RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1675
(179 letters)
>gnl|CDD|215594 PLN03129, PLN03129, NADP-dependent malic enzyme; Provisional.
Length = 581
Score = 156 bits (398), Expect = 2e-45
Identities = 47/77 (61%), Positives = 60/77 (77%)
Query: 41 MGIPVGKLSLYTALAGIKPHQCLPITLDVGTNTQQLLDDPLYIGLRQRRTTGQAYDDFIE 100
MGIPVGKL LYTA GI+P LP+ +DVGTN ++LL+DP YIGLRQ R TG+ YD+ ++
Sbjct: 194 MGIPVGKLDLYTAAGGIRPSAVLPVCIDVGTNNEKLLNDPFYIGLRQPRLTGEEYDELVD 253
Query: 101 EFMQAVVARYGQHVLIQ 117
EFM+AV R+G VL+Q
Sbjct: 254 EFMEAVKQRWGPKVLVQ 270
Score = 51.5 bits (124), Expect = 4e-08
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 118 TLSDLVTEADLDSGCLYPPPNIIKDCSLKIAAKLVEQAFKDGTATKVGT 166
L+ VTE +L G +YPP + I+D S +AA + +A+++G AT++
Sbjct: 512 ALAAQVTEEELAKGAIYPPFSRIRDISAHVAAAVAAKAYEEGLATRLPR 560
>gnl|CDD|237414 PRK13529, PRK13529, malate dehydrogenase; Provisional.
Length = 563
Score = 140 bits (356), Expect = 1e-39
Identities = 45/77 (58%), Positives = 59/77 (76%), Gaps = 1/77 (1%)
Query: 41 MGIPVGKLSLYTALAGIKPHQCLPITLDVGTNTQQLLDDPLYIGLRQRRTTGQAYDDFIE 100
MGIP+GKLSLYTA GI P + LP+ LDVGTN +QLL+DPLY+G R R G+ YD+F++
Sbjct: 169 MGIPIGKLSLYTACGGIDPARTLPVVLDVGTNNEQLLNDPLYLGWRHPRIRGEEYDEFVD 228
Query: 101 EFMQAVVARYGQHVLIQ 117
EF+QAV R+ + L+Q
Sbjct: 229 EFVQAVKRRF-PNALLQ 244
Score = 44.7 bits (107), Expect = 7e-06
Identities = 17/58 (29%), Positives = 27/58 (46%)
Query: 117 QTLSDLVTEADLDSGCLYPPPNIIKDCSLKIAAKLVEQAFKDGTATKVGTATLFRLIK 174
L+D V A G L PP I++ S IA + + A ++G A + L + I+
Sbjct: 492 HALADCVPLAKPGEGALLPPVEDIREVSRAIAIAVAKAAIEEGLARETSDEDLEQAIE 549
>gnl|CDD|215894 pfam00390, malic, Malic enzyme, N-terminal domain.
Length = 182
Score = 131 bits (332), Expect = 3e-39
Identities = 43/78 (55%), Positives = 57/78 (73%)
Query: 40 SMGIPVGKLSLYTALAGIKPHQCLPITLDVGTNTQQLLDDPLYIGLRQRRTTGQAYDDFI 99
M I GKL+LYTA AGI P + LPI LDVGTN ++LL+DPLY+GLR +R G+ YD+F+
Sbjct: 88 GMPIMEGKLALYTAFAGIDPSRVLPIVLDVGTNNEKLLNDPLYLGLRHKRVRGEEYDEFV 147
Query: 100 EEFMQAVVARYGQHVLIQ 117
+EF++AV A + IQ
Sbjct: 148 DEFVEAVKALFPPFGGIQ 165
>gnl|CDD|240357 PTZ00317, PTZ00317, NADP-dependent malic enzyme; Provisional.
Length = 559
Score = 111 bits (279), Expect = 7e-29
Identities = 42/90 (46%), Positives = 61/90 (67%), Gaps = 8/90 (8%)
Query: 28 DVGTNTQGFSKPSMGIPVGKLSLYTALAGIKPHQCLPITLDVGTNTQQLLDDPLYIGLRQ 87
D+G N MGI +GKLSLY A GI P + LP+ LDVGTN ++LL+DPLY+GLR+
Sbjct: 165 DLGAN-------GMGISIGKLSLYVAGGGINPSRVLPVVLDVGTNNEKLLNDPLYLGLRE 217
Query: 88 RRTTGQAYDDFIEEFMQAVVARYGQHVLIQ 117
+R Y + ++EFM+AV +R+ + ++Q
Sbjct: 218 KRLDDDEYYELLDEFMEAVSSRW-PNAVVQ 246
Score = 44.2 bits (105), Expect = 1e-05
Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 112 QHVLI---QTLSDLVTEADLDSGCLYPPPNIIKDCSLKIAAKLVEQAFKDGTATK 163
+LI +L+ LV+E DL G LYPP I++ S IA ++E+A + G A
Sbjct: 483 DEMLIAAAASLATLVSEEDLREGKLYPPLEDIREISAHIAVDVIEEAQEMGIAKN 537
>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 = 55.2 bits (134), Expect = 1e-09
Identities = 18/46 (39%), Positives = 31/46 (67%)
Query: 117 QTLSDLVTEADLDSGCLYPPPNIIKDCSLKIAAKLVEQAFKDGTAT 162
+ L+ LVT+ +L G LYPP + I++ S +IA + + A+++G AT
Sbjct: 215 EALASLVTDEELARGRLYPPLSNIREISAQIAVAVAKYAYEEGLAT 260
>gnl|CDD|223358 COG0281, SfcA, Malic enzyme [Energy production and conversion].
Length = 432
Score = 44.9 bits (107), Expect = 7e-06
Identities = 16/33 (48%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 40 SMGIPVGKLSLYTALAGIKPHQCLPITLDVGTN 72
+ GK L+ A AGI LPI LDVGTN
Sbjct: 99 GKPVMEGKAVLFKAFAGID---VLPIELDVGTN 128
Score = 43.7 bits (104), Expect = 2e-05
Identities = 16/32 (50%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 1 MGIPVGKLSLYTALAGIKPHQCLPITLDVGTN 32
+ GK L+ A AGI LPI LDVGTN
Sbjct: 100 KPVMEGKAVLFKAFAGID---VLPIELDVGTN 128
Score = 26.4 bits (59), Expect = 9.6
Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 118 TLSDLVTEADLDSGCLYPPPNIIKDCSLKIAAKLVEQAFKDGTATK 163
++DL E L+ + PPP + S ++A + + A ++G A +
Sbjct: 364 AIADLAREEVLE-EYIIPPPFDPRVIS-RVAVAVAKAAMEEGVARR 407
>gnl|CDD|217809 pfam03949, Malic_M, Malic enzyme, NAD binding domain.
Length = 255
Score = 37.5 bits (88), Expect = 0.002
Identities = 13/39 (33%), Positives = 24/39 (61%)
Query: 117 QTLSDLVTEADLDSGCLYPPPNIIKDCSLKIAAKLVEQA 155
+ L++LVTE +L G + PP I++ S ++A + + A
Sbjct: 216 EALAELVTEEELGEGYIIPPLFDIREVSPRVAVAVAKAA 254
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.4 bits (68), Expect = 0.62
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 35 GFSKPSM--GIP-VGKLSLYTALAGIKPHQCLPITL 67
KP + G P VGK SL TALA + + I L
Sbjct: 1541 QVGKPILLEGSPGVGKTSLITALARKTGKKLIRINL 1576
Score = 28.8 bits (64), Expect = 2.2
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 5 VGKLSLYTALAGIKPHQCLPITL 27
VGK SL TALA + + I L
Sbjct: 1554 VGKTSLITALARKTGKKLIRINL 1576
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 29.6 bits (67), Expect = 1.1
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 17/68 (25%)
Query: 110 YGQHVLIQTLSDLVTEADLDSG---CLYPPPNI-------IKDCSLKIAAKL-------V 152
G+ VLI + + + EA + SG C+ PP + IKD KIA +L +
Sbjct: 764 DGEEVLIPGIMEHIEEAGVHSGDSTCVLPPQTLSAEIVDRIKDIVRKIAKELNVKGLMNI 823
Query: 153 EQAFKDGT 160
+ A KDG
Sbjct: 824 QFAVKDGE 831
>gnl|CDD|115787 pfam07156, Prenylcys_lyase, Prenylcysteine lyase. This family
contains prenylcysteine lyases (EC:1.8.3.5) that are
approximately 500 residues long. Prenylcysteine lyase is
a FAD-dependent thioether oxidase that degrades a
variety of prenylcysteines, producing free cysteine, an
isoprenoid aldehyde and hydrogen peroxide as products of
the reaction. It has been noted that this enzyme has
considerable homology with ClP55, a 55 kDa protein that
is associated with chloride ion pumps.
Length = 368
Score = 28.7 bits (64), Expect = 1.5
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 98 FIEEFMQAVV-ARYGQHVLIQTLSDLVTEADLDSG 131
F+ E + AV+ A YGQ I + V+ A D G
Sbjct: 85 FLNEMVAAVLRANYGQSTDINAFAGAVSLAGADGG 119
>gnl|CDD|182646 PRK10683, PRK10683, putrescine transporter subunit: membrane
component of ABC superfamily; Provisional.
Length = 317
Score = 28.5 bits (64), Expect = 1.8
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 63 LPITLDVGTNTQQLLDDPLYI 83
L ITL++G N QL DDPLY
Sbjct: 77 LSITLNLG-NFLQLTDDPLYF 96
>gnl|CDD|224450 COG1533, SplB, DNA repair photolyase [DNA replication,
recombination, and repair].
Length = 297
Score = 28.1 bits (63), Expect = 2.2
Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 15/66 (22%)
Query: 64 PITLDVGTNTQQLLDDPLYIGLRQRRTTGQAYDDFIEEFMQAVVARYGQHVLIQTLSDLV 123
+ + + T DP ++ R T + I E + +YG V I T S LV
Sbjct: 83 RTVIAISSVT-----DPYQPIEKEYRLTRK-----ILEIL----LKYGFPVSIVTKSALV 128
Query: 124 TEADLD 129
DLD
Sbjct: 129 LR-DLD 133
>gnl|CDD|182090 PRK09813, PRK09813, fructoselysine 6-kinase; Provisional.
Length = 260
Score = 27.4 bits (61), Expect = 3.7
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 77 LDDPLYIGLRQRRTTGQAY----DDFIEEFMQAVVARYGQHVLIQTLSD 121
D PL+ L A D+F+ M+A+VAR G V+I TL +
Sbjct: 147 WDSPLWQTLVPHLDYAFASAPQEDEFLRLKMKAIVAR-GAGVVIVTLGE 194
>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 = 27.2 bits (60), Expect = 4.5
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 123 VTEADLDSGCLYPPPNIIKDCSLKIAAKLVEQA 155
VTE L G LYPP I++ SL IA + + A
Sbjct: 222 VTEESLKPGRLYPPLFDIQEVSLNIAVAVAKYA 254
>gnl|CDD|218700 pfam05697, Trigger_N, Bacterial trigger factor protein (TF). In
the E. coli cytosol, a fraction of the newly synthesised
proteins requires the activity of molecular chaperones
for folding to the native state. The major chaperones
implicated in this folding process are the
ribosome-associated Trigger Factor (TF), and the DnaK
and GroEL chaperones with their respective
co-chaperones. Trigger Factor is an ATP-independent
chaperone and displays chaperone and
peptidyl-prolyl-cis-trans-isomerase (PPIase) activities
in vitro. It is composed of at least three domains, an
N-terminal domain which mediates association with the
large ribosomal subunit, a central substrate binding and
PPIase domain with homology to FKBP proteins, and a
C-terminal domain of unknown function. The positioning
of TF at the peptide exit channel, together with its
ability to interact with nascent chains as short as 57
residues renders TF a prime candidate for being the
first chaperone that binds to the nascent polypeptide
chains. This family represents the N-terminal region of
the protein.
Length = 145
Score = 26.7 bits (60), Expect = 5.0
Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 17/84 (20%)
Query: 103 MQAVVARYGQHVLIQTLSDLVTEADLDSGCLYPPPNIIKDCSLKIAA--KLVEQAFKDGT 160
V RYG+ + + L DL+ EA +K+ L+ ++ E +DG
Sbjct: 51 RSVVKKRYGKEIYQEALEDLLQEAY---------EEALKEEKLEPIGQPEIEEVELEDGK 101
Query: 161 ATKVGTATL-----FRLIKFSKIK 179
+ TA L + ++
Sbjct: 102 DFEF-TAEFEVYPEVELGDYKGLE 124
>gnl|CDD|220905 pfam10923, DUF2791, P-loop Domain of unknown function (DUF2791).
This is a family of proteins found in archaea and
bacteria. This domain contains a P-loop motif suggesting
it binds to a nucleotide such as ATP.
Length = 417
Score = 27.2 bits (61), Expect = 5.4
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 96 DDFIEEFMQAVVARYGQHVLI---QTLSDLV 123
D+++ FMQ V R G V + + + D V
Sbjct: 361 DEYLAAFMQHVAGRLGGAVFVTPREFIRDFV 391
>gnl|CDD|221798 pfam12831, FAD_oxidored, FAD dependent oxidoreductase. This family
of proteins contains FAD dependent oxidoreductases and
related proteins.
Length = 415
Score = 27.1 bits (61), Expect = 5.6
Identities = 17/75 (22%), Positives = 26/75 (34%), Gaps = 22/75 (29%)
Query: 70 GTNTQQLL--DDPLYIGLRQRRTTGQAYDDFIEEFMQAVVARYGQ-------------HV 114
G T L+ DD Y R + G EF++ + AR G V
Sbjct: 36 GMATSGLVGTDDGNY--DRGQVIGG-----IAREFLRRLRARGGPLGNRTSGPWPFDPEV 88
Query: 115 LIQTLSDLVTEADLD 129
L +++ EA +
Sbjct: 89 AKLVLDEMLAEAGVT 103
>gnl|CDD|239495 cd03401, Band_7_prohibitin, Band_7_prohibitin. A subgroup of the
band 7 domain of flotillin (reggie) like proteins. This
subgroup group includes proteins similar to prohibitin
(a lipid raft-associated integral membrane protein).
Individual proteins of this band 7 domain family may
cluster to form membrane microdomains which may in turn
recruit multiprotein complexes. These microdomains in
addition to being stable scaffolds may also be also
dynamic units with their own regulatory functions.
Prohibitin is a mitochondrial inner-membrane protein
which may act as a chaperone for the stabilization of
mitochondrial proteins. Human prohibitin forms a
heter-oligomeric complex with Bap-37 (prohibitin 2, a
band 7 domain carrying homologue). This complex may
protect non-assembled membrane proteins against
proteolysis by the m-AAA protease. Prohibitin and Bap-37
yeast homologues have been implicated in yeast longevity
and, in the maintenance of mitochondrial morphology.
Length = 196
Score = 26.4 bits (59), Expect = 7.9
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 8/49 (16%)
Query: 86 RQRRTTGQAYDD-----FIEEFMQAVVARYGQHVLI---QTLSDLVTEA 126
R + G+ YD+ I E ++AVVA++ LI + +S L+ EA
Sbjct: 80 RIYQNLGEDYDERVLPSIINEVLKAVVAQFTAEELITQREEVSALIREA 128
>gnl|CDD|237215 PRK12815, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1068
Score = 26.9 bits (60), Expect = 8.8
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 129 DSGCLYPPPNIIKDCSLKIAAKLVEQAFKDGTATKVGTATLFRL 172
DS + PP ++ S + K+ + A K A K+G + +
Sbjct: 784 DSIAVLPPQSL----SEEQQEKIRDYAIK--IAKKLGFRGIMNI 821
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
0.321 0.139 0.407
Gapped
Lambda K H
0.267 0.0799 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,045,215
Number of extensions: 828038
Number of successful extensions: 717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 715
Number of HSP's successfully gapped: 34
Length of query: 179
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 88
Effective length of database: 6,901,388
Effective search space: 607322144
Effective search space used: 607322144
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 (21.8 bits)
S2: 56 (25.2 bits)