RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1304
(184 letters)
>gnl|CDD|225807 COG3268, COG3268, Uncharacterized conserved protein [Function
unknown].
Length = 382
Score = 75.6 bits (186), Expect = 2e-16
Identities = 29/72 (40%), Positives = 42/72 (58%)
Query: 112 DLKNESSILIMAKKCRVILNCVGPYTWYGEAVVKACIEAKTHHVDITGEPYFMEYMQYEY 171
L +++ MA + +V+LNCVGPYT YGE +V AC A T + DITGE F E Y
Sbjct: 58 PLGVPAALEAMASRTQVVLNCVGPYTRYGEPLVAACAAAGTDYADITGEIMFFENSIDLY 117
Query: 172 NTRAQESEVQKC 183
+ +A ++ +
Sbjct: 118 HAQAADAGARII 129
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 48.1 bits (115), Expect = 6e-07
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 108 IIIADLKNESSILIMAKKCRVILNCVGPYTWYGEAVVKACIEAKTHHVDITGEPYFMEYM 167
I D N +++ + K+ +++N P+ V+KACIE H+VD + ++
Sbjct: 49 AIAVDADNYEALVALLKEGDLVINLAPPF--LSLTVLKACIETGVHYVDTS----YLREA 102
Query: 168 QYEYNTRAQESEV 180
Q + +A+++ V
Sbjct: 103 QLALHEKAKDAGV 115
>gnl|CDD|224662 COG1748, LYS9, Saccharopine dehydrogenase and related proteins
[Amino acid transport and metabolism].
Length = 389
Score = 38.9 bits (91), Expect = 8e-04
Identities = 12/69 (17%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 112 DLKNESSILIMAKKCRVILNCVGPYTWYGEAVVKACIEAKTHHVDITGEPYFMEYMQYEY 171
D + +++ + K +++N P+ ++KACI+ +VD + + E ++
Sbjct: 55 DAADVDALVALIKDFDLVINAAPPF--VDLTILKACIKTGVDYVDTS----YYEEPPWKL 108
Query: 172 NTRAQESEV 180
+ A+++ +
Sbjct: 109 DEEAKKAGI 117
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most SDRs. 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 = 302
Score = 31.9 bits (73), Expect = 0.16
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 101 ENLIDIPIIIADLKNESSILIMAKKCRVILNCVGP-YT-W------YGEAVVKACIEAKT 152
L + I+ AD + SS++ A+ VI +C P YT W E VV A
Sbjct: 37 AWLPGVEIVAADAMDASSVIAAARGADVIYHCANPAYTRWEELFPPLMENVVAAAEANGA 96
Query: 153 HHV 155
V
Sbjct: 97 KLV 99
>gnl|CDD|236307 PRK08591, PRK08591, acetyl-CoA carboxylase biotin carboxylase
subunit; Validated.
Length = 451
Score = 31.7 bits (73), Expect = 0.17
Identities = 18/44 (40%), Positives = 20/44 (45%), Gaps = 12/44 (27%)
Query: 140 GEAVVKACIE-----AKTHH--VDITGEPYFMEYMQYEYNTRAQ 176
GEA VKA A T + GE YF+E M NTR Q
Sbjct: 256 GEAAVKAAKAIGYRGAGTIEFLYEKNGEFYFIE-M----NTRIQ 294
>gnl|CDD|223516 COG0439, AccC, Biotin carboxylase [Lipid metabolism].
Length = 449
Score = 29.9 bits (68), Expect = 0.74
Identities = 24/88 (27%), Positives = 31/88 (35%), Gaps = 20/88 (22%)
Query: 92 LGARDC-LYRENLIDIPIIIADLKNESSILIMAKKCRVILNCVGPYTWYGEAVVKACIEA 150
LG RDC + R + I + L E + + +G Y G
Sbjct: 224 LGERDCSIQRRHQKVIEEAPSPLLTEELREKIGEAAVRAAKLIG-YRGAG---------- 272
Query: 151 KTHH--VDITGEPYFMEYMQYEYNTRAQ 176
T D GE YF+E M NTR Q
Sbjct: 273 -TVEFLYDSNGEFYFIE-M----NTRLQ 294
>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 = 28.4 bits (64), Expect = 2.0
Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 16/71 (22%)
Query: 94 ARDCLYRENLIDIPIIIADLKNESSILIMAKKCRVILNCVGPYTWYG------------- 140
AR L +L + + DL+++ SI + V++N VG Y
Sbjct: 37 ARRLLVMGDLGQVLFVEFDLRDDESIRKALEGSDVVINLVG--RLYETKNFSFEDVHVEG 94
Query: 141 -EAVVKACIEA 150
E + KA EA
Sbjct: 95 PERLAKAAKEA 105
>gnl|CDD|147051 pfam04698, MOBP_C-Myrip, Myelin-associated oligodendrocytic basic
protein (MOBP). MOBP is abundantly expressed in central
nervous system myelin, and shares several
characteristics with myelin basic protein (MBP), in
terms of regional distribution and function. This family
is the middle and C-terminal regions of MOBP which has
been shown to be essential for normal arrangement of the
radial component in central nervous system myelin. Most
member-proteins carry a FVHE-PHD type zinc-finger at
their N-terminus.
Length = 710
Score = 28.6 bits (63), Expect = 2.1
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 29 GTVTAKVLSSRKQRKEDRIGESQPFRGQTLSVQDKIRPGRGSNPRPSAYKADA 81
GT+ K++ +K + E + E +P S K G++ P +KA A
Sbjct: 87 GTILQKIIRKQKDKAELQAEEEEPEWPHPQSCSTKAA-DEGTSAPPGGHKAPA 138
>gnl|CDD|220420 pfam09815, XK-related, XK-related protein. Members of this family
comprise various XK-related proteins, that are involved
in sodium-dependent transport of neutral amino acids or
oligopeptides. These proteins are responsible for the Kx
blood group system - defects results in McLeod syndrome,
an X-linked multi-system disorder characterized by late
onset abnormalities in the neuromuscular and
hematopoietic systems.
Length = 334
Score = 27.6 bits (62), Expect = 4.4
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 3/41 (7%)
Query: 132 CVGPYTWYGEAVVKACIEAKTHHVDITGEPYFMEYMQYEYN 172
+G Y A+ + + EPYF Y+ +E
Sbjct: 80 QLGILIRYLHALRLGLRVWRREE---SEEPYFYRYLVFEEA 117
>gnl|CDD|239141 cd02678, MIT_VPS4, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. This sub-family
of MIT domains is found in intracellular protein
transport proteins of the AAA-ATPase family. The
molecular function of the MIT domain is unclear.
Length = 75
Score = 25.3 bits (56), Expect = 6.5
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 162 YFMEYMQYEYNTRAQESEVQKCT 184
YFM ++YE N +++ES KCT
Sbjct: 35 YFMHALKYEKNPKSKESIRAKCT 57
>gnl|CDD|238299 cd00537, MTHFR, Methylenetetrahydrofolate reductase (MTHFR).
5,10-Methylenetetrahydrofolate is reduced to
5-methyltetrahydrofolate by methylenetetrahydrofolate
reductase, a cytoplasmic, NAD(P)-dependent enzyme.
5-methyltetrahydrofolate is utilized by methionine
synthase to convert homocysteine to methionine. The
enzymatic mechanism is a ping-pong bi-bi mechanism, in
which NAD(P)+ release precedes the binding of
methylenetetrahydrofolate and the acceptor is free FAD.
The family includes the 5,10-methylenetetrahydrofolate
reductase EC:1.7.99.5 from prokaryotes and
methylenetetrahydrofolate reductase EC: 1.5.1.20 from
eukaryotes. The bacterial enzyme is a homotetramer and
NADH is the preferred reductant while the eukaryotic
enzyme is a homodimer and NADPH is the preferred
reductant. In humans, there are several clinically
significant mutations in MTHFR that result in
hyperhomocysteinemia, which is a risk factor for the
development of cardiovascular disease.
Length = 274
Score = 26.4 bits (59), Expect = 8.9
Identities = 10/29 (34%), Positives = 12/29 (41%), Gaps = 2/29 (6%)
Query: 100 RENLIDIPII--IADLKNESSILIMAKKC 126
R I +PII I L + AK C
Sbjct: 183 RAAGITVPIIPGIMPLTSYKQAKRFAKLC 211
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
0.319 0.135 0.394
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,963,066
Number of extensions: 798729
Number of successful extensions: 533
Number of sequences better than 10.0: 1
Number of HSP's gapped: 531
Number of HSP's successfully gapped: 15
Length of query: 184
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 93
Effective length of database: 6,901,388
Effective search space: 641829084
Effective search space used: 641829084
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 (21.7 bits)
S2: 56 (25.3 bits)