycosyltransferase Family GT2
of unknown function. GT-2 includes diverse families of
glycosyltransferases with a common GT-A type structural
fold, which has two tightly associated beta/alpha/beta
domains that tend to form a continuous central sheet of
at least eight beta-strands. These are enzymes that
catalyze the transfer of sugar moieties from activated
donor molecules to specific acceptor molecules, forming
glycosidic bonds. Glycosyltransferases have been
classified into more than 90 distinct sequence based
families.
Length = 202
Score = 26.4 bits (59), Expect = 0.94
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 13 DRIWMMDIDGLLAKG 27
D IW+MD D +
Sbjct: 81 DWIWLMDDDAIPDPD 95
>gnl|CDD|236500 PRK09405, aceE, pyruvate dehydrogenase subunit E1; Reviewed.
Length = 891
Score = 26.3 bits (59), Expect = 1.1
Identities = 10/14 (71%), Positives = 11/14 (78%), Gaps = 3/14 (21%)
Query: 32 VRGNGKYYSLIQEL 45
VRGNGK +IQEL
Sbjct: 271 VRGNGK---IIQEL 281
>gnl|CDD|185266 PRK15368, PRK15368, pathogenicity island chaperone protein SpiC;
Provisional.
Length = 127
Score = 26.1 bits (57), Expect = 1.2
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 10 EARDRIWMMDIDGLLAKGRV 29
E R W+M IDG A+G +
Sbjct: 17 EGNSRSWIMTIDGHPARGEI 36
>gnl|CDD|145308 pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29).
Length = 404
Score = 26.1 bits (58), Expect = 1.3
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 18 MDIDGLLAKGRVEVVRGNGK 37
+DIDG+ G E + NG
Sbjct: 384 IDIDGITKDGTREPIFRNGN 403
>gnl|CDD|235976 PRK07232, PRK07232, bifunctional malic enzyme
oxidoreductase/phosphotransacetylase; Reviewed.
Length = 752
Score = 25.4 bits (57), Expect = 1.9
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 12 RDRIWMMDIDGLLAKGRVE 30
++ I + D G++ KGR E
Sbjct: 211 KENIIVCDSKGVIYKGRTE 229
>gnl|CDD|235660 PRK05976, PRK05976, dihydrolipoamide dehydrogenase; Validated.
Length = 472
Score = 25.6 bits (57), Expect = 1.9
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 20 IDGLLAKGRVEVVRGNGK 37
+ LL KG+++V G G+
Sbjct: 98 VAALLKKGKIDVFHGIGR 115
>gnl|CDD|183798 PRK12861, PRK12861, malic enzyme; Reviewed.
Length = 764
Score = 25.2 bits (55), Expect = 2.2
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 12 RDRIWMMDIDGLLAKGRVEVV 32
+ IW+ DI+G++ +GR ++
Sbjct: 215 VENIWVTDIEGVVYRGRTTLM 235
>gnl|CDD|240453 cd12873, SPRY_DDX1, SPRY domain associated with DEAD box gene
DDX1. This SPRY domain is associated with the DEAD box
gene, DDX1, an RNA-dependent ATPase involved in HIV-1
Rev function and virus replication. It is suggested
that DDX1 acts as a cellular cofactor by promoting
oligomerization of Rev on the Rev response element
(RRE). DDX1 RNA is overexpressed in breast cancer, data
showing a strong and independent association between
poor prognosis and deregulation of the DEAD box protein
DDX1, thus potentially serving as an effective
prognostic biomarker for early recurrence in primary
breast cancer. DDX1 also interacts with RelA and
enhances nuclear factor kappaB-mediated transcription.
DEAD-box proteins are associated with all levels of RNA
metabolism and function, and have been implicated in
translation initiation, transcription, RNA splicing,
ribosome assembly, RNA transport, and RNA decay.
Length = 155
Score = 25.2 bits (56), Expect = 2.2
Identities = 14/41 (34%), Positives = 17/41 (41%), Gaps = 10/41 (24%)
Query: 9 QEARDRIWMMDIDGLLAKGRVEV----------VRGNGKYY 39
RD + DGLL + R E V+G GKYY
Sbjct: 3 PYDRDAALAISPDGLLCQSREEKGWQGCRATKGVKGKGKYY 43
>gnl|CDD|221676 pfam12632, Vezatin, Mysoin-binding motif of peroxisomes. Vezatin
is a peroxisome transmembrane receptor that is involved
in membrane-membrane and cell-cell adhesions. In the
movement of peroxisomes it binds to class V and class
VIIa myosins to guide the organelle through the
microtubules and allow pathogens to internalise
themselves into host cells. Vezatin is crucial for
spermatozoan production. In mouse cells it interacts
with the cadherin-catenin complex bridging it to the
C-terminal FERM domain of myosin VIIA.
Length = 246
Score = 25.1 bits (55), Expect = 2.3
Identities = 7/17 (41%), Positives = 8/17 (47%)
Query: 37 KYYSLIQELNLNRPAYL 53
K LIQE+ L Y
Sbjct: 73 KALILIQEVELVSRGYR 89
>gnl|CDD|224789 COG1877, OtsB, Trehalose-6-phosphatase [Carbohydrate transport
and metabolism].
Length = 266
Score = 25.0 bits (55), Expect = 2.5
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 2/47 (4%)
Query: 1 MQTEGSTVQEARDRIWMMDIDGLLAKG--RVEVVRGNGKYYSLIQEL 45
AR R+ +D DG L + E + + SL+Q+L
Sbjct: 6 SNQLLEPYLNARKRLLFLDYDGTLTEIVPHPEAAVPDDRLLSLLQDL 52
>gnl|CDD|223358 COG0281, SfcA, Malic enzyme [Energy production and conversion].
Length = 432
Score = 25.2 bits (56), Expect = 2.6
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 11 ARDRIWMMDIDGLLAKGR 28
+ I+++D GLL GR
Sbjct: 224 KEENIFVVDRKGLLYDGR 241
>gnl|CDD|235092 PRK02963, PRK02963, carbon starvation induced protein; Validated.
Length = 316
Score = 25.0 bits (55), Expect = 2.7
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 1 MQTEGSTVQEARDRIWMMDID 21
+ +G+ V+E D + MM ID
Sbjct: 153 LHNDGTYVEEITDYVLMMKID 173
>gnl|CDD|185695 cd01081, Aldose_epim, aldose 1-epimerase superfamily. Aldose
1-epimerases or mutarotases are key enzymes of
carbohydrate metabolism; they catalyze the
interconversion of the alpha- and beta-anomers of
hexose sugars such as glucose and galactose. This
interconversion is an important step that allows anomer
specific metabolic conversion of sugars. Studies of the
catalytic mechanism of the best known member of the
family, galactose mutarotase, have shown a glutamate
and a histidine residue to be critical for catalysis;
the glutamate serves as the active site base to
initiate the reaction by removing the proton from the
C-1 hydroxyl group of the sugar substrate and the
histidine as the active site acid to protonate the C-5
ring oxygen.
Length = 284
Score = 24.7 bits (54), Expect = 3.1
Identities = 9/44 (20%), Positives = 14/44 (31%)
Query: 18 MDIDGLLAKGRVEVVRGNGKYYSLIQELNLNRPAYLAWLVARLP 61
+I L KG V+++ G A L R+
Sbjct: 10 ANIISLKVKGDVDLLWGYPDAEEYPLAPTGGGGAILFPFANRIS 53
>gnl|CDD|216542 pfam01512, Complex1_51K, Respiratory-chain NADH dehydrogenase 51 Kd
subunit.
Length = 150
Score = 24.7 bits (55), Expect = 3.4
Identities = 12/31 (38%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 20 IDGLLAKGRVEVVRGNGKY-----YSLIQEL 45
I A G +EVV GKY +LI L
Sbjct: 91 IAEAPAAGDIEVVLLPGKYPCGEEKALIYSL 121
>gnl|CDD|149877 pfam08943, CsiD, CsiD. This family consists of various bacterial
proteins pertaining to the non-haem Fe(II)-dependent
oxygenase family. Exact function is unknown, but a
putative role includes involvement in the control of
utilisation of gamma-aminobutyric acid.
Length = 297
Score = 24.6 bits (54), Expect = 3.4
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 1 MQTEGSTVQEARDRIWMMDID 21
+ +G+ V+E D + MM ID
Sbjct: 140 LHNDGTYVEEITDWVLMMKID 160
>gnl|CDD|240436 PTZ00486, PTZ00486, apyrase Superfamily; Provisional.
Length = 352
Score = 24.6 bits (54), Expect = 3.5
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 12 RDRIWMMDIDGLLAKGRVEVVRGNGKYYSLIQELNLNRPAYL 53
R+ +++ ID G+VEVV + Y S+ L ++ P Y+
Sbjct: 195 RNPMYIKKIDK---NGKVEVVNWSNVYNSIRNALGISYPGYI 233
>gnl|CDD|216713 pfam01804, Penicil_amidase, Penicillin amidase. Penicillin
amidase or penicillin acylase EC:3.5.1.11 catalyzes the
hydrolysis of benzylpenicillin to phenylacetic acid and
6-aminopenicillanic acid (6-APA) a key intermediate in
the the synthesis of penicillins. Also in the family
are cephalosporin acylase and aculeacin A acylase,
which are involved in the synthesis of related peptide
antibiotics.
Length = 668
Score = 24.7 bits (54), Expect = 4.2
Identities = 5/20 (25%), Positives = 14/20 (70%)
Query: 10 EARDRIWMMDIDGLLAKGRV 29
+A+DR++ +++ A+G +
Sbjct: 30 QAQDRLFQLELLRRTARGEL 49
>gnl|CDD|238575 cd01170, THZ_kinase, 4-methyl-5-beta-hydroxyethylthiazole (Thz)
kinase catalyzes the phosphorylation of the
hydroxylgroup of Thz. A reaction that allows cells to
recycle Thz into the thiamine biosynthesis pathway, as
an alternative to its synthesis from cysteine, tyrosine
and 1-deoxy-D-xylulose-5-phosphate.
Length = 242
Score = 24.4 bits (54), Expect = 4.5
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 20 IDGLLAKGRVEVVRGN 35
LLA+G+ V+RGN
Sbjct: 99 AKELLAEGQPTVIRGN 114
>gnl|CDD|235798 PRK06416, PRK06416, dihydrolipoamide dehydrogenase; Reviewed.
Length = 462
Score = 24.3 bits (54), Expect = 5.1
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 22 GLLAKGRVEVVRGNGKY 38
GLL K +V+++RG K
Sbjct: 100 GLLKKNKVDIIRGEAKL 116
>gnl|CDD|218344 pfam04951, Peptidase_M55, D-aminopeptidase. Bacillus subtilis
DppA is a binuclear zinc-dependent, D-specific
aminopeptidase. The structure reveals that DppA is a
new example of a 'self-compartmentalising protease', a
family of proteolytic complexes. Proteasomes are the
most extensively studied representatives of this
family. The DppA enzyme is composed of identical 30 kDa
subunits organised in a decamer with 52 point-group
symmetry. A 20 A wide channel runs through the complex,
giving access to a central chamber holding the active
sites. The structure shows DppA to be a prototype of a
new family of metalloaminopeptidases characterized by
the SXDXEG key sequence. The only known substrates are
D-ala-D-ala and D-ala-gly-gly.
Length = 265
Score = 24.0 bits (53), Expect = 6.2
Identities = 13/73 (17%), Positives = 23/73 (31%), Gaps = 28/73 (38%)
Query: 2 QTEGSTVQEARDRIWMMD-----IDGLLAKG-----------------------RVEVVR 33
Q + + R R M + I+G A G R ++
Sbjct: 20 QVDPGNPEYERARKLMTEEVNAAIEGAFAGGATEVVVNDSHGGMRNLLPEELDPRARLIS 79
Query: 34 GNGKYYSLIQELN 46
G + S++Q L+
Sbjct: 80 GKPRPLSMMQGLD 92
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 0.137 0.422
Gapped
Lambda K H
0.267 0.0886 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,301,583
Number of extensions: 238891
Number of successful extensions: 269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 269
Number of HSP's successfully gapped: 31
Length of query: 64
Length of database: 10,937,602
Length adjustment: 35
Effective length of query: 29
Effective length of database: 9,385,212
Effective search space: 272171148
Effective search space used: 272171148
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 (23.9 bits)