RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy818
(214 letters)
>gnl|CDD|238117 cd00195, UBCc, Ubiquitin-conjugating enzyme E2, catalytic (UBCc)
domain. This is part of the ubiquitin-mediated protein
degradation pathway in which a thiol-ester linkage forms
between a conserved cysteine and the C-terminus of
ubiquitin and complexes with ubiquitin protein ligase
enzymes, E3. This pathway regulates many fundamental
cellular processes. There are also other E2s which form
thiol-ester linkages without the use of E3s as well as
several UBC homologs (TSG101, Mms2, Croc-1 and similar
proteins) which lack the active site cysteine essential
for ubiquitination and appear to function in DNA repair
pathways which were omitted from the scope of this CD.
Length = 141
Score = 133 bits (336), Expect = 7e-40
Identities = 44/114 (38%), Positives = 68/114 (59%), Gaps = 4/114 (3%)
Query: 11 RLKQDYMKLKKDPIPYVIAEPNPANILEWFYVVIGPENTQYEGGMYLGKLVFPRDFPFKP 70
RL+++ LKKDP + AEP N+LEW + GP +T YEGG++ + FP D+PFKP
Sbjct: 3 RLQKELKDLKKDPPSGISAEPVEENLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYPFKP 62
Query: 71 PSIYMIT--PNGRFKTNTRLCLSMSDFHPDTWNPAWSVSTILTGLLSFMVERSP 122
P + +T + N ++CLS+ H W+PA+++ T+L L S + E +P
Sbjct: 63 PKVRFVTKIYHPNVDENGKICLSILKTH--GWSPAYTLRTVLLSLQSLLNEPNP 114
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 116 bits (292), Expect = 4e-33
Identities = 43/122 (35%), Positives = 64/122 (52%), Gaps = 8/122 (6%)
Query: 1 MSSKHCGATARLKQDYMKLKKDPIPYVIAEP-NPANILEWFYVVIGPENTQYEGGMYLGK 59
MSS A RL ++ KL+KDP P + A P + N+ W + GP +T YEGG++
Sbjct: 1 MSSP--SALKRLLKELKKLQKDPPPGISAGPVDDDNLFHWEATITGPPDTPYEGGIFKLT 58
Query: 60 LVFPRDFPFKPPSIYMITPNGRFK--TNTRLCLSMSDFHPDTWNPAWSVSTILTGLLSFM 117
L FP D+PFKPP + T + +CL + D W+P +++ TIL L S +
Sbjct: 59 LEFPEDYPFKPPKVRFTTKIFHPNVDPSGNVCLDILK---DRWSPVYTLETILLSLQSLL 115
Query: 118 VE 119
+
Sbjct: 116 LS 117
>gnl|CDD|215772 pfam00179, UQ_con, Ubiquitin-conjugating enzyme. Proteins destined
for proteasome-mediated degradation may be
ubiquitinated. Ubiquitination follows conjugation of
ubiquitin to a conserved cysteine residue of UBC
homologues. TSG101 is one of several UBC homologues that
lacks this active site cysteine.
Length = 139
Score = 115 bits (290), Expect = 5e-33
Identities = 39/111 (35%), Positives = 61/111 (54%), Gaps = 8/111 (7%)
Query: 11 RLKQDYMKLKKDPIPYVIAEPNPANILEWFYVVIGPENTQYEGGMYLGKLVFPRDFPFKP 70
RL+++ +L KDP P + A P N+ EW +IGPE T YEGG++ + FP D+PFKP
Sbjct: 1 RLQKELKELLKDPPPGISAFPVDDNLFEWEVTIIGPEGTPYEGGVFKLDIEFPEDYPFKP 60
Query: 71 PSIYMIT----PNGRFKTNTRLCLSMSDFHPDTWNPAWSVSTILTGLLSFM 117
P + T PN + +CL + + W+PA ++ +L + S +
Sbjct: 61 PKVKFTTKIYHPN--VDPSGEICLDI--LKDENWSPALTIEQVLLSIQSLL 107
>gnl|CDD|214562 smart00212, UBCc, Ubiquitin-conjugating enzyme E2, catalytic domain
homologues. Proteins destined for proteasome-mediated
degradation may be ubiquitinated. Ubiquitination follows
conjugation of ubiquitin to a conserved cysteine residue
of UBC homologues. This pathway functions in regulating
many fundamental processes required for cell
viability.TSG101 is one of several UBC homologues that
lacks this active site cysteine.
Length = 145
Score = 110 bits (276), Expect = 7e-31
Identities = 40/112 (35%), Positives = 63/112 (56%), Gaps = 5/112 (4%)
Query: 11 RLKQDYMKLKKDPIPYVIAEPNP-ANILEWFYVVIGPENTQYEGGMYLGKLVFPRDFPFK 69
RL ++ +L+KDP P A P N+LEW ++GP T YEGG++ + FP D+PFK
Sbjct: 1 RLLKELKELRKDPPPGFTAYPVDDENLLEWTGTIVGPPGTPYEGGVFKLTIEFPEDYPFK 60
Query: 70 PPSIYMITP--NGRFKTNTRLCLSMSDFHPDTWNPAWSVSTILTGLLSFMVE 119
PP + IT + ++ +CL + + W+PA ++ T+L L S + E
Sbjct: 61 PPKVKFITKIYHPNVDSSGEICLDIL--KQEKWSPALTLETVLLSLQSLLSE 110
>gnl|CDD|177768 PLN00172, PLN00172, ubiquitin conjugating enzyme; Provisional.
Length = 147
Score = 74.8 bits (183), Expect = 4e-17
Identities = 41/119 (34%), Positives = 66/119 (55%), Gaps = 9/119 (7%)
Query: 8 ATARLKQDYMKLKKDPIPYVIAEPNPANILEWFYVVIGPENTQYEGGMYLGKLVFPRDFP 67
AT R+++++ L KDP A P+ N+ W +IGP ++ Y GG++ ++FP D+P
Sbjct: 2 ATKRIQKEHKDLLKDPPSNCSAGPSDENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYP 61
Query: 68 FKPPSIYMIT----PNGRFKTNTRLCLSMSDFHPDTWNPAWSVSTILTGLLSFMVERSP 122
FKPP + T PN +N +CL D D W+PA +VS +L + S + + +P
Sbjct: 62 FKPPKVQFTTKIYHPN--INSNGSICL---DILRDQWSPALTVSKVLLSISSLLTDPNP 115
>gnl|CDD|240397 PTZ00390, PTZ00390, ubiquitin-conjugating enzyme; Provisional.
Length = 152
Score = 64.8 bits (158), Expect = 2e-13
Identities = 36/107 (33%), Positives = 56/107 (52%), Gaps = 9/107 (8%)
Query: 8 ATARLKQDYMKLKKDPIPYVIAEPNPANILEWFYVVIGPENTQYEGGMYLGKLVFPRDFP 67
+ R++++ L DP P + AEP+P N + ++ GP+ T YEGG Y +L P +P
Sbjct: 3 ISKRIEKETQNLANDPPPGIKAEPDPGNYRHFKILMEGPDGTPYEGGYYKLELFLPEQYP 62
Query: 68 FKPPSIYMIT----PNGRFKTNTRLCLSMSDFHPDTWNPAWSVSTIL 110
+PP + +T PN R+CL D D W+PA + T+L
Sbjct: 63 MEPPKVRFLTKIYHPN--IDKLGRICL---DILKDKWSPALQIRTVL 104
>gnl|CDD|187601 cd05343, Mgc4172-like_SDR_c, human Mgc4172-like, classical (c)
SDRs. Human Mgc4172-like proteins, putative SDRs. These
proteins are members of the SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes 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 (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) 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. Extended SDRs have additional elements in
the C-terminal region, 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. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 61.4 bits (149), Expect = 2e-11
Identities = 25/56 (44%), Positives = 38/56 (67%), Gaps = 2/56 (3%)
Query: 159 VQSISPGLVKSQIFKSSLGDKFDKS--LYEAHPCLQAEDIANTVEFILSSPPHVQV 212
SISPGLV+++ + +K+ YE+ PCL+ ED+AN V ++LS+PPHVQ+
Sbjct: 187 ATSISPGLVETEFAFKLHDNDPEKAAATYESIPCLKPEDVANAVLYVLSTPPHVQI 242
>gnl|CDD|226674 COG4221, COG4221, Short-chain alcohol dehydrogenase of unknown
specificity [General function prediction only].
Length = 246
Score = 51.1 bits (123), Expect = 6e-08
Identities = 24/85 (28%), Positives = 34/85 (40%), Gaps = 20/85 (23%)
Query: 134 RRQLAARSLRFNLNDKNFCELFPDLVQSISPGLVKSQIFK----SSLGDKFDKSLYEAHP 189
R++LA +R V ISPGLV++ F ++ DK
Sbjct: 168 RQELAGTGIR---------------VTVISPGLVETTEFSTVRFEGDDERADKVYKGGTA 212
Query: 190 CLQAEDIANTVEFILSSPPHVQVSR 214
L EDIA V F + P HV ++
Sbjct: 213 -LTPEDIAEAVLFAATQPQHVNINE 236
>gnl|CDD|187604 cd05346, SDR_c5, classical (c) SDR, subgroup 5. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a typical Gly-rich NAD-binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRs are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes 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 (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) 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. Extended SDRs have additional elements in
the C-terminal region, 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. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 249
Score = 48.0 bits (115), Expect = 7e-07
Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 159 VQSISPGLVKSQI----FKSSLGDKFD-KSLYEAHPCLQAEDIANTVEFILSSPPHVQVS 213
V +I PGLV+++ F GDK +YE L EDIA T+ ++ S P HV ++
Sbjct: 176 VTNIEPGLVETEFSLVRFH---GDKEKADKVYEGVEPLTPEDIAETILWVASRPAHVNIN 232
Query: 214 R 214
Sbjct: 233 D 233
>gnl|CDD|187639 cd08934, CAD_SDR_c, clavulanic acid dehydrogenase (CAD), classical
(c) SDR. CAD catalyzes the NADP-dependent reduction of
clavulanate-9-aldehyde to clavulanic acid, a
beta-lactamase inhibitor. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes 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 (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) 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. Extended SDRs have additional
elements in the C-terminal region, 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.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 243
Score = 38.3 bits (89), Expect = 0.001
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 159 VQSISPGLVKSQIFKSSLGDKFDKSLYEAHPC----LQAEDIANTVEFILSSPPHVQV 212
V I PG V ++ + + K YE LQAEDIA V + +++P HV V
Sbjct: 177 VVVIEPGTVDTE-LRDHITHTITKEAYEERISTIRKLQAEDIAAAVRYAVTAPHHVTV 233
>gnl|CDD|187623 cd05365, 7_alpha_HSDH_SDR_c, 7 alpha-hydroxysteroid dehydrogenase
(7 alpha-HSDH), classical (c) SDRs. This bacterial
subgroup contains 7 alpha-HSDHs, including Escherichia
coli 7 alpha-HSDH. 7 alpha-HSDH, a member of the SDR
family, catalyzes the NAD+ -dependent dehydrogenation of
a hydroxyl group at position 7 of the steroid skeleton
of bile acids. In humans the two primary bile acids are
cholic and chenodeoxycholic acids, these are formed from
cholesterol in the liver. Escherichia coli 7 alpha-HSDH
dehydroxylates these bile acids in the human intestine.
Mammalian 7 alpha-HSDH activity has been found in
livers. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 242
Score = 37.5 bits (87), Expect = 0.003
Identities = 26/95 (27%), Positives = 44/95 (46%), Gaps = 14/95 (14%)
Query: 126 SIEMSDYERRQLAA----RSLRFNLNDKNFCELFPDLVQSISPGLVKSQIFKSSLGDKFD 181
++ ++ Y + A R+L F+L K V +++PG VK+ S L + +
Sbjct: 143 NVRIAAYGSSKAAVNHMTRNLAFDLGPKGI------RVNAVAPGAVKTDALASVLTPEIE 196
Query: 182 KSLYEAHPCL---QAEDIANTVEFILSSPPHVQVS 213
+++ + P + EDIAN F L SP VS
Sbjct: 197 RAMLKHTPLGRLGEPEDIANAALF-LCSPASAWVS 230
>gnl|CDD|212491 cd05233, SDR_c, classical (c) SDRs. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes 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 prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) 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. Extended SDRs have additional elements in
the C-terminal region, 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. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 234
Score = 37.3 bits (87), Expect = 0.003
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 159 VQSISPGLVKSQIFKSSLGDKFDKSLYEAHP---CLQAEDIANTVEFILS 205
V +++PGLV + + ++ +K L A P E++A V F+ S
Sbjct: 171 VNAVAPGLVDTPMLAKLGPEEAEKELAAAIPLGRLGTPEEVAEAVVFLAS 220
>gnl|CDD|130624 TIGR01561, gde_arch, glycogen debranching enzyme, archaeal type,
putative. The seed for this model is composed of two
uncharacterized archaeal proteins from Methanosarcina
acetivorans and Sulfolobus solfataricus. Trusted cutoff
is set so that essentially only archaeal members hit the
model. The notable exceptions to archaeal membership are
the Gram positive Clostridium perfringens which scores
much better than some other archaea and the
Cyanobacterium Nostoc sp. which scores just above the
trusted cutoff. Noise cutoff is set to exclude the
characterized eukaryotic glycogen debranching enzyme in
S. cerevisiae. These cutoffs leave the prokaryotes
Porphyromonas gingivalis and Deinococcus radiodurans
below trusted but above noise. Multiple alignments
including these last two species exhibit sequence
divergence which may suggest a subtly different function
for these prokaryotic proteins [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 575
Score = 33.9 bits (77), Expect = 0.057
Identities = 32/142 (22%), Positives = 53/142 (37%), Gaps = 18/142 (12%)
Query: 38 EWFYVVIGPENTQYEGGMYLGKLVFPRDFPFKPPSIYMITPNG------RFKTNTRLCLS 91
E+F GP T+ + GK R F F+ + +G + + L L
Sbjct: 145 EFFTQEAGPAGTEL--ALSEGK----RIFNFEIHDKLELFNDGIWYFNFEYDLDKELGL- 197
Query: 92 MSDFHPDTWNPAWSVSTILTGLLSFMVERSPT-LGSIEMSDYERRQL--AARSLRFNLND 148
+F D +NP S + G F V P + S E+ + +L AA L+
Sbjct: 198 --NFIEDIFNPFCFESKLEKGASRFFVAARPKDISSEELEHVDILKLLEAAGQNLLILDS 255
Query: 149 KNFCELFPDLVQSISPGLVKSQ 170
K L+++ +VK+
Sbjct: 256 KLIESFALKLLRATDDFVVKNH 277
>gnl|CDD|187634 cd08929, SDR_c4, classical (c) SDR, subgroup 4. This subgroup has
a canonical active site tetrad and a typical Gly-rich
NAD-binding motif. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes 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 (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) 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. Extended SDRs have additional
elements in the C-terminal region, 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.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 226
Score = 32.9 bits (75), Expect = 0.079
Identities = 18/56 (32%), Positives = 23/56 (41%), Gaps = 9/56 (16%)
Query: 159 VQSISPGLVKSQIFKSSLGDKFDKSLYEAHPCLQAEDIANTVEFILSSPPHVQVSR 214
V ++ PG V + F S + K L ED+A V F L P VSR
Sbjct: 171 VVNVMPGSVDTG-FAGSPEGQAWK--------LAPEDVAQAVLFALEMPARALVSR 217
>gnl|CDD|182531 PRK10538, PRK10538, malonic semialdehyde reductase; Provisional.
Length = 248
Score = 32.0 bits (73), Expect = 0.17
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 159 VQSISPGLVK----SQI-FKSSLGDKFDKSLYEAHPCLQAEDIANTVEFILSSPPHVQV 212
V I PGLV S + FK K +K+ Y+ L ED++ V ++ + P HV +
Sbjct: 172 VTDIEPGLVGGTEFSNVRFKGD-DGKAEKT-YQNTVALTPEDVSEAVWWVATLPAHVNI 228
>gnl|CDD|235914 PRK07041, PRK07041, short chain dehydrogenase; Provisional.
Length = 230
Score = 31.5 bits (72), Expect = 0.21
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 153 ELFPDLVQSISPGLVKSQIFKSSLGDKFDKSLYEAHPCL------QAEDIANTVEFILSS 206
EL P V ++SPGLV + ++ GD + A L Q ED+AN + F+ ++
Sbjct: 154 ELAPVRVNTVSPGLVDTPLWSKLAGDAREAMFAAAAERLPARRVGQPEDVANAILFLAAN 213
Query: 207 P 207
Sbjct: 214 G 214
>gnl|CDD|235693 PRK06077, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 252
Score = 31.6 bits (72), Expect = 0.25
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 153 ELFPDL-VQSISPGLVKSQIFKS---SLG---DKFDKSLYEAHPCLQAEDIANTVEFILS 205
EL P + V +I+PG VK+++ +S LG +F + L E++A V IL
Sbjct: 171 ELAPKIRVNAIAPGFVKTKLGESLFKVLGMSEKEFAEKFTLMGKILDPEEVAEFVAAILK 230
Query: 206 SP 207
Sbjct: 231 IE 232
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 31.4 bits (72), Expect = 0.30
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 159 VQSISPGLVKSQIFKS-SLGDKFDKSLYEAHPCL---QAEDIANTVEFILS 205
V +++PG + ++++ S S DK L E P + E+IA V F+ S
Sbjct: 180 VNAVAPGAIDTEMWSSFSEEDKE--GLAEEIPLGRLGKPEEIAKVVLFLAS 228
>gnl|CDD|187600 cd05341, 3beta-17beta-HSD_like_SDR_c, 3beta17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs. This subgroup
includes members identified as 3beta17beta
hydroxysteroid dehydrogenase, 20beta hydroxysteroid
dehydrogenase, and R-alcohol dehydrogenase. These
proteins exhibit the canonical active site tetrad and
glycine rich NAD(P)-binding motif of the classical SDRs.
17beta-dehydrogenases are a group of isozymes that
catalyze activation and inactivation of estrogen and
androgens, and include members of the SDR family. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 247
Score = 30.4 bits (69), Expect = 0.47
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 159 VQSISPGLVKSQIFKSSLGDKFDKSLYEAHPCLQA---EDIANTVEFILS 205
V S+ PG + + + L + + Y P +A ++IA V ++ S
Sbjct: 178 VNSVHPGYIYTPMTDELLIAQGEMGNYPNTPMGRAGEPDEIAYAVVYLAS 227
>gnl|CDD|233590 TIGR01830, 3oxo_ACP_reduc, 3-oxoacyl-(acyl-carrier-protein)
reductase. This model represents 3-oxoacyl-[ACP]
reductase, also called 3-ketoacyl-acyl carrier protein
reductase, an enzyme of fatty acid biosynthesis [Fatty
acid and phospholipid metabolism, Biosynthesis].
Length = 239
Score = 30.6 bits (70), Expect = 0.51
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 21/76 (27%)
Query: 135 RQLAARSLRFNLNDKNFCELFPDLVQSISPGLVKSQIFKSSLGDKFDKSLYEAHPCL--- 191
++LA+R++ N +++PG + + L +K K + P L
Sbjct: 164 KELASRNITVN---------------AVAPGFIDTD-MTDKLSEKVKKKILSQIP-LGRF 206
Query: 192 -QAEDIANTVEFILSS 206
E++AN V F+ S
Sbjct: 207 GTPEEVANAVAFLASD 222
>gnl|CDD|235990 PRK07326, PRK07326, short chain dehydrogenase; Provisional.
Length = 237
Score = 30.0 bits (68), Expect = 0.64
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 191 LQAEDIANTVEFILSSPPHVQVSR 214
+Q EDIA V +L PP S+
Sbjct: 203 IQPEDIAQLVLDLLKMPPRTLPSK 226
>gnl|CDD|181298 PRK08219, PRK08219, short chain dehydrogenase; Provisional.
Length = 227
Score = 28.7 bits (65), Expect = 1.6
Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 159 VQSISPGLVKS---QIFKSSLGDKFDKSLYEAHPCLQAEDIANTVEFILSSPPHVQV 212
V S+ PG + + + G ++D Y L+ E +A V F + +PP +
Sbjct: 166 VTSVHPGRTDTDMQRGLVAQEGGEYDPERY-----LRPETVAKAVRFAVDAPPDAHI 217
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 29.1 bits (66), Expect = 1.7
Identities = 11/49 (22%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 159 VQSISPGLVKSQIFKSSLGDKFDKSLYE--AHPCLQAEDIANTVEFILS 205
V ++PG + + + ++++ + + E EDIA V F+ S
Sbjct: 181 VNMVAPGDIDTDMKEATIEEAREAKDAETPLGRSGTPEDIARAVAFLCS 229
>gnl|CDD|223549 COG0473, LeuB, Isocitrate/isopropylmalate dehydrogenase [Amino acid
transport and metabolism].
Length = 348
Score = 28.7 bits (65), Expect = 2.1
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 8/48 (16%)
Query: 163 SPGLVKSQIFKSSLGDKFDKSLYEA-H---PCLQAEDIANTVEFILSS 206
S GL S ++LGD+ +L+E H P + + IAN + ILS+
Sbjct: 251 SLGLAPS----ANLGDERGPALFEPVHGSAPDIAGKGIANPIATILSA 294
>gnl|CDD|235500 PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 248
Score = 28.2 bits (64), Expect = 3.0
Identities = 13/51 (25%), Positives = 28/51 (54%), Gaps = 6/51 (11%)
Query: 159 VQSISPGLVKSQIFKSSLGDKFDKSLYEAHPCL----QAEDIANTVEFILS 205
V +++PG +++ + + L + +++ P L Q E+IA+ V F+ S
Sbjct: 180 VNAVAPGFIETDMTDA-LPEDVKEAILAQIP-LGRLGQPEEIASAVAFLAS 228
>gnl|CDD|180300 PRK05875, PRK05875, short chain dehydrogenase; Provisional.
Length = 276
Score = 27.5 bits (61), Expect = 5.2
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 159 VQSISPGLVKSQIFKSSLGDKFDKSLYEAHPCL----QAEDIANTVEFILS 205
V SI PGL+++ + + Y A L + ED+AN F+LS
Sbjct: 184 VNSIRPGLIRTDLVAPITESPELSADYRACTPLPRVGEVEDVANLAMFLLS 234
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 27.8 bits (61), Expect = 5.8
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 95 FHPDTWNPAWS--VSTILT-GLLSFMVERSPTLGSIEM 129
+HP+ WN W V I G+ + MV P GS+ M
Sbjct: 1440 YHPEIWNLPWDKLVEEIKKYGVRNAMVTTCPPTGSVSM 1477
>gnl|CDD|193586 cd09972, LOTUS_TDRD_OSKAR, The first LOTUS domain in Oskar and
Tudor-containing proteins 5 and 7. The first LOTUS
domain in Oskar and Tudor-containing proteins 5 and 7:
The LOTUS containing proteins are germline-specific and
are found in the nuage/polar granules of germ cells.
Tudor-containing protein 5 and 7 belong to the
evolutionary conserved Tudor domain-containing protein
(TDRD) family involved in germ cell development. In
mice, TDRD5 and TDRD7 are components of the
intermitochondrial cements (IMCs) and the chromatoid
bodies (CBs), which are cytoplasmic ribonucleoprotein
granules involved in RNA processing for
spermatogenesis. Oskar protein is a critical component
of the pole plasm in the Drosophila oocyte, which is
required for germ cell formation.The exact molecular
function of LOTUS domain remains to be identified. Its
occurrence in proteins associated with RNA metabolism
suggests that it might be involved in RNA binding
function. The presence of several basic residues and
RNA fold recognition motifs support this hypothesis.
The RNA binding function might be the first step of
regulating mRNA translation or localization.
Length = 87
Score = 25.9 bits (58), Expect = 6.8
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 1 MSSKHCGATA-RLKQDYMKLKKDPIPY 26
+SSK G T L++DY +L+ +PIPY
Sbjct: 13 ISSKG-GLTLSELERDYRELEGEPIPY 38
>gnl|CDD|149965 pfam09096, Phage-tail_2, Baseplate structural protein, domain 2.
Members of this family adopt a beta barrel structure
with a Greek key topology, which is topologically
similar to the FMN-binding split barrel. They are
structural component of the viral baseplate,
predominantly found in the structural protein gp27.
Length = 168
Score = 26.7 bits (59), Expect = 7.9
Identities = 6/14 (42%), Positives = 11/14 (78%)
Query: 19 LKKDPIPYVIAEPN 32
+K++PIP ++ EP
Sbjct: 2 IKQEPIPMIVGEPR 15
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
0.320 0.136 0.420
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,850,812
Number of extensions: 997130
Number of successful extensions: 811
Number of sequences better than 10.0: 1
Number of HSP's gapped: 796
Number of HSP's successfully gapped: 36
Length of query: 214
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 121
Effective length of database: 6,812,680
Effective search space: 824334280
Effective search space used: 824334280
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: 57 (25.7 bits)