RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16161
(387 letters)
>gnl|CDD|187585 cd05324, carb_red_PTCR-like_SDR_c, Porcine testicular carbonyl
reductase (PTCR)-like, classical (c) SDRs. PTCR is a
classical SDR which catalyzes the NADPH-dependent
reduction of ketones on steroids and prostaglandins.
Unlike most SDRs, PTCR functions as a monomer. This
subgroup also includes human carbonyl reductase 1 (CBR1)
and CBR3. CBR1 is an NADPH-dependent SDR with broad
substrate specificity and may be responsible for the in
vivo reduction of quinones, prostaglandins, and other
carbonyl-containing compounds. In addition it includes
poppy NADPH-dependent salutaridine reductase which
catalyzes the stereospecific reduction of salutaridine
to 7(S)-salutaridinol in the biosynthesis of morphine,
and Arabidopsis SDR1,a menthone reductase, which
catalyzes the reduction of menthone to neomenthol, a
compound with antimicrobial activity; SDR1 can also
carry out neomenthol oxidation. 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, 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 = 225
Score = 88.1 bits (219), Expect = 3e-20
Identities = 58/231 (25%), Positives = 77/231 (33%), Gaps = 104/231 (45%)
Query: 153 APFGQQAETTLATNFFALVTVCHMLFPLLRP--HARVVNVASQYGMLYKVPSQELKQTLL 210
P +QA T+ TNFF V V L PLL+ R+VNV+S G
Sbjct: 97 TPTREQARETMKTNFFGTVDVTQALLPLLKKSPAGRIVNVSSGLG--------------- 141
Query: 211 NDSLTEDQLVGMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRP 270
SLT Y VSK + L+ I L+K+
Sbjct: 142 --SLTS---------------------------AYGVSKAALNALTRI----LAKELKET 168
Query: 271 DIIVNAVHPGYVNTDLTGHKGILTMTIHTLKVGVIKLSFIQHATLSKDQTRPDIIVNAVH 330
I VNA PG+V TD+ G K T P+
Sbjct: 169 GIKVNACCPGWVKTDMGGGKAPKT---------------------------PE------- 194
Query: 331 PGYVNTDLTGHKGILTTEQGSVSSVKGALIPPDAKEPRGQFIWYDGSIVDW 381
+G+ + V AL+PPD EP G+F + D +V W
Sbjct: 195 ------------------EGAETPVYLALLPPDG-EPTGKF-FSDKKVVPW 225
>gnl|CDD|212492 cd05327, retinol-DH_like_SDR_c_like, retinol dehydrogenase
(retinol-DH), Light dependent Protochlorophyllide
(Pchlide) OxidoReductase (LPOR) and related proteins,
classical (c) SDRs. Classical SDR subgroup containing
retinol-DHs, LPORs, and related proteins. Retinol is
processed by a medium chain alcohol dehydrogenase
followed by retinol-DHs. Pchlide reductases act in
chlorophyll biosynthesis. There are distinct enzymes
that catalyze Pchlide reduction in light or dark
conditions. Light-dependent reduction is via an
NADP-dependent SDR, LPOR. Proteins in this subfamily
share the glycine-rich NAD-binding motif of the
classical SDRs, have a partial match to the canonical
active site tetrad, but lack the typical active site
Ser. This subgroup includes the human proteins: retinol
dehydrogenase -12, -13 ,and -14, dehydrogenase/reductase
SDR family member (DHRS)-12 , -13 and -X (a DHRS on
chromosome X), and WWOX (WW domain-containing
oxidoreductase), as well as a Neurospora crassa SDR
encoded by the blue light inducible bli-4 gene. 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 = 269
Score = 47.2 bits (113), Expect = 5e-06
Identities = 28/133 (21%), Positives = 47/133 (35%), Gaps = 40/133 (30%)
Query: 160 ETTLATNFFALVTVCHMLFPLLR--PHARVVNVASQYGMLYKVPSQELKQTLLNDSLTED 217
E A N+ + ++L P+L+ +R+VNV+S
Sbjct: 103 ELQFAVNYLGHFLLTNLLLPVLKASAPSRIVNVSS------------------------- 137
Query: 218 QLVGMMHDYVKLAKEGKDQEAGWPD-DPYTV---SKVGVIKLSFIQHATLSKDQTRPDII 273
+ H + + PY SK+ I L + L++ +
Sbjct: 138 ----IAHRAGPIDFN-DLDLENNKEYSPYKAYGQSKLANI-LFTRE---LARRLEGTGVT 188
Query: 274 VNAVHPGYVNTDL 286
VNA+HPG V T+L
Sbjct: 189 VNALHPGVVRTEL 201
Score = 32.6 bits (75), Expect = 0.27
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 13/63 (20%)
Query: 324 IIVNAVHPGYVNTDLTGHKGIL-------------TTEQGSVSSVKGALIPPDAKEPRGQ 370
+ VNA+HPG V T+L G + EQG+ +++ A P
Sbjct: 187 VTVNALHPGVVRTELLRRNGSFFLLYKLLRPFLKKSPEQGAQTALYAATSPELEGVSGKY 246
Query: 371 FIW 373
F
Sbjct: 247 FSD 249
>gnl|CDD|223959 COG1028, FabG, Dehydrogenases with different specificities (related
to short-chain alcohol dehydrogenases) [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 251
Score = 46.7 bits (111), Expect = 6e-06
Identities = 24/132 (18%), Positives = 40/132 (30%), Gaps = 45/132 (34%)
Query: 158 QAETTLATNFFALVTVCHMLFPLLRPHARVVNVASQYGMLYKVPSQELKQTLLNDSLTED 217
+ + N + PL++ R+VN++S G+
Sbjct: 110 DWDRVIDVNLLGAFLLTRAALPLMKK-QRIVNISSVAGLG-------------------- 148
Query: 218 QLVGMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAV 277
Y SK +I L+ L+ + I VNAV
Sbjct: 149 --------------------GPPGQAAYAASKAALIGLT----KALALELAPRGIRVNAV 184
Query: 278 HPGYVNTDLTGH 289
PGY++T +T
Sbjct: 185 APGYIDTPMTAA 196
Score = 35.9 bits (83), Expect = 0.020
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 314 TLSKDQTRPDIIVNAVHPGYVNTDLTGH 341
L+ + I VNAV PGY++T +T
Sbjct: 169 ALALELAPRGIRVNAVAPGYIDTPMTAA 196
>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 = 46.1 bits (110), Expect = 9e-06
Identities = 28/173 (16%), Positives = 50/173 (28%), Gaps = 57/173 (32%)
Query: 160 ETTLATNFFALVTVCHMLFPLL--RPHARVVNVASQYGMLYKVPSQELKQTLLNDSLTED 217
+ L N + + P + + R+VN++S G L +P Q
Sbjct: 99 DRVLDVNLTGVFLLTRAALPHMKKQGGGRIVNISSVAG-LRPLPGQ-------------- 143
Query: 218 QLVGMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAV 277
Y SK + L+ +L+ + I VNAV
Sbjct: 144 -------------------------AAYAASKAALEGLT----RSLALELAPYGIRVNAV 174
Query: 278 HPGYVNTDLTGHKGILTMTIHTLKVGVIKLSFIQHATLSKDQTRPDIIVNAVH 330
PG V+T + + + + + P+ + AV
Sbjct: 175 APGLVDTPMLAK-----LGPEEAEKELAAAIPLGRL------GTPEEVAEAVV 216
Score = 31.9 bits (73), Expect = 0.40
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 314 TLSKDQTRPDIIVNAVHPGYVNTDLTGH 341
+L+ + I VNAV PG V+T +
Sbjct: 159 SLALELAPYGIRVNAVAPGLVDTPMLAK 186
>gnl|CDD|187586 cd05325, carb_red_sniffer_like_SDR_c, carbonyl reductase
sniffer-like, classical (c) SDRs. Sniffer is an
NADPH-dependent carbonyl reductase of the classical SDR
family. Studies in Drosophila melanogaster implicate
Sniffer in the prevention of neurodegeneration due to
aging and oxidative-stress. This subgroup also includes
Rhodococcus sp. AD45 IsoH, which is an NAD-dependent
1-hydroxy-2-glutathionyl-2-methyl-3-butene dehydrogenase
involved in isoprene metabolism, Aspergillus nidulans
StcE encoded by a gene which is part of a proposed
sterigmatocystin biosynthesis gene cluster, Bacillus
circulans SANK 72073 BtrF encoded by a gene found in the
butirosin biosynthesis gene cluster, and Aspergillus
parasiticus nor-1 involved in the biosynthesis of
aflatoxins. 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 = 233
Score = 44.2 bits (105), Expect = 4e-05
Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 10/74 (13%)
Query: 314 TLSKDQTRPDIIVNAVHPGYVNTDLTG----HKGILTTEQGSVSSVKG--ALIPPDAKEP 367
+L+ + R I V ++HPG+V TD+ G +KG +T E+ SV G +I +E
Sbjct: 164 SLAVELKRDGITVVSLHPGWVRTDMGGPFAKNKGPITPEE----SVAGLLKVIDNLNEED 219
Query: 368 RGQFIWYDGSIVDW 381
G+F+ YDG+ + W
Sbjct: 220 SGKFLDYDGTEIPW 233
Score = 34.6 bits (80), Expect = 0.059
Identities = 28/144 (19%), Positives = 51/144 (35%), Gaps = 47/144 (32%)
Query: 157 QQAETTLATNFFALVTVCHMLFPLLRP--HARVVNVASQYGMLYKVPSQELKQTLLNDSL 214
+ N + + PLL A+++N++S+ G S+
Sbjct: 98 EDLLEVFQVNVLGPLLLTQAFLPLLLKGARAKIINISSRVG-----------------SI 140
Query: 215 TEDQLVGMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIV 274
++ G Y SK + L+ +L+ + R I V
Sbjct: 141 GDNTSGGWY--------------------SYRASKAALNMLT----KSLAVELKRDGITV 176
Query: 275 NAVHPGYVNTDLTG----HKGILT 294
++HPG+V TD+ G +KG +T
Sbjct: 177 VSLHPGWVRTDMGGPFAKNKGPIT 200
>gnl|CDD|187610 cd05352, MDH-like_SDR_c, mannitol dehydrogenase (MDH)-like,
classical (c) SDRs. NADP-mannitol dehydrogenase
catalyzes the conversion of fructose to mannitol, an
acyclic 6-carbon sugar. MDH is a tetrameric member of
the SDR family. This subgroup also includes various
other tetrameric SDRs, including Pichia stipitis
D-arabinitol dehydrogenase (aka polyol dehydrogenase),
Candida albicans Sou1p, a sorbose reductase, and Candida
parapsilosis (S)-specific carbonyl reductase (SCR, aka
S-specific alcohol dehydrogenase) which catalyzes the
enantioselective reduction of 2-hydroxyacetophenone into
(S)-1-phenyl-1,2-ethanediol. 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).
Length = 252
Score = 43.9 bits (104), Expect = 5e-05
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGH 289
Y SK VI L+ +L+ + + I VN++ PGY++TDLT
Sbjct: 159 AYNASKAAVIHLA----KSLAVEWAKYFIRVNSISPGYIDTDLTDF 200
Score = 37.7 bits (88), Expect = 0.006
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 298 HTLKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGH 341
+ K VI L+ +L+ + + I VN++ PGY++TDLT
Sbjct: 161 NASKAAVIHLA----KSLAVEWAKYFIRVNSISPGYIDTDLTDF 200
>gnl|CDD|237099 PRK12428, PRK12428, 3-alpha-hydroxysteroid dehydrogenase;
Provisional.
Length = 241
Score = 43.5 bits (103), Expect = 8e-05
Identities = 36/136 (26%), Positives = 45/136 (33%), Gaps = 20/136 (14%)
Query: 149 VKGNAPFGQQAETTLATNFFALVTVCHMLFPLLRPHARVVNVASQYGMLYKVPSQELKQT 208
V G AP E NF L + L P + P +VNVAS G + + K
Sbjct: 58 VPGTAP----VELVARVNFLGLRHLTEALLPRMAPGGAIVNVASLAGAEWPQRLELHKAL 113
Query: 209 LLNDSLTEDQLVGMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQT 268
S E LA G Y +SK +I + Q +
Sbjct: 114 AATASFDEGAAW--------LAAHPVALATG-----YQLSKEALILWTMRQAQPWFGAR- 159
Query: 269 RPDIIVNAVHPGYVNT 284
I VN V PG V T
Sbjct: 160 --GIRVNCVAPGPVFT 173
>gnl|CDD|180774 PRK06953, PRK06953, short chain dehydrogenase; Provisional.
Length = 222
Score = 42.0 bits (99), Expect = 2e-04
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 319 QTRPDIIVNAVHPGYVNTDLTGHKGILTTEQGSVSSVKG--ALIPPDAKEPRGQFIWYDG 376
Q R + A+HPG+V TD+ G + L Q SV G +I + G+F YDG
Sbjct: 163 QARHATCI-ALHPGWVRTDMGGAQAALDPAQ----SVAGMRRVIAQATRRDNGRFFQYDG 217
Query: 377 SIVDW 381
+ W
Sbjct: 218 VELSW 222
>gnl|CDD|214818 smart00784, SPT2, SPT2 chromatin protein. This entry includes the
Saccharomyces cerevisiae protein SPT2 which is a
chromatin protein involved in transcriptional
regulation.
Length = 106
Score = 35.8 bits (83), Expect = 0.005
Identities = 9/26 (34%), Positives = 20/26 (76%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
+++ E EEE EK+++++K+ +K+K
Sbjct: 81 LARLEDREEERLEKEEEREKRARKRK 106
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 37.7 bits (88), Expect = 0.008
Identities = 15/36 (41%), Positives = 25/36 (69%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILT 38
S +E EE+EEE ++++ + +K+K +L T RILT
Sbjct: 149 SDEELSEEDEEEAAEEEEAEAEKEKASELATTRILT 184
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal.
This domain is found to the N-terminus of bacterial
signal peptidases of the S49 family (pfam01343).
Length = 154
Score = 36.4 bits (85), Expect = 0.008
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNR 35
++ KKE + E+ EKK +K K K +KK + + +
Sbjct: 62 LLDKKELKAWEKAEKKAEKAKAKAEKKKAKKEEPK 96
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 37.6 bits (88), Expect = 0.008
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRKFYQQERISQHR 59
K EEE +EE ++KK++KKK+++ ++ RK ++ER Q R
Sbjct: 273 LKAAEEERQEEAQEKKEEKKKEER-------EAKLAKLSPEEQRKLEEKERKKQAR 321
>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 = 37.2 bits (87), Expect = 0.009
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
Y SK GVI + +L+K+ +I VNAV PG+++TD+T
Sbjct: 148 YAASKAGVIGFT----KSLAKELASRNITVNAVAPGFIDTDMT 186
Score = 32.2 bits (74), Expect = 0.33
Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 4/39 (10%)
Query: 301 KVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 339
K GVI + +L+K+ +I VNAV PG+++TD+T
Sbjct: 152 KAGVIGFT----KSLAKELASRNITVNAVAPGFIDTDMT 186
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 37.4 bits (87), Expect = 0.010
Identities = 15/25 (60%), Positives = 21/25 (84%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+ KE+E +EEEEK++KKKK KK K+
Sbjct: 55 TDKEEEVDEEEEKEEKKKKTKKVKE 79
Score = 36.7 bits (85), Expect = 0.021
Identities = 12/24 (50%), Positives = 19/24 (79%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKK 26
++EEE +EE++K++KKKK KK
Sbjct: 53 KTTDKEEEVDEEEEKEEKKKKTKK 76
Score = 35.9 bits (83), Expect = 0.036
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
K +EEE +E+++K++KKKK KK
Sbjct: 52 EKTTDKEEEVDEEEEKEEKKKKTKK 76
Score = 35.1 bits (81), Expect = 0.059
Identities = 13/25 (52%), Positives = 20/25 (80%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+ ++EE +EEE+K++KKKK KK K
Sbjct: 54 TTDKEEEVDEEEEKEEKKKKTKKVK 78
Score = 28.6 bits (64), Expect = 7.0
Identities = 8/25 (32%), Positives = 19/25 (76%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+++ ++EEE ++++K++KKKK
Sbjct: 50 EEEKTTDKEEEVDEEEEKEEKKKKT 74
>gnl|CDD|171821 PRK12937, PRK12937, short chain dehydrogenase; Provisional.
Length = 245
Score = 37.0 bits (86), Expect = 0.011
Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDL 286
PY SK V L + L+ + I VNAV PG V T+L
Sbjct: 152 PYAASKAAVEGLVHV----LANELRGRGITVNAVAPGPVATEL 190
Score = 32.0 bits (73), Expect = 0.43
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 315 LSKDQTRPDIIVNAVHPGYVNTDL 338
L+ + I VNAV PG V T+L
Sbjct: 167 LANELRGRGITVNAVAPGPVATEL 190
>gnl|CDD|183775 PRK12826, PRK12826, 3-ketoacyl-(acyl-carrier-protein) reductase;
Reviewed.
Length = 251
Score = 36.4 bits (85), Expect = 0.013
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTG 288
Y SK G++ F + L+ + +I VN+VHPG V+T + G
Sbjct: 156 YAASKAGLV--GFTR--ALALELAARNITVNSVHPGGVDTPMAG 195
Score = 31.8 bits (73), Expect = 0.43
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 301 KVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTG 340
K G++ F + L+ + +I VN+VHPG V+T + G
Sbjct: 160 KAGLV--GFTR--ALALELAARNITVNSVHPGGVDTPMAG 195
>gnl|CDD|235500 PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 248
Score = 36.3 bits (85), Expect = 0.016
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
Y SK GVI + +L+++ I VNAV PG++ TD+T
Sbjct: 155 YAASKAGVIGFT----KSLARELASRGITVNAVAPGFIETDMT 193
Score = 31.7 bits (73), Expect = 0.47
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 301 KVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 339
K GVI + +L+++ I VNAV PG++ TD+T
Sbjct: 159 KAGVIGFT----KSLARELASRGITVNAVAPGFIETDMT 193
>gnl|CDD|221857 pfam12923, RRP7, Ribosomal RNA-processing protein 7 (RRP7). RRP7
is an essential protein in yeast that is involved in
pre-rRNA processing and ribosome assembly. It is
speculated to be required for correct assembly of rpS27
into the pre-ribosomal particle.
Length = 131
Score = 34.9 bits (81), Expect = 0.016
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKKF 28
S+ + EE + K+KKKKKKK+ + F
Sbjct: 65 GASRNKAAEERRKLKEKKKKKKKELENF 92
>gnl|CDD|187605 cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like,
classical (c) SDRs. Ga5DH catalyzes the NADP-dependent
conversion of carbon source D-gluconate and
5-keto-D-gluconate. This SDR subgroup has a classical
Gly-rich NAD(P)-binding motif and a conserved active
site tetrad pattern. However, it has been proposed that
Arg104 (Streptococcus suis Ga5DH numbering), as well as
an active site Ca2+, play a critical role in catalysis.
In addition to Ga5DHs this subgroup contains Erwinia
chrysanthemi KduD which is involved in pectin
degradation, and is a putative
2,5-diketo-3-deoxygluconate dehydrogenase. 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 = 248
Score = 36.2 bits (84), Expect = 0.019
Identities = 24/130 (18%), Positives = 39/130 (30%), Gaps = 46/130 (35%)
Query: 162 TLATNFFALVTVCHMLFPLLRP--HARVVNVASQYGMLYKVPSQELKQTLLNDSLTEDQL 219
+ N + V + + H +++N+ S
Sbjct: 109 VIDVNLNGVFFVSQAVARHMIKQGHGKIINICS--------------------------- 141
Query: 220 VGMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHP 279
+ G P Y SK GV L+ L+ + R I VNA+ P
Sbjct: 142 ---LLSE----------LGGPPVPAYAASKGGVAGLT----KALATEWARHGIQVNAIAP 184
Query: 280 GYVNTDLTGH 289
GY T++T
Sbjct: 185 GYFATEMTEA 194
>gnl|CDD|187648 cd08944, SDR_c12, classical (c) SDR, subgroup 12. These are
classical SDRs, with the canonical active site tetrad
and glycine-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 = 246
Score = 35.9 bits (83), Expect = 0.023
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
Y SK + L+ A L R NA+ PG ++T L
Sbjct: 150 YGASKAAIRNLTRTLAAELRHAGIR----CNALAPGLIDTPLL 188
Score = 30.5 bits (69), Expect = 1.1
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 4/39 (10%)
Query: 301 KVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 339
K + L+ A L R NA+ PG ++T L
Sbjct: 154 KAAIRNLTRTLAAELRHAGIR----CNALAPGLIDTPLL 188
>gnl|CDD|187594 cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase (BKR),
involved in Type II FAS, classical (c) SDRs. This
subgroup includes the Escherichai coli K12 BKR, FabG.
BKR catalyzes the NADPH-dependent reduction of ACP in
the first reductive step of de novo fatty acid synthesis
(FAS). FAS consists of four elongation steps, which are
repeated to extend the fatty acid chain through the
addition of two-carbo units from malonyl acyl-carrier
protein (ACP): condensation, reduction, dehydration, and
a final reduction. Type II FAS, typical of plants and
many bacteria, maintains these activities on discrete
polypeptides, while type I FAS utilizes one or two
multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) 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: TGxxxGxG in classical SDRs. 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 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. 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-151 and
Lys-155, and well as Asn-111 (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 = 240
Score = 35.6 bits (83), Expect = 0.028
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
Y SK GVI +L+K+ I VNAV PG+++TD+T
Sbjct: 149 YAASKAGVIGF----TKSLAKELASRGITVNAVAPGFIDTDMT 187
Score = 31.7 bits (73), Expect = 0.47
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 301 KVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 339
K GVI +L+K+ I VNAV PG+++TD+T
Sbjct: 153 KAGVIGF----TKSLAKELASRGITVNAVAPGFIDTDMT 187
>gnl|CDD|183833 PRK12939, PRK12939, short chain dehydrogenase; Provisional.
Length = 250
Score = 35.7 bits (83), Expect = 0.028
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
Y SK VI ++ +L+++ I VNA+ PG T+ T
Sbjct: 155 AYVASKGAVIGMT----RSLARELGGRGITVNAIAPGLTATEAT 194
Score = 31.5 bits (72), Expect = 0.56
Identities = 19/70 (27%), Positives = 25/70 (35%), Gaps = 14/70 (20%)
Query: 324 IIVNAVHPGYVNTDLTG-----------HKGILTTEQGSVSSVKGA---LIPPDAKEPRG 369
I VNA+ PG T+ T KG V GA L+ A+ G
Sbjct: 179 ITVNAIAPGLTATEATAYVPADERHAYYLKGRALERLQVPDDVAGAVLFLLSDAARFVTG 238
Query: 370 QFIWYDGSIV 379
Q + +G V
Sbjct: 239 QLLPVNGGFV 248
>gnl|CDD|236173 PRK08177, PRK08177, short chain dehydrogenase; Provisional.
Length = 225
Score = 35.4 bits (82), Expect = 0.028
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 318 DQTRPDIIVNAVHPGYVNTDLTGHKGILTTEQGSVSSVKGALIPPDAKEPRG--QFIWYD 375
+ P + V ++HPG+V TD+ G L E SVKG + +A +G +FI Y
Sbjct: 164 ELGEPTLTVLSMHPGWVKTDMGGDNAPLDVET----SVKGLVEQIEAASGKGGHRFIDYQ 219
Query: 376 GSIVDW 381
G + W
Sbjct: 220 GETLPW 225
Score = 30.0 bits (68), Expect = 1.8
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 266 DQTRPDIIVNAVHPGYVNTDLTGHKGILTMT 296
+ P + V ++HPG+V TD+ G L +
Sbjct: 164 ELGEPTLTVLSMHPGWVKTDMGGDNAPLDVE 194
>gnl|CDD|187662 cd09761, A3DFK9-like_SDR_c, Clostridium thermocellum A3DFK9-like, a
putative carbohydrate or polyalcohol metabolizing SDR,
classical (c) SDRs. This subgroup includes a putative
carbohydrate or polyalcohol metabolizing SDR (A3DFK9)
from Clostridium thermocellum. Its members have a
TGXXXGXG classical-SDR glycine-rich NAD-binding motif,
and some have a canonical SDR active site tetrad (A3DFK9
lacks the upstream Asn). 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 = 242
Score = 35.6 bits (82), Expect = 0.029
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 6/45 (13%)
Query: 241 PD-DPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNT 284
PD + Y SK G++ L+ +L PDI VN + PG++NT
Sbjct: 141 PDSEAYAASKGGLVALTHALAMSLG-----PDIRVNCISPGWINT 180
>gnl|CDD|219761 pfam08243, SPT2, SPT2 chromatin protein. This family includes the
Saccharomyces cerevisiae protein SPT2 which is a
chromatin protein involved in transcriptional
regulation.
Length = 116
Score = 34.1 bits (78), Expect = 0.031
Identities = 13/20 (65%), Positives = 16/20 (80%)
Query: 4 KKEQEEEEEEEKKKKKKKKK 23
++E EEEEEK+KKKKK K
Sbjct: 97 ERELAREEEEEKRKKKKKNK 116
Score = 32.5 bits (74), Expect = 0.091
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
+++ E E E E++++K+KKKKK K
Sbjct: 91 MARLEDERELAREEEEEKRKKKKKNK 116
>gnl|CDD|180413 PRK06128, PRK06128, oxidoreductase; Provisional.
Length = 300
Score = 35.6 bits (82), Expect = 0.032
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 8/92 (8%)
Query: 157 QQAETTLATNFFALVTVCHMLFPLLRPHARVVNVASQYGMLYKVPSQELKQTLLNDSLTE 216
+Q + T TN +A+ +C P L P A ++N S + S + TLL+ + T+
Sbjct: 157 EQFDATFKTNVYAMFWLCKAAIPHLPPGASIINTGS-------IQSYQPSPTLLDYASTK 209
Query: 217 DQLVGMMHDYVK-LAKEGKDQEAGWPDDPYTV 247
+V K +A++G A P +T
Sbjct: 210 AAIVAFTKALAKQVAEKGIRVNAVAPGPVWTP 241
>gnl|CDD|220237 pfam09428, DUF2011, Fungal protein of unknown function (DUF2011).
This is a family of fungal proteins whose function is
unknown.
Length = 130
Score = 34.2 bits (79), Expect = 0.034
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKKF 28
I + +E +E +K+K+ +K ++KKF
Sbjct: 94 IALRLRRERTKERAEKEKRTRKNREKKF 121
Score = 33.4 bits (77), Expect = 0.064
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
+ ++ +E E+EK+ +K ++KK K+
Sbjct: 97 RLRRERTKERAEKEKRTRKNREKKFKR 123
Score = 32.2 bits (74), Expect = 0.13
Identities = 7/25 (28%), Positives = 18/25 (72%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
++ +E E+E++ +K ++KK K++
Sbjct: 100 RERTKERAEKEKRTRKNREKKFKRR 124
Score = 27.2 bits (61), Expect = 7.7
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+K E+E E+EKKKK+K+ KK++
Sbjct: 69 AKVEKELLREKEKKKKRKRPGKKRR 93
>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 = 35.1 bits (81), Expect = 0.039
Identities = 19/54 (35%), Positives = 23/54 (42%), Gaps = 6/54 (11%)
Query: 238 AGWPDDP----YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
G DP Y SK V + A L I VN+VHPGY+ T +T
Sbjct: 140 EGLVGDPALAAYNASKGAV--RGLTKSAALECATQGYGIRVNSVHPGYIYTPMT 191
Score = 28.1 bits (63), Expect = 7.7
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 301 KVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 339
K V + A L I VN+VHPGY+ T +T
Sbjct: 155 KGAV--RGLTKSAALECATQGYGIRVNSVHPGYIYTPMT 191
>gnl|CDD|187608 cd05350, SDR_c6, classical (c) SDR, subgroup 6. These proteins are
members of the classical SDR family, with a canonical
active site tetrad and a fairly well conserved 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 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 = 239
Score = 35.0 bits (81), Expect = 0.041
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 238 AGWPDDP-YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT--GHKGILT 294
G P Y+ SK + L+ +L D + I V ++PG+++T LT
Sbjct: 139 RGLPGAAAYSASKAALSSLA----ESLRYDVKKRGIRVTVINPGFIDTPLTANMFTMPFL 194
Query: 295 MTIHT 299
M++
Sbjct: 195 MSVEQ 199
Score = 29.2 bits (66), Expect = 3.4
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 315 LSKDQTRPDIIVNAVHPGYVNTDLT--GHK--GILTTEQGSVSSVKG 357
L D + I V ++PG+++T LT +++ EQ + K
Sbjct: 161 LRYDVKKRGIRVTVINPGFIDTPLTANMFTMPFLMSVEQAAKRIYKA 207
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 35.6 bits (82), Expect = 0.041
Identities = 17/36 (47%), Positives = 20/36 (55%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRIL 37
I K + E E E K KK KK KKKK L T+ +L
Sbjct: 233 IEKPQAEAENEAGKSDKKDKKSKKKKVLGKGTSAVL 268
>gnl|CDD|218188 pfam04641, Rtf2, Replication termination factor 2. It is vital for
effective cell-replication that replication is not
stalled at any point by, for instance, damaged bases.
Rtf2 stabilizes the replication fork stalled at the
site-specific replication barrier RTS1 by preventing
replication restart until completion of DNA synthesis by
a converging replication fork initiated at a flanking
origin. The RTS1 element terminates replication forks
that are moving in the cen2-distal direction while
allowing forks moving in the cen2-proximal direction to
pass through the region. Rtf2 contains a C2HC2 motif
related to the C3HC4 RING-finger motif, and would appear
to fold up, creating a RING finger-like structure but
forming only one functional Zn2+ ion-binding site.
Length = 254
Score = 35.0 bits (81), Expect = 0.042
Identities = 15/23 (65%), Positives = 17/23 (73%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKK 26
K + EEE +KKKKKKKKK KK
Sbjct: 172 LKARLEEERAKKKKKKKKKKTKK 194
Score = 35.0 bits (81), Expect = 0.043
Identities = 17/29 (58%), Positives = 19/29 (65%), Gaps = 6/29 (20%)
Query: 5 KEQEE------EEEEEKKKKKKKKKKKKK 27
+E+ E EEE KKKKKKKKKK KK
Sbjct: 166 EEEVELLKARLEEERAKKKKKKKKKKTKK 194
Score = 29.6 bits (67), Expect = 2.8
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
++ + +EE +++KKKKKKK KK
Sbjct: 171 LLKARLEEERAKKKKKKKKKKTKKNNA 197
>gnl|CDD|235545 PRK05650, PRK05650, short chain dehydrogenase; Provisional.
Length = 270
Score = 35.0 bits (81), Expect = 0.044
Identities = 29/126 (23%), Positives = 43/126 (34%), Gaps = 46/126 (36%)
Query: 163 LATNFFALVTVCHMLFPLLRP--HARVVNVASQYGMLYKVPSQELKQTLLNDSLTEDQLV 220
+A N +V C PL + R+VN+AS G++ Q
Sbjct: 105 IAINLMGVVKGCKAFLPLFKRQKSGRIVNIASMAGLM--------------------QGP 144
Query: 221 GMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPG 280
M Y V+K GV+ LS TL + +I V+ V P
Sbjct: 145 AM--------------------SSYNVAKAGVVALS----ETLLVELADDEIGVHVVCPS 180
Query: 281 YVNTDL 286
+ T+L
Sbjct: 181 FFQTNL 186
>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19.
Med19 represents a family of conserved proteins which
are members of the multi-protein co-activator Mediator
complex. Mediator is required for activation of RNA
polymerase II transcription by DNA binding
transactivators.
Length = 178
Score = 34.4 bits (79), Expect = 0.045
Identities = 14/24 (58%), Positives = 22/24 (91%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K+++ E+++E+KKKKK+KKKKKK
Sbjct: 144 HKKKKHEDDKERKKKKKEKKKKKK 167
Score = 33.6 bits (77), Expect = 0.086
Identities = 15/24 (62%), Positives = 22/24 (91%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK++ E+++E KKKKK+KKKKKK+
Sbjct: 145 KKKKHEDDKERKKKKKEKKKKKKR 168
Score = 31.7 bits (72), Expect = 0.37
Identities = 14/24 (58%), Positives = 21/24 (87%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK+ E+++E +KKKK+KKKKKK+
Sbjct: 146 KKKHEDDKERKKKKKEKKKKKKRH 169
Score = 31.0 bits (70), Expect = 0.68
Identities = 13/24 (54%), Positives = 22/24 (91%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK ++++ E++K++KKKKK+KKKK
Sbjct: 142 KKHKKKKHEDDKERKKKKKEKKKK 165
Score = 31.0 bits (70), Expect = 0.70
Identities = 12/24 (50%), Positives = 22/24 (91%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K ++++ E+++++KKKKK+KKKKK
Sbjct: 143 KHKKKKHEDDKERKKKKKEKKKKK 166
>gnl|CDD|218482 pfam05178, Kri1, KRI1-like family. The yeast member of this
family (Kri1p) is found to be required for 40S ribosome
biogenesis in the nucleolus.
Length = 99
Score = 33.0 bits (76), Expect = 0.056
Identities = 8/23 (34%), Positives = 18/23 (78%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKK 27
KE++EEE+ +++++ K+ K K+
Sbjct: 1 KERKEEEKAQREEELKRLKNLKR 23
Score = 31.5 bits (72), Expect = 0.17
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKK 26
+KE+E+ + EE+ K+ K K+++
Sbjct: 3 RKEEEKAQREEELKRLKNLKREE 25
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 33.5 bits (77), Expect = 0.064
Identities = 11/25 (44%), Positives = 20/25 (80%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
K+E+++ ++EEK KK+ K++KKK
Sbjct: 70 QKREEKKRKDEEKTAKKRAKRQKKK 94
Score = 31.9 bits (73), Expect = 0.23
Identities = 11/24 (45%), Positives = 21/24 (87%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+K++++EE+ KK+ K++KKK+KK
Sbjct: 74 EKKRKDEEKTAKKRAKRQKKKQKK 97
Score = 31.2 bits (71), Expect = 0.37
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 9/33 (27%)
Query: 4 KKEQEEEEEE---------EKKKKKKKKKKKKK 27
++E++ ++EE +KKK+KKKKKKK K
Sbjct: 72 REEKKRKDEEKTAKKRAKRQKKKQKKKKKKKAK 104
>gnl|CDD|236210 PRK08267, PRK08267, short chain dehydrogenase; Provisional.
Length = 260
Score = 34.5 bits (80), Expect = 0.071
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 158 QAETTLATNFFALVTVCHMLFPLLR--PHARVVNVASQ---YGM 196
+ + N ++ H P L+ P ARV+N +S YG
Sbjct: 100 AHDRVIDINVKGVLNGAHAALPYLKATPGARVINTSSASAIYGQ 143
>gnl|CDD|146145 pfam03357, Snf7, Snf7. This family of proteins are involved in
protein sorting and transport from the endosome to the
vacuole/lysosome in eukaryotic cells.
Vacuoles/lysosomes play an important role in the
degradation of both lipids and cellular proteins. In
order to perform this degradative function,
vacuoles/lysosomes contain numerous hydrolases which
have been transported in the form of inactive
precursors via the biosynthetic pathway and are
proteolytically activated upon delivery to the
vacuole/lysosome. The delivery of transmembrane
proteins, such as activated cell surface receptors to
the lumen of the vacuole/lysosome, either for
degradation/downregulation, or in the case of
hydrolases, for proper localisation, requires the
formation of multivesicular bodies (MVBs). These late
endosomal structures are formed by invaginating and
budding of the limiting membrane into the lumen of the
compartment. During this process, a subset of the
endosomal membrane proteins is sorted into the forming
vesicles. Mature MVBs fuse with the vacuole/lysosome,
thereby releasing cargo containing vesicles into its
hydrolytic lumen for degradation. Endosomal proteins
that are not sorted into the intralumenal MVB vesicles
are either recycled back to the plasma membrane or
Golgi complex, or remain in the limiting membrane of
the MVB and are thereby transported to the limiting
membrane of the vacuole/lysosome as a consequence of
fusion. Therefore, the MVB sorting pathway plays a
critical role in the decision between recycling and
degradation of membrane proteins. A few archaeal
sequences are also present within this family.
Length = 169
Score = 33.8 bits (78), Expect = 0.074
Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 5/67 (7%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRKFYQQ-ERISQHRF 60
E++ ++ E + KK KK K L L + L + Q + Q R
Sbjct: 17 QESLEKKIKKLEAEIKKLAKKGNKDAALILLKQKKRYEKQ----LDQLDGQLANLEQVRM 72
Query: 61 LIEGVNA 67
IE
Sbjct: 73 AIENAKT 79
Score = 27.6 bits (62), Expect = 9.2
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRKFYQQERISQHRFL 61
+ KK++ E++ +K + + KK KK D IL + + K Q +++
Sbjct: 13 LDKKQESLEKKIKKLEAEIKKLAKKG--NKDAALILLK--QKKRYEK--QLDQLDGQLAN 66
Query: 62 IEGVN 66
+E V
Sbjct: 67 LEQVR 71
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 34.2 bits (79), Expect = 0.077
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKK 27
E+ + E+ K KKKK K K K
Sbjct: 192 NEKLKAEKAAKGGKKKKGKAKAK 214
Score = 33.9 bits (78), Expect = 0.087
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKK 25
+I++K + E+ + KKKK K K K
Sbjct: 190 LINEKLKAEKAAKGGKKKKGKAKAK 214
Score = 30.4 bits (69), Expect = 1.3
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+KE+E+ + K K KK K K +
Sbjct: 43 EEKEEEKAKVAAKAKAKKALKAKIE 67
Score = 30.0 bits (68), Expect = 1.7
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 6 EQEEEEEEEKKKKKKKKKKKKK 27
E++EE+EEEK K K K KK
Sbjct: 40 EEDEEKEEEKAKVAAKAKAKKA 61
Score = 30.0 bits (68), Expect = 1.8
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 6 EQEEEEEEEKKKKKKKKKKKKK 27
++EE+EE+E++K K K K K
Sbjct: 38 DEEEDEEKEEEKAKVAAKAKAK 59
Score = 29.6 bits (67), Expect = 2.0
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 9 EEEEEEKKKKKKKKKKKKKFLQL 31
E+ + EK K KKKK K +L
Sbjct: 193 EKLKAEKAAKGGKKKKGKAKAKL 215
Score = 29.6 bits (67), Expect = 2.4
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 6 EQEEEEEEEKKKKKKKKKKKKKFLQ 30
E+E+EE+EE+K K K K KK L+
Sbjct: 39 EEEDEEKEEEKAKVAAKAKAKKALK 63
Score = 29.2 bits (66), Expect = 3.0
Identities = 11/30 (36%), Positives = 21/30 (70%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDT 33
KK + + EE++K K++K++K + L+ DT
Sbjct: 59 KKALKAKIEEKEKAKREKEEKGLRELEEDT 88
Score = 28.9 bits (65), Expect = 4.0
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTR 39
K + + EE+EK K++K++K ++ + L
Sbjct: 60 KALKAKIEEKEKAKREKEEKGLRELEEDTPEDELAE 95
Score = 28.5 bits (64), Expect = 6.2
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K+E++ + + K KK K K ++
Sbjct: 45 KEEEKAKVAAKAKAKKALKAKIEE 68
>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex. This
entry is characterized by proteins with alternating
conserved and low-complexity regions. Bud13 together
with Snu17p and a newly identified factor,
Pml1p/Ylr016c, form a novel trimeric complex. called
The RES complex, pre-mRNA retention and splicing
complex. Subunits of this complex are not essential for
viability of yeasts but they are required for efficient
splicing in vitro and in vivo. Furthermore,
inactivation of this complex causes pre-mRNA leakage
from the nucleus. Bud13 contains a unique,
phylogenetically conserved C-terminal region of unknown
function.
Length = 141
Score = 33.4 bits (77), Expect = 0.077
Identities = 12/27 (44%), Positives = 23/27 (85%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
II +E+ EE+E EK++K++K++K+K+
Sbjct: 11 IIDIEEKREEKEREKEEKERKEEKEKE 37
Score = 29.2 bits (66), Expect = 2.0
Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 8/66 (12%)
Query: 2 ISKKEQEEEEEEEKKKKKKK-------KKKKKKFLQLDTNRILTRSMNARFLRKFYQQER 54
+KE+E+EE+E K++K+K+ K++++K L+ + + + + + Y +E
Sbjct: 18 REEKEREKEEKERKEEKEKEWGKGLVQKEEREKRLE-ELEKAKNKPLARYADDEDYDEEL 76
Query: 55 ISQHRF 60
Q R+
Sbjct: 77 KEQERW 82
>gnl|CDD|180576 PRK06463, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 255
Score = 34.4 bits (79), Expect = 0.080
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
Y ++K G+I L+ L+ + + I VNAV PG+V TD+T
Sbjct: 152 YAITKAGIIILT----RRLAFELGKYGIRVNAVAPGWVETDMT 190
Score = 30.1 bits (68), Expect = 1.8
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 301 KVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 339
K G+I L+ L+ + + I VNAV PG+V TD+T
Sbjct: 156 KAGIIILT----RRLAFELGKYGIRVNAVAPGWVETDMT 190
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 33.9 bits (78), Expect = 0.081
Identities = 15/24 (62%), Positives = 19/24 (79%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK+++E+ E K KKKKKKKKKK
Sbjct: 170 KKDKKEKMVEPKGSKKKKKKKKKK 193
Score = 31.6 bits (72), Expect = 0.44
Identities = 14/25 (56%), Positives = 20/25 (80%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+++ E EEEEKK+KKKKK+ KK+
Sbjct: 142 KVEKEAEVEEEEKKEKKKKKEVKKE 166
Score = 30.8 bits (70), Expect = 0.78
Identities = 14/22 (63%), Positives = 16/22 (72%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKK 24
KKE+ E + KKKKKKKKKK
Sbjct: 172 DKKEKMVEPKGSKKKKKKKKKK 193
Score = 30.5 bits (69), Expect = 1.2
Identities = 16/24 (66%), Positives = 21/24 (87%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+KE E EEEE+K+KKKKK+ KK+K
Sbjct: 144 EKEAEVEEEEKKEKKKKKEVKKEK 167
Score = 30.1 bits (68), Expect = 1.6
Identities = 12/25 (48%), Positives = 21/25 (84%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
KKE+++++E +K+KK+KK KK+K
Sbjct: 153 EKKEKKKKKEVKKEKKEKKDKKEKM 177
Score = 29.7 bits (67), Expect = 1.7
Identities = 10/25 (40%), Positives = 20/25 (80%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+K++++E ++EKK+KK KK+K +
Sbjct: 155 KEKKKKKEVKKEKKEKKDKKEKMVE 179
Score = 29.3 bits (66), Expect = 2.7
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKK 25
K+++ E + KKKKKKKKKK
Sbjct: 171 KDKKEKMVEPKGSKKKKKKKKKK 193
Score = 28.9 bits (65), Expect = 3.1
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
KKE+++++E+ + K KKKKKKK
Sbjct: 166 EKKEKKDKKEKMVEPKGSKKKKKKK 190
Score = 28.9 bits (65), Expect = 3.6
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+K+ ++E+ E K KKKKKKKKK
Sbjct: 168 KEKKDKKEKMVEPKGSKKKKKKKKK 192
Score = 27.8 bits (62), Expect = 7.9
Identities = 13/25 (52%), Positives = 20/25 (80%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+ K ++E E EE++KK+KKKKK+ K
Sbjct: 140 TAKVEKEAEVEEEEKKEKKKKKEVK 164
Score = 27.8 bits (62), Expect = 8.7
Identities = 15/24 (62%), Positives = 21/24 (87%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+ E EEEE++EKKKKK+ KK+KK+
Sbjct: 146 EAEVEEEEKKEKKKKKEVKKEKKE 169
>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional.
Length = 135
Score = 33.1 bits (76), Expect = 0.083
Identities = 11/27 (40%), Positives = 22/27 (81%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
++ +K ++++++++KKKKKKKK KK
Sbjct: 104 VLKEKAKQKKQKKKKKKKKKKKTSKKA 130
Score = 30.8 bits (70), Expect = 0.54
Identities = 10/25 (40%), Positives = 21/25 (84%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+K++++++++++KKKKK KK KK
Sbjct: 109 AKQKKQKKKKKKKKKKKTSKKAAKK 133
Score = 30.8 bits (70), Expect = 0.58
Identities = 11/27 (40%), Positives = 20/27 (74%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
+ K +Q+++++++KKKKKKK KK
Sbjct: 105 LKEKAKQKKQKKKKKKKKKKKTSKKAA 131
Score = 30.0 bits (68), Expect = 0.81
Identities = 15/26 (57%), Positives = 22/26 (84%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
I K+ +E+ +++K+KKKKKKKKKKK
Sbjct: 100 IVKQVLKEKAKQKKQKKKKKKKKKKK 125
Score = 29.7 bits (67), Expect = 1.2
Identities = 11/24 (45%), Positives = 20/24 (83%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+K+Q+++++++KKKK KK KKK
Sbjct: 111 QKKQKKKKKKKKKKKTSKKAAKKK 134
Score = 29.7 bits (67), Expect = 1.3
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
K+++++++++KKKKKK KK K
Sbjct: 107 EKAKQKKQKKKKKKKKKKKTSKKAAK 132
Score = 29.3 bits (66), Expect = 1.9
Identities = 13/27 (48%), Positives = 22/27 (81%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
I+ + +E+ +++++KKKKKKKKKKK
Sbjct: 100 IVKQVLKEKAKQKKQKKKKKKKKKKKT 126
Score = 28.5 bits (64), Expect = 2.7
Identities = 11/24 (45%), Positives = 20/24 (83%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK+++++++++KKK KK KKKK
Sbjct: 112 KKQKKKKKKKKKKKTSKKAAKKKK 135
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 34.7 bits (80), Expect = 0.087
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKF 28
I + +E EE K KKKK+KKK+ F
Sbjct: 412 IEEIREELIEEGLLKSKKKKRKKKEWF 438
Score = 31.2 bits (71), Expect = 1.1
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTN 34
I ++ EE + KKKK+KKK+ +KF ++
Sbjct: 415 IREELIEEGLLKSKKKKRKKKEWFEKFRWFVSS 447
Score = 30.8 bits (70), Expect = 1.5
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
++ +EE EE K KKKK+KKK++ +
Sbjct: 413 EEIREELIEEGLLKSKKKKRKKKEWFE 439
Score = 28.5 bits (64), Expect = 6.5
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKK 26
I + +E + +KKK+KKK+ +K
Sbjct: 415 IREELIEEGLLKSKKKKRKKKEWFEK 440
>gnl|CDD|187665 cd09805, type2_17beta_HSD-like_SDR_c, human 17beta-hydroxysteroid
dehydrogenase type 2 (type 2 17beta-HSD)-like, classical
(c) SDRs. 17beta-hydroxysteroid dehydrogenases are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. This
classical-SDR subgroup includes the human proteins: type
2 17beta-HSD, type 6 17beta-HSD, type 2 11beta-HSD,
dehydrogenase/reductase SDR family member 9,
short-chain dehydrogenase/reductase family 9C member 7,
3-hydroxybutyrate dehydrogenase type 1, and retinol
dehydrogenase 5. 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 = 281
Score = 34.2 bits (79), Expect = 0.094
Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 163 LATNFFALVTVCHMLFPLLR-PHARVVNVASQYGMLYKVPSQEL 205
+ N F V V PLLR RVVNV+S M +VP
Sbjct: 107 MEVNLFGTVEVTKAFLPLLRRAKGRVVNVSS---MGGRVPFPAG 147
>gnl|CDD|236372 PRK09072, PRK09072, short chain dehydrogenase; Provisional.
Length = 263
Score = 34.1 bits (79), Expect = 0.094
Identities = 19/49 (38%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 153 APFGQQAETT----LATNFFALVTVCHMLFPLLR--PHARVVNVASQYG 195
A Q LA N A + + L PLLR P A VVNV S +G
Sbjct: 94 ALLEDQDPEAIERLLALNLTAPMQLTRALLPLLRAQPSAMVVNVGSTFG 142
>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 156 to 174 amino acids in length. This domain is
found associated with pfam07780, pfam01728.
Length = 154
Score = 33.0 bits (76), Expect = 0.099
Identities = 6/23 (26%), Positives = 17/23 (73%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKK 27
+ E+E + K++K+++ ++K+K
Sbjct: 122 ELLEKELAKLKREKRRENERKQK 144
Score = 30.7 bits (70), Expect = 0.65
Identities = 10/39 (25%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMN 42
+E++ +E EK+ K K++K+++ + IL M
Sbjct: 115 DEEEQIDELLEKELAKLKREKRRE-NERKQKEILKEQMK 152
Score = 29.6 bits (67), Expect = 1.7
Identities = 7/25 (28%), Positives = 17/25 (68%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
++EQ +E E++ K K++K+++
Sbjct: 115 DEEEQIDELLEKELAKLKREKRREN 139
Score = 28.8 bits (65), Expect = 3.1
Identities = 5/31 (16%), Positives = 21/31 (67%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKKFLQL 31
++ K+ + + E+ ++ ++K+K+ K+ +++
Sbjct: 123 LLEKELAKLKREKRRENERKQKEILKEQMKM 153
Score = 28.0 bits (63), Expect = 4.7
Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 12/46 (26%)
Query: 2 ISKKEQEEEE------------EEEKKKKKKKKKKKKKFLQLDTNR 35
++E+ E E E+E K K++K+++ + Q + +
Sbjct: 103 EEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEILK 148
>gnl|CDD|187589 cd05328, 3alpha_HSD_SDR_c, alpha hydroxysteroid dehydrogenase
(3alpha_HSD), classical (c) SDRs. Bacterial
3-alpha_HSD, which catalyzes the NAD-dependent
oxidoreduction of hydroxysteroids, is a dimeric member
of the classical 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 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 = 34.0 bits (78), Expect = 0.10
Identities = 34/133 (25%), Positives = 48/133 (36%), Gaps = 20/133 (15%)
Query: 159 AETTLATNFFALVTVCHMLFPLLRPHA--RVVNVASQYGMLYKVPSQELKQTLLNDSLTE 216
A L N+F L + L P LR V V+S G + EL + L + TE
Sbjct: 76 AGLVLKVNYFGLRALMEALLPRLRKGHGPAAVVVSSIAGAGWAQDKLELAKALA--AGTE 133
Query: 217 DQLVGMMHDYVKLAKEGKDQEAGWPDDP-YTVSKVGVIKLSFIQHATLSKDQTRPDIIVN 275
+ V + + AG P Y SK + + + AT + VN
Sbjct: 134 ARAVAL------------AEHAGQPGYLAYAGSKEALTVWTRRRAATW---LYGAGVRVN 178
Query: 276 AVHPGYVNTDLTG 288
V PG V T +
Sbjct: 179 TVAPGPVETPILQ 191
>gnl|CDD|168574 PRK06484, PRK06484, short chain dehydrogenase; Validated.
Length = 520
Score = 34.4 bits (79), Expect = 0.11
Identities = 29/115 (25%), Positives = 44/115 (38%), Gaps = 16/115 (13%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGHKGILTMTIHTLKVGV 304
Y+ SK VI L+ +L+ + I VNAV PGYV T M + G
Sbjct: 154 YSASKAAVISLT----RSLACEWAAKGIRVNAVLPGYVRTQ---------MVAELERAGK 200
Query: 305 IKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTG-HKGILTTEQGSVSSVKGA 358
+ S ++ RP+ I AV ++ +D G G + G+
Sbjct: 201 LDPSAVRSRIPLGRLGRPEEIAEAVF--FLASDQASYITGSTLVVDGGWTVYGGS 253
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 34.2 bits (79), Expect = 0.11
Identities = 14/24 (58%), Positives = 22/24 (91%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK++EE++ +++KKKKK+KKK KK
Sbjct: 384 KKKREEKKPQKRKKKKKRKKKGKK 407
Score = 33.8 bits (78), Expect = 0.13
Identities = 13/24 (54%), Positives = 20/24 (83%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK +E++ ++ KKKKK+KKK KK+
Sbjct: 385 KKREEKKPQKRKKKKKRKKKGKKR 408
Score = 33.0 bits (76), Expect = 0.24
Identities = 13/24 (54%), Positives = 20/24 (83%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K++ EE++ +K+KKKKK+KKK K
Sbjct: 383 PKKKREEKKPQKRKKKKKRKKKGK 406
Score = 33.0 bits (76), Expect = 0.26
Identities = 12/25 (48%), Positives = 21/25 (84%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKF 28
K+E+++ ++ +KKKK+KKK KK+K
Sbjct: 386 KREEKKPQKRKKKKKRKKKGKKRKK 410
Score = 31.1 bits (71), Expect = 1.2
Identities = 10/24 (41%), Positives = 21/24 (87%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
++++ ++ +++KK+KKK KK+KKK
Sbjct: 388 EEKKPQKRKKKKKRKKKGKKRKKK 411
Score = 30.3 bits (69), Expect = 1.6
Identities = 11/24 (45%), Positives = 20/24 (83%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK Q+ ++++++KKK KK+KKK +
Sbjct: 390 KKPQKRKKKKKRKKKGKKRKKKGR 413
Score = 29.6 bits (67), Expect = 3.5
Identities = 10/24 (41%), Positives = 19/24 (79%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K ++ +++++ KKK KK+KKK +K
Sbjct: 391 KPQKRKKKKKRKKKGKKRKKKGRK 414
>gnl|CDD|237219 PRK12827, PRK12827, short chain dehydrogenase; Provisional.
Length = 249
Score = 33.5 bits (77), Expect = 0.12
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGHKGILTMTIHTLK 301
Y SK G+I L+ TL+ + I VNAV PG +NT + + T H L
Sbjct: 159 NYAASKAGLIGLT----KTLANELAPRGITVNAVAPGAINTPMADN---AAPTEHLLN 209
Score = 28.1 bits (63), Expect = 7.9
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 324 IIVNAVHPGYVNTDL 338
I VNAV PG +NT +
Sbjct: 183 ITVNAVAPGAINTPM 197
>gnl|CDD|240576 cd12932, RRP7_like, RRP7 domain ribosomal RNA-processing protein
7 (Rrp7p), ribosomal RNA-processing protein 7 homolog A
(Rrp7A), and similar proteins. This CD corresponds to
the RRP7 domain of Rrp7p and Rrp7A. Rrp7p is encoded by
YCL031C gene from Saccharomyces cerevisiae. It is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. Rrp7A, also termed gastric cancer antigen
Zg14, is the Rrp7p homolog mainly found in Metazoans.
The cellular function of Rrp7A remains unclear
currently. Both Rrp7p and Rrp7A harbor an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal RRP7 domain.
Length = 118
Score = 32.2 bits (74), Expect = 0.12
Identities = 12/26 (46%), Positives = 20/26 (76%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKF 28
+++E E + +EK+KKKKKKK+ + F
Sbjct: 66 AREEAVEAKAKEKEKKKKKKKELEDF 91
Score = 32.2 bits (74), Expect = 0.12
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
K EE E K K+K+KKKKKKK L+
Sbjct: 62 KGKTAREEAVEAKAKEKEKKKKKKKELE 89
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase;
Provisional.
Length = 330
Score = 33.7 bits (78), Expect = 0.15
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
++ KKE + + +KKK+K++ K K
Sbjct: 60 LLDKKELKAWHKAQKKKEKQEAKAAKA 86
Score = 28.3 bits (64), Expect = 6.5
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K + ++++EK++ K K K K
Sbjct: 67 KAWHKAQKKKEKQEAKAAKAKSKP 90
>gnl|CDD|187649 cd08945, PKR_SDR_c, Polyketide ketoreductase, classical (c) SDR.
Polyketide ketoreductase (KR) is a classical SDR with a
characteristic NAD-binding pattern and active site
tetrad. Aromatic polyketides include various aromatic
compounds of pharmaceutical interest. Polyketide KR,
part of the type II polyketide synthase (PKS) complex,
is comprised of stand-alone domains that resemble the
domains found in fatty acid synthase and multidomain
type I PKS. 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 = 258
Score = 33.3 bits (76), Expect = 0.15
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNT 284
PY+ SK GV+ + L + R I VNAV PG+V T
Sbjct: 153 PYSASKHGVVGFT----KALGLELARTGITVNAVCPGFVET 189
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 33.8 bits (78), Expect = 0.16
Identities = 9/26 (34%), Positives = 19/26 (73%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
++K+ +++E+E+EK K KK+ + K
Sbjct: 396 LAKRAEKKEKEKEKPKVKKRHRDTKN 421
Score = 33.0 bits (76), Expect = 0.24
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
SKK + E+++K+K+K K KK+
Sbjct: 392 SKKVLAKRAEKKEKEKEKPKVKKRH 416
Score = 30.7 bits (70), Expect = 1.5
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+ E++E+E+E+ K KK+ + K
Sbjct: 399 RAEKKEKEKEKPKVKKRHRDTKNI 422
Score = 29.1 bits (66), Expect = 4.2
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTR 39
K ++ + +KK+K+K+K K K DT I R
Sbjct: 388 TGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKR 425
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 33.4 bits (77), Expect = 0.18
Identities = 13/27 (48%), Positives = 20/27 (74%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
I+ K E++ EEE+++KKKK KKK+
Sbjct: 415 IVEKAEKKREEEKKEKKKKAFAGKKKE 441
Score = 33.4 bits (77), Expect = 0.19
Identities = 13/27 (48%), Positives = 19/27 (70%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
I +K +++ EEE+K+KKKK KKK
Sbjct: 414 KIVEKAEKKREEEKKEKKKKAFAGKKK 440
Score = 31.8 bits (73), Expect = 0.72
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
I K ++ E++ E++KK+KKKK
Sbjct: 411 KIKKIVEKAEKKREEEKKEKKKKAFAG 437
Score = 31.4 bits (72), Expect = 0.91
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
I E+ E++ EE+KK+KKKK K
Sbjct: 412 IKKIVEKAEKKREEEKKEKKKKAFAGK 438
Score = 30.7 bits (70), Expect = 1.6
Identities = 10/24 (41%), Positives = 19/24 (79%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK +EE++E++KK KKK++++
Sbjct: 421 KKREEEKKEKKKKAFAGKKKEEEE 444
Score = 30.7 bits (70), Expect = 1.6
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+++ EEE++EKKKK KKK++
Sbjct: 419 AEKKREEEKKEKKKKAFAGKKKEE 442
Score = 30.7 bits (70), Expect = 1.6
Identities = 11/24 (45%), Positives = 20/24 (83%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+K++EEE++E+KKK KKK+++
Sbjct: 420 EKKREEEKKEKKKKAFAGKKKEEE 443
Score = 30.7 bits (70), Expect = 1.6
Identities = 12/25 (48%), Positives = 21/25 (84%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+KK ++ E+ EKK++++KK+KKKK
Sbjct: 409 TKKIKKIVEKAEKKREEEKKEKKKK 433
Score = 29.1 bits (66), Expect = 4.8
Identities = 14/26 (53%), Positives = 23/26 (88%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFL 29
+KE+EEEE EE+K+++++KKKK+ L
Sbjct: 454 EKEEEEEEAEEEKEEEEEKKKKQATL 479
Score = 28.3 bits (64), Expect = 6.8
Identities = 11/25 (44%), Positives = 20/25 (80%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKF 28
K ++ E+ E+K++++KK+KKKK F
Sbjct: 411 KIKKIVEKAEKKREEEKKEKKKKAF 435
>gnl|CDD|219547 pfam07741, BRF1, Brf1-like TBP-binding domain. This region
covers both the Brf homology II and III regions. This
region is involved in binding TATA binding protein.
Length = 95
Score = 31.1 bits (71), Expect = 0.19
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
+KE +++ +E KKKKK+K K
Sbjct: 32 QEEKELKQKADEGNNSGKKKKKRKAK 57
Score = 30.7 bits (70), Expect = 0.33
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKK 27
+Q+ +E KKKKK+K KKK
Sbjct: 37 LKQKADEGNNSGKKKKKRKAKKK 59
Score = 29.9 bits (68), Expect = 0.62
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
K+ +++ +E KKKKK+K KK
Sbjct: 34 EKELKQKADEGNNSGKKKKKRKAKK 58
Score = 27.6 bits (62), Expect = 3.6
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
+ ++E+E +++ ++ KKKKK+K
Sbjct: 29 LEEQEEKELKQKADEGNNSGKKKKKRK 55
>gnl|CDD|187636 cd08931, SDR_c9, classical (c) SDR, subgroup 9. This subgroup has
the canonical active site tetrad and NAD-binding motif
of the classical 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 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 = 227
Score = 32.8 bits (75), Expect = 0.19
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 166 NFFALVTVCHMLFPLLR--PHARVVNVASQ---YGM 196
N ++ + P L+ P ARV+N AS YG
Sbjct: 107 NVKGVLNGAYAALPYLKATPGARVINTASSSAIYGQ 142
>gnl|CDD|235739 PRK06200, PRK06200, 2,3-dihydroxy-2,3-dihydrophenylpropionate
dehydrogenase; Provisional.
Length = 263
Score = 33.0 bits (76), Expect = 0.21
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 13/49 (26%)
Query: 244 PYTVSK---VGVIK-LSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTG 288
YT SK VG+++ L++ + P I VN V PG TDL G
Sbjct: 155 LYTASKHAVVGLVRQLAY---------ELAPKIRVNGVAPGGTVTDLRG 194
Score = 30.3 bits (69), Expect = 1.7
Identities = 15/36 (41%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 322 PDIIVNAVHPGYVNTDLTGHKGILTTEQGSVSSVKG 357
P I VN V PG TDL G + E S+S G
Sbjct: 176 PKIRVNGVAPGGTVTDLRGPASLGQGET-SISDSPG 210
>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
Length = 158
Score = 32.0 bits (73), Expect = 0.24
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
S+KEQ+E +E ++K+ K KK+KK
Sbjct: 95 SEKEQKEVSKETEEKEAIKAKKEKK 119
Score = 30.5 bits (69), Expect = 0.89
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+KE +E EE++ K KK+KK+KK
Sbjct: 99 QKEVSKETEEKEAIKAKKEKKEKK 122
Score = 30.1 bits (68), Expect = 1.2
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K+ +E EE+E K KK+KK+KK+
Sbjct: 100 KEVSKETEEKEAIKAKKEKKEKKE 123
Score = 29.7 bits (67), Expect = 1.6
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKK 26
KE EE+E + KK+KK+KK+KK
Sbjct: 102 VSKETEEKEAIKAKKEKKEKKEKK 125
Score = 29.3 bits (66), Expect = 1.8
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
K+++E +E E+K+ K KK+KK+
Sbjct: 95 SEKEQKEVSKETEEKEAIKAKKEKKE 120
Score = 29.0 bits (65), Expect = 2.3
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+ +E EE+E K KK+KK+KK+K
Sbjct: 100 KEVSKETEEKEAIKAKKEKKEKKEK 124
Score = 28.2 bits (63), Expect = 4.7
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
++ EE+E K KK+KK+KK+KK +
Sbjct: 102 VSKETEEKEAIKAKKEKKEKKEKKVAE 128
Score = 27.4 bits (61), Expect = 8.0
Identities = 7/26 (26%), Positives = 17/26 (65%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
I+ +E E+E+++ K+ ++K+ K
Sbjct: 88 INLFPEESEKEQKEVSKETEEKEAIK 113
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to
be DNA-binding and may be a transcription factor.
Length = 238
Score = 32.7 bits (75), Expect = 0.24
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQL 31
S E+E E+E +++++ KKKK+ K
Sbjct: 68 SDDEEEGEKELQREERLKKKKRVKTKAYK 96
Score = 30.4 bits (69), Expect = 1.1
Identities = 9/25 (36%), Positives = 18/25 (72%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
++EE E+E +++++ KKKK+ K
Sbjct: 67 ESDDEEEGEKELQREERLKKKKRVK 91
Score = 30.0 bits (68), Expect = 1.6
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKF 28
+KE + EE +KKK+ K K K+
Sbjct: 75 EKELQREERLKKKKRVKTKAYKEPT 99
Score = 28.5 bits (64), Expect = 5.0
Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 23/77 (29%)
Query: 7 QEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRS-----------MNARFLRKFYQQER- 54
+E E KK + K +K+K+K + + LT+ +N + L ++ +QE
Sbjct: 157 LKEREIRRKKIQAKARKRKEKKKE----KELTQEERLAEAKETERINLKSLERYEEQEEE 212
Query: 55 -------ISQHRFLIEG 64
+ R L EG
Sbjct: 213 KKKAKIQALKKRRLYEG 229
>gnl|CDD|168186 PRK05693, PRK05693, short chain dehydrogenase; Provisional.
Length = 274
Score = 32.8 bits (75), Expect = 0.24
Identities = 18/34 (52%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 165 TNFFALVTVCHMLFPLL-RPHARVVNVASQYGML 197
TN FA+V V LFPLL R VVN+ S G+L
Sbjct: 102 TNVFAVVGVTRALFPLLRRSRGLVVNIGSVSGVL 135
>gnl|CDD|181198 PRK08017, PRK08017, oxidoreductase; Provisional.
Length = 256
Score = 32.8 bits (75), Expect = 0.25
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 157 QQAETTLATNFFALVTVCHMLFPLLRPH--ARVVNVASQYGML 197
QQ E +TNFF + +L P + PH R+V +S G++
Sbjct: 96 QQMEQQFSTNFFGTHQLTMLLLPAMLPHGEGRIVMTSSVMGLI 138
>gnl|CDD|235924 PRK07063, PRK07063, short chain dehydrogenase; Provisional.
Length = 260
Score = 32.7 bits (75), Expect = 0.27
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 10/47 (21%)
Query: 244 PYTVSKVGVIKLSF---IQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
PY V+K G++ L+ I++A ++ VNA+ PGY+ T LT
Sbjct: 157 PYPVAKHGLLGLTRALGIEYA-------ARNVRVNAIAPGYIETQLT 196
>gnl|CDD|240597 cd12933, eIF3G, eIF3G domain found in eukaryotic translation
initiation factor 3 subunit G (eIF-3G) and similar
proteins. eIF-3G, also termed eIF-3 subunit 4, or
eIF-3-delta, or eIF3-p42, or eIF3-p44, is the
RNA-binding subunit of eIF3. eIF3 is a large
multi-subunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. Besides, eIF-3G is one
of the cytosolic targets; it interacts with mature
apoptosis-inducing factor (AIF). This family also
includes yeast eIF3-p33, a homolog of vertebrate
eIF-3G; it plays an important role in the initiation
phase of protein synthesis in yeast. It binds both mRNA
and rRNA fragments due to an RNA recognition motif near
its C-terminus.
Length = 114
Score = 30.7 bits (70), Expect = 0.36
Identities = 17/24 (70%), Positives = 19/24 (79%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKK 24
+I KE+ EEEEEE KKKKKK KK
Sbjct: 71 LIRNKEELEEEEEEAKKKKKKGKK 94
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 32.1 bits (74), Expect = 0.36
Identities = 18/43 (41%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
Y SK VI L+ A L D+ R VNAV P V T L
Sbjct: 154 YNASKGAVITLTKALAAELGPDKIR----VNAVAPVVVETGLL 192
Score = 28.6 bits (65), Expect = 5.5
Identities = 11/19 (57%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 322 PDII-VNAVHPGYVNTDLT 339
PD I VNAV P V T L
Sbjct: 174 PDKIRVNAVAPVVVETGLL 192
>gnl|CDD|180371 PRK06057, PRK06057, short chain dehydrogenase; Provisional.
Length = 255
Score = 32.0 bits (73), Expect = 0.37
Identities = 20/45 (44%), Positives = 24/45 (53%), Gaps = 10/45 (22%)
Query: 245 YTVSKVGVIKLSF---IQHATLSKDQTRPDIIVNAVHPGYVNTDL 286
YT SK GV+ +S +Q A R I VNA+ PG VNT L
Sbjct: 154 YTASKGGVLAMSRELGVQFA-------RQGIRVNALCPGPVNTPL 191
>gnl|CDD|149515 pfam08492, SRP72, SRP72 RNA-binding domain. This region has been
identified as the binding site of the SRP72 protein to
SRP RNA.
Length = 57
Score = 29.3 bits (66), Expect = 0.37
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKF 28
K +++ E+KKKK KKK+K K
Sbjct: 5 PKKIAKKKPGTEQKKKKSAKKKRKPKL 31
>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional.
Length = 1832
Score = 32.8 bits (75), Expect = 0.38
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTR 39
+K EE+ E KK+K KK+ K + + + L R
Sbjct: 1554 EKNIEEDYAESDIKKRKNKKQYKSNTEAELDFFLKR 1589
Score = 32.0 bits (73), Expect = 0.61
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKK 26
++S +E+ EE+ + KK+K KK+
Sbjct: 1549 VLSNQEKNIEEDYAESDIKKRKNKKQ 1574
>gnl|CDD|222291 pfam13655, RVT_N, N-terminal domain of reverse transcriptase.
This domain is found at the N-terminus of bacterial
reverse transcriptases.
Length = 84
Score = 30.2 bits (69), Expect = 0.40
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 16 KKKKKKKKKKKKFLQLDTNRILTRSMNARFL 46
K K+ KK + LQ ++LTRS +A+ L
Sbjct: 22 KASKEGDWKKVRKLQ----KLLTRSFSAKLL 48
>gnl|CDD|187590 cd05329, TR_SDR_c, tropinone reductase-I and II (TR-1, and
TR-II)-like, classical (c) SDRs. This subgroup includes
TR-I and TR-II; these proteins are members of the SDR
family. TRs catalyze the NADPH-dependent reductions of
the 3-carbonyl group of tropinone, to a beta-hydroxyl
group. TR-I and TR-II produce different stereoisomers
from tropinone, TR-I produces tropine
(3alpha-hydroxytropane), and TR-II, produces
pseudotropine (sigma-tropine, 3beta-hydroxytropane).
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 = 251
Score = 32.0 bits (73), Expect = 0.46
Identities = 26/125 (20%), Positives = 44/125 (35%), Gaps = 46/125 (36%)
Query: 165 TNFFALVTVCHMLFPLLRPHAR--VVNVASQYGMLYKVPSQELKQTLLNDSLTEDQLVGM 222
TNF A + + PLL+ +V ++S G++ VPS
Sbjct: 114 TNFEAAYHLSRLAHPLLKASGNGNIVFISSVAGVI-AVPSGA------------------ 154
Query: 223 MHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYV 282
PY +K + +L+ +L+ + + +I VNAV P +
Sbjct: 155 ---------------------PYGATKGALNQLT----RSLACEWAKDNIRVNAVAPWVI 189
Query: 283 NTDLT 287
T L
Sbjct: 190 ATPLV 194
Score = 27.8 bits (62), Expect = 9.7
Identities = 21/68 (30%), Positives = 25/68 (36%), Gaps = 15/68 (22%)
Query: 324 IIVNAVHPGYVNTDLTG---------HKGILTT------EQGSVSSVKGALIPPDAKEPR 368
I VNAV P + T L K I T E V+++ L P A
Sbjct: 179 IRVNAVAPWVIATPLVEPVIQQKENLDKVIERTPLKRFGEPEEVAALVAFLCMPAASYIT 238
Query: 369 GQFIWYDG 376
GQ I DG
Sbjct: 239 GQIIAVDG 246
>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM).
This family consists of several Plasmodium falciparum
SPAM (secreted polymorphic antigen associated with
merozoites) proteins. Variation among SPAM alleles is
the result of deletions and amino acid substitutions in
non-repetitive sequences within and flanking the
alanine heptad-repeat domain. Heptad repeats in which
the a and d position contain hydrophobic residues
generate amphipathic alpha-helices which give rise to
helical bundles or coiled-coil structures in proteins.
SPAM is an example of a P. falciparum antigen in which
a repetitive sequence has features characteristic of a
well-defined structural element.
Length = 164
Score = 31.4 bits (71), Expect = 0.48
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKK 24
I+ +E+EEE+EE+ K +KK
Sbjct: 74 IVEDEEEEEEDEEDNVDLKDIEKK 97
Score = 29.4 bits (66), Expect = 2.2
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKK 25
I + E+EEEE+EE K +KK
Sbjct: 74 IVEDEEEEEEDEEDNVDLKDIEKK 97
Score = 28.7 bits (64), Expect = 3.6
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 6 EQEEEEEEEKKKKKKKKKKKKK 27
E EEEEEE+++ K +KK
Sbjct: 76 EDEEEEEEDEEDNVDLKDIEKK 97
Score = 28.3 bits (63), Expect = 4.7
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKK 26
+++EEEEE+E+ K +KK
Sbjct: 76 EDEEEEEEDEEDNVDLKDIEKK 97
>gnl|CDD|236094 PRK07774, PRK07774, short chain dehydrogenase; Provisional.
Length = 250
Score = 31.6 bits (72), Expect = 0.50
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 238 AGW-PDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
A W + Y ++KVG+ L+ L+++ +I VNA+ PG ++T+ T
Sbjct: 147 AAWLYSNFYGLAKVGLNGLT----QQLARELGGMNIRVNAIAPGPIDTEAT 193
>gnl|CDD|187620 cd05362, THN_reductase-like_SDR_c,
tetrahydroxynaphthalene/trihydroxynaphthalene
reductase-like, classical (c) SDRs.
1,3,6,8-tetrahydroxynaphthalene reductase (4HNR) of
Magnaporthe grisea and the related
1,3,8-trihydroxynaphthalene reductase (3HNR) are typical
members of the SDR family containing the canonical
glycine rich NAD(P)-binding site and active site tetrad,
and function in fungal melanin biosynthesis. This
subgroup also includes an SDR from Norway spruce that
may function to protect against both biotic and abitoic
stress. 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 = 31.9 bits (73), Expect = 0.50
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDL 286
Y SK V + + L+K+ I VNAV PG V+TD+
Sbjct: 151 YAGSKAAVEAFTRV----LAKELGGRGITVNAVAPGPVDTDM 188
Score = 29.6 bits (67), Expect = 2.6
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 314 TLSKDQTRPDIIVNAVHPGYVNTDL 338
L+K+ I VNAV PG V+TD+
Sbjct: 164 VLAKELGGRGITVNAVAPGPVDTDM 188
>gnl|CDD|188169 TIGR01829, AcAcCoA_reduct, acetoacetyl-CoA reductase. This model
represent acetoacetyl-CoA reductase, a member of the
family short-chain-alcohol dehydrogenases. Note that,
despite the precision implied by the enzyme name, the
reaction of EC 1.1.1.36 is defined more generally as
(R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH.
Members of this family may act in the biosynthesis of
poly-beta-hydroxybutyrate (e.g. Rhizobium meliloti) and
related poly-beta-hydroxyalkanoates. Note that the
member of this family from Azospirillum brasilense,
designated NodG, appears to lack acetoacetyl-CoA
reductase activity and to act instead in the production
of nodulation factor. This family is downgraded to
subfamily for this NodG. Other proteins designated NodG,
as from Rhizobium, belong to related but distinct
protein families.
Length = 242
Score = 31.6 bits (72), Expect = 0.53
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
Y+ +K G+I + L+++ + VN + PGY+ TD+
Sbjct: 150 YSAAKAGMIGFT----KALAQEGATKGVTVNTISPGYIATDMV 188
Score = 27.8 bits (62), Expect = 8.3
Identities = 11/39 (28%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 301 KVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 339
K G+I + L+++ + VN + PGY+ TD+
Sbjct: 154 KAGMIGFT----KALAQEGATKGVTVNTISPGYIATDMV 188
>gnl|CDD|188170 TIGR01832, kduD, 2-deoxy-D-gluconate 3-dehydrogenase. This model
describes 2-deoxy-D-gluconate 3-dehydrogenase (also
called 2-keto-3-deoxygluconate oxidoreductase), a member
of the family of short-chain-alcohol dehydrogenases
(pfam00106). This protein has been characterized in
Erwinia chrysanthemi as an enzyme of pectin degradation
[Energy metabolism, Biosynthesis and degradation of
polysaccharides].
Length = 248
Score = 31.7 bits (72), Expect = 0.54
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
YT SK V L+ + L+ + I VNA+ PGY+ T+ T
Sbjct: 153 YTASKHAVAGLTKL----LANEWAAKGINVNAIAPGYMATNNT 191
>gnl|CDD|235816 PRK06500, PRK06500, short chain dehydrogenase; Provisional.
Length = 249
Score = 31.5 bits (72), Expect = 0.54
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGHKGI 292
Y SK ++ L+ TLS + I VNAV PG V T L G G+
Sbjct: 150 YAASKAALLSLA----KTLSGELLPRGIRVNAVSPGPVQTPLYGKLGL 193
Score = 29.9 bits (68), Expect = 1.8
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 283 NTDLTGHKGILTMTIHTL-KVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGH 341
N + H G+ +++ K ++ L+ TLS + I VNAV PG V T L G
Sbjct: 135 NGSINAHIGMPNSSVYAASKAALLSLA----KTLSGELLPRGIRVNAVSPGPVQTPLYGK 190
Query: 342 KGILTTEQGSVSSVKGALIP 361
G+ +V++ AL+P
Sbjct: 191 LGLPEATLDAVAAQIQALVP 210
>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992). This
bacterial family of proteins has no known function.
However, the cis-regulatory yjdF motif, just upstream
from the gene encoding the proteins for this family, is
a small non-coding RNA, Rfam:RF01764. The yjdF motif is
found in many Firmicutes, including Bacillus subtilis.
In most cases, it resides in potential 5' UTRs of
homologues of the yjdF gene whose function is unknown.
However, in Streptococcus thermophilus, a yjdF RNA motif
is associated with an operon whose protein products
synthesise nicotinamide adenine dinucleotide (NAD+).
Also, the S. thermophilus yjdF RNA lacks typical yjdF
motif consensus features downstream of and including the
P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the
S. thermophilus RNAs might sense a distinct compound
that structurally resembles the ligand bound by other
yjdF RNAs. On the ohter hand, perhaps these RNAs have an
alternative solution forming a similar binding site, as
is observed with some SAM riboswitches.
Length = 132
Score = 30.7 bits (70), Expect = 0.54
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
KE++EEE+E K++ K++KKK K
Sbjct: 105 RSKEKKEEEKERKRQLKQQKKKAKH 129
Score = 29.5 bits (67), Expect = 1.3
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKK 25
KKE+E+E + + K++KKK K +
Sbjct: 109 KKEEEKERKRQLKQQKKKAKHR 130
Score = 29.1 bits (66), Expect = 1.6
Identities = 11/26 (42%), Positives = 21/26 (80%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
SK+++EEE+E +++ K++KKK K +
Sbjct: 105 RSKEKKEEEKERKRQLKQQKKKAKHR 130
Score = 27.2 bits (61), Expect = 7.5
Identities = 12/24 (50%), Positives = 21/24 (87%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK +E++EEEK++K++ K++KKK
Sbjct: 103 KKRSKEKKEEEKERKRQLKQQKKK 126
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 31.8 bits (73), Expect = 0.55
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 239 GWPDD-PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTD 285
GWP Y +K G++ L+ L+++ I VN V PG ++TD
Sbjct: 149 GWPGRSNYAAAKAGLVGLT----KALARELAEYGITVNMVAPGDIDTD 192
Score = 27.9 bits (63), Expect = 9.2
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 324 IIVNAVHPGYVNTD 337
I VN V PG ++TD
Sbjct: 179 ITVNMVAPGDIDTD 192
>gnl|CDD|187632 cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. 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 = 248
Score = 31.4 bits (72), Expect = 0.56
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 157 QQAETTLATNFFALVTVCHMLFPLLR--PHARVVNVAS 192
++ N F + V PL+R R+VNV+S
Sbjct: 96 EEVRELFEVNVFGPLRVTRAFLPLMRKQGSGRIVNVSS 133
>gnl|CDD|183778 PRK12829, PRK12829, short chain dehydrogenase; Provisional.
Length = 264
Score = 31.6 bits (72), Expect = 0.67
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNT 284
PY SK V + ++ +L+ + I VNA+ PG V
Sbjct: 159 PYAASKWAV--VGLVK--SLAIELGPLGIRVNAILPGIVRG 195
>gnl|CDD|187654 cd08951, DR_C-13_KR_SDR_c_like, daunorubicin C-13 ketoreductase
(KR), classical (c)-like SDRs. Daunorubicin is a
clinically important therapeutic compound used in some
cancer treatments. Daunorubicin C-13 ketoreductase is
member of the classical SDR family with a canonical
glycine-rich NAD(P)-binding motif, but lacking a
complete match to the active site tetrad characteristic
of this group. The critical Tyr, plus the Lys and
upstream Asn are present, but the catalytic Ser is
replaced, generally by Gln. 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 KRs 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 = 260
Score = 31.3 bits (71), Expect = 0.68
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 11/53 (20%)
Query: 239 GWPDDP-YTVSKVGVIKLSFIQHATLSKDQTR--PDIIVNAVHPGYVNTDLTG 288
G D P Y+ SK+ V TL+ R D+ NAVHPG+V T + G
Sbjct: 151 GENDSPAYSDSKLHV--------LTLAAAVARRWKDVSSNAVHPGWVPTKMGG 195
Score = 30.5 bits (69), Expect = 1.4
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 308 SFIQHATLSKDQTR--PDIIVNAVHPGYVNTDLTG 340
S + TL+ R D+ NAVHPG+V T + G
Sbjct: 161 SKLHVLTLAAAVARRWKDVSSNAVHPGWVPTKMGG 195
>gnl|CDD|218336 pfam04935, SURF6, Surfeit locus protein 6. The surfeit locus
protein SURF-6 is shown to be a component of the
nucleolar matrix and has a strong binding capacity for
nucleic acids.
Length = 206
Score = 30.7 bits (70), Expect = 0.81
Identities = 8/24 (33%), Positives = 17/24 (70%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
++ + E+ + KK+K+K+ KKK+
Sbjct: 11 RRRKREQRKARKKQKRKEAKKKED 34
Score = 30.4 bits (69), Expect = 1.1
Identities = 8/27 (29%), Positives = 21/27 (77%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
++ ++ ++ E+ + +KK+K+K+ KKK+
Sbjct: 7 LLEQRRRKREQRKARKKQKRKEAKKKE 33
Score = 28.8 bits (65), Expect = 3.5
Identities = 13/29 (44%), Positives = 20/29 (68%), Gaps = 3/29 (10%)
Query: 4 KKEQE---EEEEEEKKKKKKKKKKKKKFL 29
KK +E + ++++K KKKKK KKK + L
Sbjct: 178 KKREENLKKRKDDKKNKKKKKAKKKGRIL 206
>gnl|CDD|183773 PRK12824, PRK12824, acetoacetyl-CoA reductase; Provisional.
Length = 245
Score = 30.9 bits (70), Expect = 0.83
Identities = 25/134 (18%), Positives = 46/134 (34%), Gaps = 46/134 (34%)
Query: 157 QQAETTLATNFFALVTVCHMLFPLLRPH--ARVVNVASQYGMLYKVPSQELKQTLLNDSL 214
Q+ + TN ++ V LF + R++N++S +N
Sbjct: 102 QEWNDVINTNLNSVFNVTQPLFAAMCEQGYGRIINISS-----------------VN--- 141
Query: 215 TEDQLVGMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIV 274
G + G + Y+ +K G+I + L+ + R I V
Sbjct: 142 ------------------GLKGQFGQTN--YSAAKAGMIGFT----KALASEGARYGITV 177
Query: 275 NAVHPGYVNTDLTG 288
N + PGY+ T +
Sbjct: 178 NCIAPGYIATPMVE 191
Score = 27.8 bits (62), Expect = 9.1
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 282 VN-TDLTGHKGILTMTIHTL-KVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 339
+N + + G KG T ++ K G+I + L+ + R I VN + PGY+ T +
Sbjct: 135 INISSVNGLKGQFGQTNYSAAKAGMIGFT----KALASEGARYGITVNCIAPGYIATPMV 190
Query: 340 G 340
Sbjct: 191 E 191
>gnl|CDD|219978 pfam08701, GN3L_Grn1, GNL3L/Grn1 putative GTPase. Grn1 (yeast)
and GNL3L (human) are putative GTPases which are
required for growth and play a role in processing of
nucleolar pre-rRNA. This family contains a potential
nuclear localisation signal.
Length = 80
Score = 29.1 bits (66), Expect = 0.85
Identities = 8/24 (33%), Positives = 18/24 (75%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK ++EEE+E +K+ +K ++ + +
Sbjct: 54 KKRKQEEEKERRKEARKAERAEAR 77
>gnl|CDD|206228 pfam14058, PcfK, PcfK-like protein. The PcfK-like protein family
includes the Enterococcus faecalis PcfK protein, which
is functionally uncharacterized. This family of proteins
is found in bacteria and viruses. Proteins in this
family are typically between 137 and 257 amino acids in
length. There are two completely conserved residues (D
and L) that may be functionally important.
Length = 136
Score = 30.0 bits (68), Expect = 0.87
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
+ ++EE K +K+ KK KK + +Q
Sbjct: 101 EALKAYQQEELRKIQKRSKKSKKAEPVQ 128
Score = 27.7 bits (62), Expect = 5.7
Identities = 8/25 (32%), Positives = 17/25 (68%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
++KE + ++E+ +K +K+ KK K
Sbjct: 98 ARKEALKAYQQEELRKIQKRSKKSK 122
Score = 27.7 bits (62), Expect = 6.2
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDT 33
K+ + ++EE +K +K+ KK KK +
Sbjct: 100 KEALKAYQQEELRKIQKRSKKSKKAEPVQG 129
>gnl|CDD|233042 TIGR00598, rad14, DNA repair protein. All proteins in this family
for which functions are known are used for the
recognition of DNA damage as part of nucleotide excision
repair. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 172
Score = 30.5 bits (69), Expect = 0.91
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 6 EQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRKFYQQERISQHRF 60
++E+E EE K++ K+KK +KK +L R RS + + R+ +H F
Sbjct: 97 DEEKERREESKEEMKEKKFEKKLKEL---RRAVRSSEYTNKK----EGRVHEHEF 144
>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein.
Genome duplication is precisely regulated by
cyclin-dependent kinases CDKs, which bring about the
onset of S phase by activating replication origins and
then prevent relicensing of origins until mitosis is
completed. The optimum sequence motif for CDK
phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found
to have at least 11 potential phosphorylation sites.
Drc1 is required for DNA synthesis and S-M replication
checkpoint control. Drc1 associates with Cdc2 and is
phosphorylated at the onset of S phase when Cdc2 is
activated. Thus Cdc2 promotes DNA replication by
phosphorylating Drc1 and regulating its association with
Cut5. Sld2 and Sld3 represent the minimal set of S-CDK
substrates required for DNA replication.
Length = 397
Score = 31.3 bits (71), Expect = 0.91
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKK 26
E+ +EE E+K+K KKK +K+K
Sbjct: 345 EDDEESKEEVEKKQKVKKKPRKRK 368
Score = 29.4 bits (66), Expect = 3.6
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+E +EE E+++K KKK +K+K
Sbjct: 346 DDEESKEEVEKKQKVKKKPRKRKVN 370
Score = 29.0 bits (65), Expect = 4.1
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTN 34
++ EE +EE +KK+K KKK +K+ + +N
Sbjct: 343 EDEDDEESKEEVEKKQKVKKKPRKRKVNPVSN 374
>gnl|CDD|220818 pfam10595, UPF0564, Uncharacterized protein family UPF0564. This
family of proteins has no known function. However, one
of the members is annotated as an EF-hand family
protein.
Length = 349
Score = 31.3 bits (71), Expect = 0.93
Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQ--------LDTNRILTRSMNARFLRKFYQQER 54
+KE+E +E++EKK+ +++KKKKK+ D + L + K ++E+
Sbjct: 281 ERKEKEAKEQQEKKELEQRKKKKKEMAPKVKQRFEANDPAQKLQEERKEQLA-KLRKEEK 339
>gnl|CDD|220252 pfam09468, RNase_H2-Ydr279, Ydr279p protein family (RNase H2
complex component). RNases H are enzymes that
specifically hydrolyse RNA when annealed to a
complementary DNA and are present in all living
organisms. In yeast RNase H2 is composed of a complex of
three proteins (Rnh2Ap, Ydr279p and Ylr154p), this
family represents the homologues of Ydr279p. It is not
known whether non yeast proteins in this family fulfil
the same function.
Length = 287
Score = 30.8 bits (70), Expect = 1.00
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQLDT 33
+++ + +EE KKKK K+ K K ++
Sbjct: 247 RAEKKRKSKEEIKKKKPKESKGVKALKKVVA 277
Score = 30.8 bits (70), Expect = 1.1
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
S+ E++ + +EE KKKK K+ K K
Sbjct: 245 ESRAEKKRKSKEEIKKKKPKESKGVK 270
>gnl|CDD|181335 PRK08264, PRK08264, short chain dehydrogenase; Validated.
Length = 238
Score = 30.6 bits (70), Expect = 1.1
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 271 DIIVNAVHPGYVNTDLTGH 289
V VHPG ++TD+
Sbjct: 168 GTRVLGVHPGPIDTDMAAG 186
Score = 30.6 bits (70), Expect = 1.1
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 323 DIIVNAVHPGYVNTDLTGH 341
V VHPG ++TD+
Sbjct: 168 GTRVLGVHPGPIDTDMAAG 186
>gnl|CDD|234422 TIGR03971, SDR_subfam_1, oxidoreductase, SDR family. Members of
this protein subfamily are putative oxidoreductases
belonging to the larger SDR family. Members of the
present subfamily may occur several to a genome and are
largely restricted to genomes that contain members of
families TIGR03962, TIGR03967, and TIGR03969. Many
members have been annotated by homology as carveol
dehydrogenases.
Length = 265
Score = 30.6 bits (69), Expect = 1.1
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
Y +K G++ L+ TL+ + I VN++HP V+T +
Sbjct: 166 YAAAKHGLVGLT----KTLANELAEYGIRVNSIHPYSVDTPMI 204
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 31.1 bits (71), Expect = 1.2
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKK 25
+K +++ E+EE +K KKK +
Sbjct: 419 RKAEKKAEKEEAEKAAAKKKAE 440
Score = 30.7 bits (70), Expect = 1.5
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K E+EE E+ KKK + KK K
Sbjct: 424 KAEKEEAEKAAAKKKAEAAAKKAK 447
Score = 30.7 bits (70), Expect = 1.5
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K E++ E+EE +K KKK +
Sbjct: 420 KAEKKAEKEEAEKAAAKKKAEAAA 443
Score = 29.1 bits (66), Expect = 4.1
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK ++EE E+ KKK + KK
Sbjct: 423 KKAEKEEAEKAAAKKKAEAAAKKA 446
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 30.6 bits (69), Expect = 1.4
Identities = 14/25 (56%), Positives = 22/25 (88%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
S KE+E+E+E+ K++KKKKK+K K+
Sbjct: 102 SGKEEEKEKEQVKEEKKKKKEKPKE 126
Score = 30.2 bits (68), Expect = 2.1
Identities = 13/25 (52%), Positives = 20/25 (80%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
K E +EEE+EK++ K++KKKKK+
Sbjct: 98 PKNESGKEEEKEKEQVKEEKKKKKE 122
Score = 30.2 bits (68), Expect = 2.1
Identities = 12/25 (48%), Positives = 21/25 (84%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
++ +EEE+E+E+ K++KKKKK+K
Sbjct: 100 NESGKEEEKEKEQVKEEKKKKKEKP 124
Score = 29.1 bits (65), Expect = 5.1
Identities = 12/25 (48%), Positives = 20/25 (80%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
++EE+E+E+ K++KKKKK+K K
Sbjct: 101 ESGKEEEKEKEQVKEEKKKKKEKPK 125
Score = 28.7 bits (64), Expect = 5.5
Identities = 11/25 (44%), Positives = 19/25 (76%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
K + +EEE++K++ K++KKKKK
Sbjct: 97 EPKNESGKEEEKEKEQVKEEKKKKK 121
Score = 28.7 bits (64), Expect = 6.7
Identities = 10/26 (38%), Positives = 20/26 (76%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
+K+ + E +EE+K+K++ K++KKK
Sbjct: 94 PAKEPKNESGKEEEKEKEQVKEEKKK 119
>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are approximately 90 amino acids in
length. There are two completely conserved L residues
that may be functionally important.
Length = 70
Score = 28.1 bits (63), Expect = 1.4
Identities = 11/26 (42%), Positives = 21/26 (80%)
Query: 6 EQEEEEEEEKKKKKKKKKKKKKFLQL 31
++EEEEE K++++K+++K K F +L
Sbjct: 35 KREEEEEARKREERKEREKNKSFEEL 60
Score = 28.1 bits (63), Expect = 1.7
Identities = 10/24 (41%), Positives = 21/24 (87%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K E+E+ EEEE+ +K++++K+++K
Sbjct: 30 KAEEEKREEEEEARKREERKEREK 53
Score = 27.3 bits (61), Expect = 3.2
Identities = 8/24 (33%), Positives = 20/24 (83%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KKE + EEE+ +++++ +K++++K
Sbjct: 26 KKELKAEEEKREEEEEARKREERK 49
Score = 26.9 bits (60), Expect = 4.0
Identities = 6/25 (24%), Positives = 22/25 (88%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+KK++ + EEE+++++++ +K++++
Sbjct: 24 AKKKELKAEEEKREEEEEARKREER 48
Score = 26.9 bits (60), Expect = 4.5
Identities = 10/24 (41%), Positives = 21/24 (87%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
++E+ EEEEE +K++++K+++K K
Sbjct: 32 EEEKREEEEEARKREERKEREKNK 55
Score = 25.8 bits (57), Expect = 9.2
Identities = 8/22 (36%), Positives = 17/22 (77%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKK 24
K+E+EEE + +++K+++K K
Sbjct: 34 EKREEEEEARKREERKEREKNK 55
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 30.8 bits (70), Expect = 1.4
Identities = 12/35 (34%), Positives = 24/35 (68%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRI 36
+KE +E++ +K KK+++KKKK+ +L+ +I
Sbjct: 557 KEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAKI 591
Score = 28.8 bits (65), Expect = 5.6
Identities = 8/27 (29%), Positives = 21/27 (77%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
++E+EE+E +++K+ +K KK+++ +
Sbjct: 554 QREKEEKEALKEQKRLRKLKKQEEKKK 580
Score = 28.8 bits (65), Expect = 6.4
Identities = 9/27 (33%), Positives = 19/27 (70%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
+ K+E + E+EE++ K++K+ +K K
Sbjct: 547 LDDKEELQREKEEKEALKEQKRLRKLK 573
Score = 28.5 bits (64), Expect = 6.6
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
K+ +E++ K KK+++KKKK+
Sbjct: 557 KEEKEALKEQKRLRKLKKQEEKKKKEL 583
>gnl|CDD|184861 PRK14859, tatA, twin arginine translocase protein A; Provisional.
Length = 63
Score = 28.2 bits (63), Expect = 1.4
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KK E+EE E K KK+ KKKKK
Sbjct: 40 KKATSEKEEIEIKPTKKEDKKKKK 63
>gnl|CDD|181136 PRK07825, PRK07825, short chain dehydrogenase; Provisional.
Length = 273
Score = 30.3 bits (69), Expect = 1.4
Identities = 31/154 (20%), Positives = 50/154 (32%), Gaps = 56/154 (36%)
Query: 154 PFGQQAETT----LATNFFALVTVCHMLFPLLRPHAR--VVNVASQYGMLYKVPSQELKQ 207
PF + + L N + ++ + P + P R VVNVAS G +
Sbjct: 93 PFLDEPDAVTRRILDVNVYGVILGSKLAAPRMVPRGRGHVVNVASLAGKIP--------- 143
Query: 208 TLLNDSLTEDQLVGMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQ 267
+ GM Y SK V+ + ++ +
Sbjct: 144 -----------VPGMA--------------------TYCASKHAVVGFT-----DAARLE 167
Query: 268 TRPD-IIVNAVHPGYVNTDLT----GHKGILTMT 296
R + V+ V P +VNT+L G KG +
Sbjct: 168 LRGTGVHVSVVLPSFVNTELIAGTGGAKGFKNVE 201
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 30.2 bits (69), Expect = 1.5
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 10/45 (22%)
Query: 244 PYTVSKVGVIKLSFIQHAT---LSKDQTRPDIIVNAVHPGYVNTD 285
Y+ SK V + A L+ R VNAV PG ++T+
Sbjct: 154 LYSASKGAVNAFT---KALAKELAPSGIR----VNAVAPGAIDTE 191
>gnl|CDD|135631 PRK05867, PRK05867, short chain dehydrogenase; Provisional.
Length = 253
Score = 30.4 bits (68), Expect = 1.5
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDL 286
Y SK VI L+ L+ + R VN+V PGY+ T+L
Sbjct: 161 YCASKAAVIHLTKAMAVELAPHKIR----VNSVSPGYILTEL 198
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical 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
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 = 239
Score = 30.3 bits (69), Expect = 1.5
Identities = 11/44 (25%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 156 GQQAETTLATNFFALVTVCHMLFPLL--RPHARVVNVASQYGML 197
++ E + N+F + V H + PL+ + +V V+SQ ++
Sbjct: 103 AEEFERGMDVNYFGSLNVAHAVLPLMKEQRPGHIVFVSSQAALV 146
>gnl|CDD|171531 PRK12481, PRK12481, 2-deoxy-D-gluconate 3-dehydrogenase;
Provisional.
Length = 251
Score = 30.3 bits (68), Expect = 1.5
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
YT SK V+ L+ L+ + ++ +I VNA+ PGY+ TD T
Sbjct: 156 YTASKSAVMGLT----RALATELSQYNINVNAIAPGYMATDNT 194
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 30.1 bits (68), Expect = 1.6
Identities = 7/23 (30%), Positives = 21/23 (91%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKK 26
K +Q++++ EE+++K++KK++++
Sbjct: 191 KLKQQQQKREEERRKQRKKQQEE 213
Score = 29.3 bits (66), Expect = 3.4
Identities = 6/26 (23%), Positives = 22/26 (84%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKF 28
KK ++++++ E++++K++KK++++
Sbjct: 189 LKKLKQQQQKREEERRKQRKKQQEEE 214
Score = 28.5 bits (64), Expect = 5.8
Identities = 7/24 (29%), Positives = 22/24 (91%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
++++EEE +++KK+++++++K+K
Sbjct: 196 QQKREEERRKQRKKQQEEEERKQK 219
>gnl|CDD|240578 cd12951, RRP7_Rrp7A, RRP7 domain ribosomal RNA-processing protein
7 homolog A (Rrp7A) and similar proteins. The family
corresponds to the RRP7 domain of Rrp7A, also termed
gastric cancer antigen Zg14, and similar proteins which
are yeast ribosomal RNA-processing protein 7 (Rrp7p)
homologs mainly found in Metazoans. The cellular
function of Rrp7A remains unclear currently. Rrp7A
harbors an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RRP7
domain.
Length = 129
Score = 29.2 bits (66), Expect = 1.6
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKF 28
++KE + EK+KKKKKKK+ K F
Sbjct: 64 TARKESVAAKAAEKEKKKKKKKELKNF 90
Score = 27.2 bits (61), Expect = 8.8
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
K +E K +K+KKKKKKK
Sbjct: 61 RPKTARKESVAAKAAEKEKKKKKKK 85
>gnl|CDD|180411 PRK06123, PRK06123, short chain dehydrogenase; Provisional.
Length = 248
Score = 30.1 bits (68), Expect = 1.6
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 315 LSKDQTRPDIIVNAVHPGYVNTDLTGHKGILTTEQGSVSSVKGALIP 361
L+K+ I VNAV PG + T++ G E G V VK IP
Sbjct: 171 LAKEVAAEGIRVNAVRPGVIYTEIHASGG----EPGRVDRVKAG-IP 212
>gnl|CDD|240577 cd12950, RRP7_Rrp7p, RRP7 domain ribosomal RNA-processing protein
7 (Rrp7p) and similar proteins. This CD corresponds to
the RRP7 domain of Rrp7p. Rrp7p is encoded by YCL031C
gene from Saccharomyces cerevisiae. It is an essential
yeast protein involved in pre-rRNA processing and
ribosome assembly. Rrp7p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain.
Length = 128
Score = 29.2 bits (66), Expect = 1.7
Identities = 13/23 (56%), Positives = 19/23 (82%)
Query: 6 EQEEEEEEEKKKKKKKKKKKKKF 28
+ EEE++EK+KKKKKKK+ + F
Sbjct: 72 KAAEEEKKEKEKKKKKKKELEDF 94
Score = 29.2 bits (66), Expect = 1.7
Identities = 14/25 (56%), Positives = 20/25 (80%)
Query: 6 EQEEEEEEEKKKKKKKKKKKKKFLQ 30
E+ + EE+KK+K+KKKKKKK L+
Sbjct: 68 EEAGKAAEEEKKEKEKKKKKKKELE 92
Score = 27.2 bits (61), Expect = 7.2
Identities = 12/21 (57%), Positives = 18/21 (85%)
Query: 4 KKEQEEEEEEEKKKKKKKKKK 24
K +EE++E+EKKKKKKK+ +
Sbjct: 72 KAAEEEKKEKEKKKKKKKELE 92
>gnl|CDD|217502 pfam03343, SART-1, SART-1 family. SART-1 is a protein involved in
cell cycle arrest and pre-mRNA splicing. It has been
shown to be a component of U4/U6 x U5 tri-snRNP complex
in human, Schizosaccharomyces pombe and Saccharomyces
cerevisiae. SART-1 is a known tumour antigen in a range
of cancers recognised by T cells.
Length = 603
Score = 30.5 bits (69), Expect = 1.7
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 9 EEEEEEKKKKKKKKKKKKK 27
+ E K KK KKKKKKKK
Sbjct: 268 DVSEMVKFKKPKKKKKKKK 286
Score = 30.1 bits (68), Expect = 2.4
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 7 QEEEEEEEKKKKKKKKKKKKKFLQLD 32
E + KK KKKKKKKKK+ LD
Sbjct: 268 DVSEMVKFKKPKKKKKKKKKRRKDLD 293
Score = 28.2 bits (63), Expect = 9.2
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 7 QEEEEEEEKKKKKKKKKKKKK 27
+ + E K KK KKKKKK
Sbjct: 264 SDYYDVSEMVKFKKPKKKKKK 284
>gnl|CDD|180440 PRK06172, PRK06172, short chain dehydrogenase; Provisional.
Length = 253
Score = 30.1 bits (68), Expect = 1.7
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDL 286
Y SK VI L+ + + + + I VNAV P ++TD+
Sbjct: 157 YAASKHAVIGLT----KSAAIEYAKKGIRVNAVCPAVIDTDM 194
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 30.3 bits (69), Expect = 1.7
Identities = 8/26 (30%), Positives = 19/26 (73%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKKFLQ 30
+ +EE+E E ++K++K+KK ++ +
Sbjct: 106 ERIQEEDEAEAQEKREKQKKLREEID 131
Score = 29.9 bits (68), Expect = 2.0
Identities = 9/27 (33%), Positives = 21/27 (77%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
++ QEE+E E ++K++K+KK +++ +
Sbjct: 106 ERIQEEDEAEAQEKREKQKKLREEIDE 132
Score = 29.5 bits (67), Expect = 2.8
Identities = 7/27 (25%), Positives = 18/27 (66%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
+ E +EE++ + ++K++K+KK +
Sbjct: 102 DEIIERIQEEDEAEAQEKREKQKKLRE 128
Score = 29.1 bits (66), Expect = 4.1
Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 19/74 (25%)
Query: 4 KKEQEEEEEEEKKKKK--------------KKKKKKKKFLQLDTNRILTRSMNARFLRKF 49
K EEEE E K+K++ ++K++++++ + R + R
Sbjct: 53 KALAEEEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQEREQMDEIIER----- 107
Query: 50 YQQERISQHRFLIE 63
Q+E ++ + E
Sbjct: 108 IQEEDEAEAQEKRE 121
Score = 29.1 bits (66), Expect = 4.4
Identities = 13/55 (23%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKKFLQ-LDTNRILTRSMNARFLRKFYQQER 54
+ + QEE E +E++K+K++ +K+++ Q L R L++ +E
Sbjct: 204 LRADLYQEEYERKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAEEE 258
Score = 28.7 bits (65), Expect = 5.6
Identities = 7/26 (26%), Positives = 20/26 (76%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKKFLQ 30
+E+ E EEE + +++++K++K++ +
Sbjct: 160 REKAEREEEREAERRERKEEKEREVA 185
Score = 28.3 bits (64), Expect = 6.9
Identities = 8/26 (30%), Positives = 19/26 (73%)
Query: 7 QEEEEEEEKKKKKKKKKKKKKFLQLD 32
+ +EE+E + ++K++K+KK ++D
Sbjct: 106 ERIQEEDEAEAQEKREKQKKLREEID 131
Score = 28.3 bits (64), Expect = 7.1
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKKFLQ 30
+ EEEE ++K+K+++++ + LQ
Sbjct: 52 LKALAEEEERERKRKEERREGRAVLQ 77
Score = 28.0 bits (63), Expect = 8.1
Identities = 7/24 (29%), Positives = 18/24 (75%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKK 25
+K + EEE E +++++K++K++
Sbjct: 159 QREKAEREEEREAERRERKEEKER 182
Score = 28.0 bits (63), Expect = 8.3
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 4 KKEQEEEEEEEKKKKKKKKK 23
K EEEE E+K+K+++++
Sbjct: 52 LKALAEEEERERKRKEERRE 71
>gnl|CDD|200253 TIGR03225, benzo_boxB, benzoyl-CoA oxygenase, B subunit. Members
of this protein family are BoxB, the B subunit of
benzoyl-CoA oxygenase. This oxygen-requiring enzyme acts
in an aerobic pathway of benzoate catabolism via
coenzyme A ligation [Energy metabolism, Other].
Length = 471
Score = 30.6 bits (69), Expect = 1.7
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 242 DDPYTVSKVGVIKLSFIQ-----HATLSKDQTRPDIIVNAVHPGYVNTDLTG 288
DDPY + +GVI L IQ H +++ D ++ NA N L G
Sbjct: 267 DDPYRIRALGVIDLPTIQKYLNFHYSVTSDLFGAEVSSNAAT--AYNAGLKG 316
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 30.1 bits (69), Expect = 1.8
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
Y+ +K GVI + L+ + I VNAV PG+++TD+T
Sbjct: 153 NYSAAKAGVIGFT----KALALELASRGITVNAVAPGFIDTDMT 192
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 29.7 bits (67), Expect = 1.8
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKKF 28
K+++++++++K KK K +KK
Sbjct: 88 KKKSKKKKDKDKDKKDDKKDDKSEKKDE 115
Score = 29.3 bits (66), Expect = 2.1
Identities = 14/24 (58%), Positives = 19/24 (79%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+K ++E EE++K K KKKK KKKK
Sbjct: 72 EKVKKEYEEKQKWKWKKKKSKKKK 95
Score = 29.3 bits (66), Expect = 2.7
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 7/57 (12%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRKFYQQERISQHR 59
S+K+ E+E E++ + K + L R + YQ R+ + R
Sbjct: 110 SEKKDEKEAEDKLEDLTKSYSETLSTLSELKPRKYALH------KDIYQS-RLDRKR 159
Score = 28.9 bits (65), Expect = 2.9
Identities = 8/25 (32%), Positives = 20/25 (80%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
KK+++++++++KK K +KK +K+
Sbjct: 93 KKKDKDKDKKDDKKDDKSEKKDEKE 117
Score = 28.9 bits (65), Expect = 3.2
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
KKE EE+++ + KKKK KKKK K
Sbjct: 74 VKKEYEEKQKWKWKKKKSKKKKDKD 98
Score = 28.1 bits (63), Expect = 5.2
Identities = 14/26 (53%), Positives = 19/26 (73%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKK 27
I K ++E EE+++ K KKKK KKKK
Sbjct: 71 IEKVKKEYEEKQKWKWKKKKSKKKKD 96
Score = 28.1 bits (63), Expect = 5.5
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+ E+ ++E EEK+K K KKKK KK
Sbjct: 70 EIEKVKKEYEEKQKWKWKKKKSKK 93
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 30.4 bits (68), Expect = 1.9
Identities = 9/55 (16%), Positives = 25/55 (45%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRKFYQQERIS 56
++++E+ E +EE ++ ++ KK+ +K +F+ + I+
Sbjct: 240 VAEEEEFELDEEHEEAEEDKKEALEKIGAEGDEEKFKFDEEIKFIEHDVKDRNIA 294
>gnl|CDD|181721 PRK09242, PRK09242, tropinone reductase; Provisional.
Length = 257
Score = 30.1 bits (68), Expect = 1.9
Identities = 29/134 (21%), Positives = 47/134 (35%), Gaps = 48/134 (35%)
Query: 163 LATNFFALVTVCHMLFPLLRPHA--RVVNVASQYGMLYKVPSQELKQTLLNDSLTEDQLV 220
TN F+ + PLL+ HA +VN+ S G+
Sbjct: 116 FETNLFSAFELSRYAHPLLKQHASSAIVNIGSVSGL------------------------ 151
Query: 221 GMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPG 280
+G PY ++K +++++ ++D R VNAV P
Sbjct: 152 -------------THVRSG---APYGMTKAALLQMTRNLAVEWAEDGIR----VNAVAPW 191
Query: 281 YVNTDLTGHKGILT 294
Y+ T LT G L+
Sbjct: 192 YIRTPLT--SGPLS 203
>gnl|CDD|236207 PRK08261, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 450
Score = 30.2 bits (69), Expect = 1.9
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 245 YTVSKVGVIKL--SFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGH 289
Y SK GVI L + A L ++ I +NAV PG++ T +T
Sbjct: 356 YAASKAGVIGLVQAL---APLLAER---GITINAVAPGFIETQMTAA 396
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 29.7 bits (67), Expect = 2.1
Identities = 11/23 (47%), Positives = 19/23 (82%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKK 27
+E EEEE EE+KK ++K++ ++K
Sbjct: 21 REAEEEEREERKKLEEKREGERK 43
Score = 28.5 bits (64), Expect = 4.2
Identities = 8/28 (28%), Positives = 25/28 (89%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQL 31
++E+++EEEE K+++++ +K+++++ +L
Sbjct: 51 EREKKKEEEERKEREEQARKEQEEYEKL 78
>gnl|CDD|222649 pfam14284, PcfJ, PcfJ-like protein. The PcfJ-like protein family
includes the E. faecalis PcfJ protein, which is
functionally uncharacterized. It is found in bacteria
and viruses, and is typically between 159 and 170 amino
acids in length. There is a conserved HCV sequence
motif.
Length = 169
Score = 29.2 bits (66), Expect = 2.2
Identities = 8/31 (25%), Positives = 21/31 (67%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKFLQLD 32
++K + ++E+E+ +K +K+ + +K F +L
Sbjct: 35 VAKYQAKKEKEKAEKMRKRYPELEKIFRELK 65
>gnl|CDD|181324 PRK08251, PRK08251, short chain dehydrogenase; Provisional.
Length = 248
Score = 29.9 bits (68), Expect = 2.2
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 5/60 (8%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGHKGILTMTIHTLKVGV 304
Y SK GV L L + + I V+ + PGY+ +++ T + + GV
Sbjct: 154 YAASKAGVASLG----EGLRAELAKTPIKVSTIEPGYIRSEMNAKAK-STPFMVDTETGV 208
>gnl|CDD|219621 pfam07890, Rrp15p, Rrp15p. Rrp15p is required for the formation
of 60S ribosomal subunits.
Length = 132
Score = 28.9 bits (65), Expect = 2.2
Identities = 8/27 (29%), Positives = 19/27 (70%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
K++ + E+ EKK K++ + +K++ L+
Sbjct: 33 AKKKLKSEKLEKKAKRQLRAEKRQALE 59
Score = 27.3 bits (61), Expect = 7.5
Identities = 8/34 (23%), Positives = 20/34 (58%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRI 36
K +++ + E+ +KK K++ + +K L+ R+
Sbjct: 30 LLKAKKKLKSEKLEKKAKRQLRAEKRQALEKGRV 63
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 30.1 bits (68), Expect = 2.3
Identities = 9/24 (37%), Positives = 19/24 (79%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K +QEE E+++K++ + K+K++K
Sbjct: 406 KLKQEENEKKQKEQADEDKEKRQK 429
Score = 29.8 bits (67), Expect = 2.9
Identities = 9/22 (40%), Positives = 20/22 (90%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKK 25
+K+Q+E+ +E+K+K++K ++KK
Sbjct: 413 EKKQKEQADEDKEKRQKDERKK 434
Score = 28.6 bits (64), Expect = 6.3
Identities = 7/23 (30%), Positives = 19/23 (82%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKK 26
+++++E+ +E K+K++K ++KK
Sbjct: 412 NEKKQKEQADEDKEKRQKDERKK 434
Score = 28.6 bits (64), Expect = 6.7
Identities = 7/24 (29%), Positives = 20/24 (83%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+ E++++E+ ++ K+K++K ++KK
Sbjct: 411 ENEKKQKEQADEDKEKRQKDERKK 434
Score = 28.2 bits (63), Expect = 9.3
Identities = 7/24 (29%), Positives = 19/24 (79%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
K+E+ E++++E+ + K+K++K +
Sbjct: 408 KQEENEKKQKEQADEDKEKRQKDE 431
>gnl|CDD|215038 PLN00040, PLN00040, Protein MAK16 homolog; Provisional.
Length = 233
Score = 29.7 bits (67), Expect = 2.3
Identities = 7/40 (17%), Positives = 16/40 (40%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSM 41
++ +EE + +K KKK + ++ + M
Sbjct: 193 EVEEAEEELPKSDKNPNSKKKSRVHVEIEYEDEIEYKSLM 232
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 30.3 bits (68), Expect = 2.4
Identities = 13/29 (44%), Positives = 22/29 (75%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQL 31
++K+ EEE E+KKKK++K K+K+ +L
Sbjct: 8 AEKKILTEEELERKKKKEEKAKEKELKKL 36
Score = 28.3 bits (63), Expect = 8.3
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KKE++ +E+E KK K +K+ K K
Sbjct: 23 KKEEKAKEKELKKLKAAQKEAKAK 46
>gnl|CDD|187584 cd05323, ADH_SDR_c_like, insect type alcohol dehydrogenase
(ADH)-like, classical (c) SDRs. This subgroup contains
insect type ADH, and 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) type I; these proteins are
classical SDRs. ADH catalyzes the NAD+-dependent
oxidation of alcohols to aldehydes/ketones. This
subgroup is distinct from the zinc-dependent alcohol
dehydrogenases of the medium chain
dehydrogenase/reductase family, and evolved in fruit
flies to allow the digestion of fermenting fruit.
15-PGDH catalyzes the NAD-dependent interconversion of
(5Z,13E)-(15S)-11alpha,15-dihydroxy-9-oxoprost-13-enoate
and (5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate,
and has a typical SDR glycine-rich NAD-binding motif,
which is not fully present in ADH. 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 = 244
Score = 29.6 bits (67), Expect = 2.4
Identities = 27/137 (19%), Positives = 43/137 (31%), Gaps = 52/137 (37%)
Query: 157 QQAETTLATNFFALVTVCHMLFPLLR-----PHARVVNVASQYGMLYKVPSQELKQTLLN 211
E T+ N ++ ++ + +VN+ S G LY P +
Sbjct: 101 PPWEKTIDVNLTGVINTTYLALHYMDKNKGGKGGVIVNIGSVAG-LYPAPQFPV------ 153
Query: 212 DSLTEDQLVGMMHDYVKLAKEGKDQEAGWPDDPYTVSKVGVIKL--SFIQHATLSKDQTR 269
Y+ SK GV+ S A L + +T
Sbjct: 154 ---------------------------------YSASKHGVVGFTRSL---ADLLEYKT- 176
Query: 270 PDIIVNAVHPGYVNTDL 286
+ VNA+ PG+ NT L
Sbjct: 177 -GVRVNAICPGFTNTPL 192
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is
functionally equivalent to L7/L12 in bacteria and the
P1 and P2 proteins in eukaryotes. L12p is homologous to
P1 and P2 but is not homologous to bacterial L7/L12. It
is located in the L12 stalk, with proteins L10, L11,
and 23S rRNA. L12p is the only protein in the ribosome
to occur as multimers, always appearing as sets of
dimers. Recent data indicate that most archaeal species
contain six copies of L12p (three homodimers), while
eukaryotes have four copies (two heterodimers), and
bacteria may have four or six copies (two or three
homodimers), depending on the species. The organization
of proteins within the stalk has been characterized
primarily in bacteria, where L7/L12 forms either two or
three homodimers and each homodimer binds to the
extended C-terminal helix of L10. L7/L12 is attached to
the ribosome through L10 and is the only ribosomal
protein that does not directly interact with rRNA.
Archaeal L12p is believed to function in a similar
fashion. However, hybrid ribosomes containing the large
subunit from E. coli with an archaeal stalk are able to
bind archaeal and eukaryotic elongation factors but not
bacterial elongation factors. In several mesophilic and
thermophilic archaeal species, the binding of 23S rRNA
to protein L11 and to the L10/L12p pentameric complex
was found to be temperature-dependent and cooperative.
Length = 106
Score = 28.2 bits (63), Expect = 2.5
Identities = 10/21 (47%), Positives = 19/21 (90%)
Query: 3 SKKEQEEEEEEEKKKKKKKKK 23
+ +E+ EE+EEEKKK+++K++
Sbjct: 73 AAEEKAEEKEEEKKKEEEKEE 93
>gnl|CDD|216447 pfam01346, FKBP_N, Domain amino terminal to FKBP-type
peptidyl-prolyl isomerase. This family is only found at
the amino terminus of pfam00254. This domain is of
unknown function.
Length = 124
Score = 28.7 bits (65), Expect = 2.5
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFL 29
KK Q +++ + +KK ++ K + FL
Sbjct: 79 KKLQAKQQAKAEKKAEENKAAGEAFL 104
>gnl|CDD|220376 pfam09745, DUF2040, Coiled-coil domain-containing protein 55
(DUF2040). This entry is a conserved domain of
approximately 130 residues of proteins conserved from
fungi to humans. The proteins do contain a coiled-coil
domain, but the function is unknown.
Length = 128
Score = 28.5 bits (64), Expect = 2.5
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKF 28
+K +EEE+E E+ +++ K K
Sbjct: 103 RKLEEEEKEREELEEENDVTKGKDL 127
>gnl|CDD|132368 TIGR03325, BphB_TodD, cis-2,3-dihydrobiphenyl-2,3-diol
dehydrogenase. Members of this family occur as the BphD
protein of biphenyl catabolism and as the TodD protein
of toluene catabolism. Members catalyze the second step
in each pathway and proved interchangeable when tested;
the first and fourth enzymes in each pathway confer
metabolic specificity. In the context of biphenyl
degradation, the enzyme acts as
cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC
1.3.1.56), while in toluene degradation it acts as
cis-toluene dihydrodiol dehydrogenase.
Length = 262
Score = 29.4 bits (66), Expect = 2.6
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 10/62 (16%)
Query: 322 PDIIVNAVHPGYVNTDLTGHKGILTTEQGSVSSVK-----GALIP----PDAKEPRGQFI 372
P + VN V PG +++DL G K + ++ S+S+V +++P PDA+E G ++
Sbjct: 175 PYVRVNGVAPGGMSSDLRGPKSLGMADK-SISTVPLGDMLKSVLPIGRMPDAEEYTGAYV 233
Query: 373 WY 374
++
Sbjct: 234 FF 235
>gnl|CDD|219901 pfam08555, DUF1754, Eukaryotic family of unknown function
(DUF1754). This is a eukaryotic protein family of
unknown function.
Length = 90
Score = 27.8 bits (62), Expect = 2.6
Identities = 11/13 (84%), Positives = 11/13 (84%)
Query: 15 KKKKKKKKKKKKK 27
KKKKKKKKKK K
Sbjct: 20 KKKKKKKKKKNKS 32
Score = 27.8 bits (62), Expect = 2.8
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 14 EKKKKKKKKKKKKK 27
+ KKKKKKKKKK K
Sbjct: 18 DVKKKKKKKKKKNK 31
Score = 27.4 bits (61), Expect = 4.7
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 14 EKKKKKKKKKKKKK 27
+KKKKKKKKK K K
Sbjct: 20 KKKKKKKKKKNKSK 33
>gnl|CDD|187628 cd05370, SDR_c2, classical (c) SDR, subgroup 2. Short-chain
dehydrogenases/reductases (SDRs, aka Tyrosine-dependent
oxidoreductases) 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 = 228
Score = 29.2 bits (66), Expect = 2.7
Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 148 SVKGNAPFGQQAETTLATNFFALVTVCHMLFPLL--RPHARVVNVASQYGML 197
++ A +A+T + TN + + P L +P A +VNV+S +
Sbjct: 93 DLRDPASDLDKADTEIDTNLIGPIRLIKAFLPHLKKQPEATIVNVSSGLAFV 144
>gnl|CDD|151173 pfam10669, Phage_Gp23, Protein gp23 (Bacteriophage A118). This
is the highly conserved family of the major tail
subunit protein.
Length = 121
Score = 28.5 bits (63), Expect = 2.7
Identities = 10/38 (26%), Positives = 25/38 (65%), Gaps = 2/38 (5%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQL--DTNRILTR 39
K+E+++ E E +K+ K+ K+++ KF+ + R++ +
Sbjct: 49 KEERDKMETEREKRDKESKEERDKFISTMNEQQRLMDK 86
>gnl|CDD|187597 cd05338, DHRS1_HSDL2-like_SDR_c, human dehydrogenase/reductase (SDR
family) member 1 (DHRS1) and human hydroxysteroid
dehydrogenase-like protein 2 (HSDL2), classical (c)
SDRs. This subgroup includes human DHRS1 and human
HSDL2 and related proteins. These are members of the
classical SDR family, with a canonical Gly-rich
NAD-binding motif and the typical YXXXK active site
motif. However, the rest of the catalytic tetrad is not
strongly conserved. DHRS1 mRNA has been detected in many
tissues, liver, heart, skeletal muscle, kidney and
pancreas; a longer transcript is predominantly expressed
in the liver , a shorter one in the heart. HSDL2 may
play a part in fatty acid metabolism, as it is found in
peroxisomes. 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 = 246
Score = 29.3 bits (66), Expect = 2.7
Identities = 18/95 (18%), Positives = 31/95 (32%), Gaps = 27/95 (28%)
Query: 238 AGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGHKGILTMTI 297
D Y K G+ +L+ L+ + R I VN++ P I
Sbjct: 157 PARGDVAYAAGKAGMSRLT----LGLAAELRRHGIAVNSLWPSTA--------------I 198
Query: 298 HTLKVGVIKLSFIQHATLSKD--QTRPDIIVNAVH 330
T + + + S P+I+ +AV
Sbjct: 199 ET-------PAATELSGGSDPARARSPEILSDAVL 226
>gnl|CDD|181605 PRK08993, PRK08993, 2-deoxy-D-gluconate 3-dehydrogenase; Validated.
Length = 253
Score = 29.5 bits (66), Expect = 2.7
Identities = 15/43 (34%), Positives = 27/43 (62%), Gaps = 4/43 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLT 287
YT SK GV+ ++ + ++ + + +I VNA+ PGY+ T+ T
Sbjct: 158 YTASKSGVMGVTRL----MANEWAKHNINVNAIAPGYMATNNT 196
>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355). This
family of proteins is found in bacteria and viruses.
Proteins in this family are typically between 180 and
214 amino acids in length.
Length = 125
Score = 28.4 bits (64), Expect = 2.8
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+K+QEE++ E +K K ++K +
Sbjct: 25 EKKQEEKKSEAEKLAKMSAEEKAE 48
Score = 26.8 bits (60), Expect = 9.8
Identities = 8/34 (23%), Positives = 17/34 (50%)
Query: 8 EEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSM 41
EE+ E E +K +K+ ++ + L + + M
Sbjct: 44 EEKAEYELEKLEKELEELEAELARRELKAEAKKM 77
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 29.8 bits (67), Expect = 2.9
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 2 ISKKEQEEEEEEEKKKKKKKKKKKKKFL 29
S+ + EE KK K+KK FL
Sbjct: 246 ESRSVSDSEESSPPSKKPKEKKTSSTFL 273
>gnl|CDD|206307 pfam14138, COX16, Cytochrome c oxidase assembly protein COX16.
This family represents homologues of COX16 which has
been shown to be involved in assembly of cytochrome
oxidase. Protein in this family are typically between
106 and 134 amino acids in length.
Length = 79
Score = 27.5 bits (62), Expect = 2.9
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 4 KKEQEEEEEEEKKKKKKKKK 23
+K Q+ EEEE K KK++K
Sbjct: 31 RKVQQLEEEEALKLLKKRRK 50
>gnl|CDD|221544 pfam12353, eIF3g, Eukaryotic translation initiation factor 3
subunit G. This domain family is found in eukaryotes,
and is approximately 130 amino acids in length. The
family is found in association with pfam00076. This
family is subunit G of the eukaryotic translation
initiation factor 3. Subunit G is required for eIF3
integrity.
Length = 126
Score = 28.4 bits (64), Expect = 2.9
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKK 23
+I ++EEEEEEE+K KK KK
Sbjct: 81 LIRNWKEEEEEEEEEKAKKSGKK 103
>gnl|CDD|149438 pfam08374, Protocadherin, Protocadherin. The structure of
protocadherins is similar to that of classic cadherins
(pfam00028), but particularly on the cytoplasmic domains
they also have some unique features. They are expressed
in a variety of organisms and are found in high
concentrations in the brain where they seem to be
localised mainly at cell-cell contact sites. Their
expression seems to be developmentally regulated.
Length = 223
Score = 29.0 bits (65), Expect = 3.0
Identities = 17/34 (50%), Positives = 21/34 (61%), Gaps = 5/34 (14%)
Query: 3 SKKEQEE-----EEEEEKKKKKKKKKKKKKFLQL 31
KKE E+ +E ++KKKKK KKKK K L L
Sbjct: 75 GKKETEDWFSPNQENKQKKKKKDKKKKSPKSLLL 108
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 29.5 bits (66), Expect = 3.1
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
S K E+ +EE+ KKKKKK K KK
Sbjct: 229 SDKGGEDGDEEKSKKKKKKLAKNKK 253
Score = 29.2 bits (65), Expect = 4.3
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+++ EEE KK KK KK K KK
Sbjct: 325 EEKNEEEGGLSKKGKKLKKLKGKK 348
Score = 29.2 bits (65), Expect = 4.6
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
K ++ +EE+ KKKKKK K KKK
Sbjct: 230 DKGGEDGDEEKSKKKKKKLAKNKKK 254
Score = 29.2 bits (65), Expect = 4.7
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRS 40
E+ EEE+ E++ KK KK K L+ N +
Sbjct: 319 DSEESEEEKNEEEGGLSKKGKKLKKLKGKKNGLDKDD 355
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 28.0 bits (63), Expect = 3.2
Identities = 4/20 (20%), Positives = 15/20 (75%)
Query: 6 EQEEEEEEEKKKKKKKKKKK 25
EE++E+++++++K++
Sbjct: 74 AAAAEEKKEEEEEEEEKEES 93
Score = 27.6 bits (62), Expect = 4.0
Identities = 6/19 (31%), Positives = 15/19 (78%)
Query: 5 KEQEEEEEEEKKKKKKKKK 23
EE++EEE+++++K++
Sbjct: 75 AAAEEKKEEEEEEEEKEES 93
Score = 27.6 bits (62), Expect = 4.2
Identities = 8/17 (47%), Positives = 15/17 (88%)
Query: 4 KKEQEEEEEEEKKKKKK 20
+E++EEEEEE++K++
Sbjct: 77 AEEKKEEEEEEEEKEES 93
>gnl|CDD|227880 COG5593, COG5593, Nucleic-acid-binding protein possibly involved in
ribosomal biogenesis [Translation, ribosomal structure
and biogenesis].
Length = 821
Score = 29.6 bits (66), Expect = 3.2
Identities = 13/28 (46%), Positives = 21/28 (75%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
S++E+EEEE +E K+ KKK++K L+
Sbjct: 777 SEEEKEEEENKEVSAKRAKKKQRKNMLK 804
>gnl|CDD|211705 TIGR01963, PHB_DH, 3-hydroxybutyrate dehydrogenase. This model
represents a subfamily of the short chain
dehydrogenases. Characterized members so far as
3-hydroxybutyrate dehydrogenases and are found in
species that accumulate ester polmers called
polyhydroxyalkanoic acids (PHAs) under certain
conditions. Several members of the family are from
species not known to accumulate PHAs, including
Oceanobacillus iheyensis and Bacillus subtilis. However,
polymer formation is not required for there be a role
for 3-hydroxybutyrate dehydrogenase; it may be members
of this family have the same function in those species.
Length = 255
Score = 29.3 bits (66), Expect = 3.3
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDL 286
Y +K G+I L+ L+ + I VNA+ PGYV T L
Sbjct: 149 AYVAAKHGLIGLT----KVLALEVAEHGITVNAICPGYVRTPL 187
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 29.6 bits (66), Expect = 3.3
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRK 48
KE +EEE+E+K ++++ K K+ +L + + K
Sbjct: 271 VLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEK 316
>gnl|CDD|237187 PRK12743, PRK12743, oxidoreductase; Provisional.
Length = 256
Score = 29.2 bits (66), Expect = 3.4
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 16/51 (31%)
Query: 244 PYTVSKVG------VIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTG 288
YT +K + L ++H I+VNAV PG + T + G
Sbjct: 152 AYTAAKHALGGLTKAMALELVEH----------GILVNAVAPGAIATPMNG 192
>gnl|CDD|221654 pfam12589, WBS_methylT, Methyltransferase involved in
Williams-Beuren syndrome. This domain family is found
in eukaryotes, and is typically between 72 and 83 amino
acids in length. The family is found in association
with pfam08241. This family is made up of
S-adenosylmethionine-dependent methyltransferases. The
proteins are deleted in Williams-Beuren syndrome (WBS),
a complex developmental disorder with multisystemic
manifestations including supravalvular aortic stenosis
(SVAS) and a specific cognitive phenotype.
Length = 85
Score = 27.6 bits (62), Expect = 3.4
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
SK + + KKKKKKK KKK K
Sbjct: 30 SKVRRISQRNRRKKKKKKKLKKKSK 54
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 29.1 bits (65), Expect = 3.4
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKKFL 29
IISK E +E ++KK K KK K+++
Sbjct: 177 IISKAWSELDESKKKKYIDKYKKLKEEYD 205
>gnl|CDD|180773 PRK06949, PRK06949, short chain dehydrogenase; Provisional.
Length = 258
Score = 29.0 bits (65), Expect = 3.4
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGH 289
Y +SK V+ ++ ++ + R I VNA+ PGY++T++ H
Sbjct: 166 YCMSKAAVVHMT----RAMALEWGRHGINVNAICPGYIDTEINHH 206
Score = 28.6 bits (64), Expect = 5.5
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 324 IIVNAVHPGYVNTDLTGHKGILTTEQG 350
I VNA+ PGY++T++ H TEQG
Sbjct: 189 INVNAICPGYIDTEINHHH--WETEQG 213
>gnl|CDD|183719 PRK12747, PRK12747, short chain dehydrogenase; Provisional.
Length = 252
Score = 29.3 bits (65), Expect = 3.4
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTG 288
Y+++K + ++F TL+K I VNA+ PG++ TD+
Sbjct: 158 YSMTKGAINTMTF----TLAKQLGARGITVNAILPGFIKTDMNA 197
Score = 28.1 bits (62), Expect = 8.4
Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 15/74 (20%)
Query: 314 TLSKDQTRPDIIVNAVHPGYVNTDLTGH-------KGILTT--------EQGSVSSVKGA 358
TL+K I VNA+ PG++ TD+ K TT E ++
Sbjct: 171 TLAKQLGARGITVNAILPGFIKTDMNAELLSDPMMKQYATTISAFNRLGEVEDIADTAAF 230
Query: 359 LIPPDAKEPRGQFI 372
L PD++ GQ I
Sbjct: 231 LASPDSRWVTGQLI 244
>gnl|CDD|180723 PRK06841, PRK06841, short chain dehydrogenase; Provisional.
Length = 255
Score = 29.2 bits (66), Expect = 3.5
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGHKG 291
Y SK GV+ ++ L+ + I VNA+ P V T+L G K
Sbjct: 161 YCASKAGVVGMT----KVLALEWGPYGITVNAISPTVVLTEL-GKKA 202
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This
family consists of several bovine specific leukaemia
virus receptors which are thought to function as
transmembrane proteins, although their exact function is
unknown.
Length = 561
Score = 29.6 bits (66), Expect = 3.6
Identities = 11/29 (37%), Positives = 21/29 (72%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLD 32
K +++E++E+EK++ K KKK+ + F L
Sbjct: 201 KPKKKEKKEKEKERDKDKKKEVEGFKSLL 229
Score = 28.5 bits (63), Expect = 6.7
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTN 34
K+++E+E+E +K KKK+ + K L LD +
Sbjct: 204 KKEKKEKEKERDKDKKKEVEGFKSLLLALDDS 235
Score = 28.1 bits (62), Expect = 9.8
Identities = 9/24 (37%), Positives = 18/24 (75%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
++E+ + EK K++KKK++K+K
Sbjct: 85 EEERRHRQRLEKDKREKKKREKEK 108
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 27.7 bits (62), Expect = 3.6
Identities = 7/20 (35%), Positives = 16/20 (80%)
Query: 5 KEQEEEEEEEKKKKKKKKKK 24
EEEEEEE+++++++++
Sbjct: 73 AAAEEEEEEEEEEEEEEEES 92
Score = 27.3 bits (61), Expect = 4.9
Identities = 6/20 (30%), Positives = 16/20 (80%)
Query: 6 EQEEEEEEEKKKKKKKKKKK 25
EEEEEE++++++++++
Sbjct: 73 AAAEEEEEEEEEEEEEEEES 92
Score = 27.3 bits (61), Expect = 5.1
Identities = 3/21 (14%), Positives = 16/21 (76%)
Query: 7 QEEEEEEEKKKKKKKKKKKKK 27
EEE+++++++++++++
Sbjct: 71 AAAAAEEEEEEEEEEEEEEEE 91
>gnl|CDD|171820 PRK12936, PRK12936, 3-ketoacyl-(acyl-carrier-protein) reductase
NodG; Reviewed.
Length = 245
Score = 29.1 bits (65), Expect = 4.0
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTG 288
Y SK G+I S +L+++ ++ VN V PG++ + +TG
Sbjct: 152 YCASKAGMIGFS----KSLAQEIATRNVTVNCVAPGFIESAMTG 191
>gnl|CDD|129272 TIGR00168, infC, translation initiation factor IF-3. infC uses
abnormal initiation codons such as AUA, AUC, and CUG
which render its expression particularly sensitive to
excess of its gene product IF-3 thereby regulating its
own expression [Protein synthesis, Translation factors].
Length = 165
Score = 28.5 bits (64), Expect = 4.0
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 17/69 (24%)
Query: 14 EKKKKKKKKKKKKKFLQL---------DTNRILTRSMNA-RFLRKFYQQE-------RIS 56
E++KKKK+ KK +K +Q+ D + + + A RFL K + + R S
Sbjct: 62 EQEKKKKEAKKNQKIIQVKEVKMRPTIDEHDLQFKLKQAIRFLEKGDKVKFTVRFRGRES 121
Query: 57 QHRFLIEGV 65
H L E V
Sbjct: 122 THIELGEKV 130
>gnl|CDD|218771 pfam05835, Synaphin, Synaphin protein. This family consists of
several eukaryotic synaphin 1 and 2 proteins.
Synaphin/complexin is a cytosolic protein that
preferentially binds to syntaxin within the SNARE
complex. Synaphin promotes SNAREs to form precomplexes
that oligomerise into higher order structures. A
peptide from the central, syntaxin binding domain of
synaphin competitively inhibits these two proteins from
interacting and prevents SNARE complexes from
oligomerising. It is thought that oligomerisation of
SNARE complexes into a higher order structure creates a
SNARE scaffold for efficient, regulated fusion of
synaptic vesicles. Synaphin promotes neuronal
exocytosis by promoting interaction between the
complementary syntaxin and synaptobrevin transmembrane
regions that reside in opposing membranes prior to
fusion.
Length = 139
Score = 28.3 bits (63), Expect = 4.2
Identities = 8/38 (21%), Positives = 22/38 (57%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRS 40
+EE+EE ++ ++ ++++K K +++ R + R
Sbjct: 29 ESDAEEEDEEIQEALREAEEERKAKHRKMEEEREVMRQ 66
>gnl|CDD|181297 PRK08217, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 253
Score = 28.8 bits (65), Expect = 4.2
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTG 288
Y+ SK GV ++ T +K+ R I V A+ PG + T++T
Sbjct: 163 YSASKAGVAAMT----VTWAKELARYGIRVAAIAPGVIETEMTA 202
>gnl|CDD|241300 cd01270, PTB_CAPON-like, Carboxyl-terminal PDZ ligand of neuronal
nitric oxide synthase protein (CAPON)
Phosphotyrosine-binding (PTB) domain. CAPON (also known
as Nitric oxide synthase 1 adaptor protein, NOS1AP,
encodes a cytosolic protein that binds to the signaling
molecule, neuronal NOS (nNOS). It contains a N-terminal
PTB domain that binds to the small monomeric G protein,
Dexras1 and a C-terminal PDZ-binding domain that
mediates interactions with nNOS. Included in this cd
are C. elegan proteins dystrobrevin, DYB-1, which
controls neurotransmitter release and muscle Ca(2+)
transients by localizing BK channels and DYstrophin-like
phenotype and CAPON related,DYC-1, which is functionally
related to dystrophin homolog, DYS-1. Mutations in the
dystrophin gene causes Duchenne muscular dystrophy.
DYS-1 shares sequence similarity, including key motifs,
with their mammalian counterparts. These CAPON-like
proteins all have a single PTB domain. PTB domains have
a common PH-like fold and are found in various
eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 179
Score = 28.4 bits (64), Expect = 4.5
Identities = 16/48 (33%), Positives = 20/48 (41%), Gaps = 15/48 (31%)
Query: 16 KKKK-------------KKKKKKKKFLQLDTNRILTRSMNARFLRKFY 50
KKKK +KKKKKK D +++L M R FY
Sbjct: 67 KKKKVTITVSVDGVKVVLRKKKKKKGWTWDESKLL--LMQHPIYRIFY 112
>gnl|CDD|193580 cd09891, NGN_Bact_1, Bacterial N-Utilization Substance G (NusG)
N-terminal (NGN) domain, subgroup 1. The N-Utilization
Substance G (NusG) protein is involved in transcription
elongation and termination in bacteria. NusG is
essential in Escherichia coli and associates with RNA
polymerase elongation and Rho-termination. Homologs of
the NusG gene exist in all bacteria. The NusG
N-terminal domain (NGN) is similar in all NusG
homologs, but its C-terminal domain and the linker that
separates these two domains are different. The domain
organization of NusG suggests that the common
properties of NusG and its homologs are due to their
similar NGN domains.
Length = 107
Score = 27.4 bits (62), Expect = 4.8
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 9 EEEEEEKKKKKKKKKKKKKF 28
EE E K KKK K++K F
Sbjct: 39 TEEVVEVKNGKKKVKERKLF 58
>gnl|CDD|218660 pfam05620, DUF788, Protein of unknown function (DUF788). This
family consists of several eukaryotic proteins of
unknown function.
Length = 166
Score = 28.1 bits (63), Expect = 4.8
Identities = 6/22 (27%), Positives = 14/22 (63%)
Query: 6 EQEEEEEEEKKKKKKKKKKKKK 27
+ E E + K+++K +K+ +K
Sbjct: 145 QGAETNETKSKRQEKLEKRGEK 166
Score = 28.1 bits (63), Expect = 6.3
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKK 27
Q E E K K+++K +K+ +
Sbjct: 143 SSQGAETNETKSKRQEKLEKRGE 165
Score = 27.3 bits (61), Expect = 9.8
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
S + E E K K+++K +K+
Sbjct: 140 SLPSSQGAETNETKSKRQEKLEKRG 164
>gnl|CDD|188606 TIGR04091, LTA_dltB, D-alanyl-lipoteichoic acid biosynthesis
protein DltB. Members of this protein family are DltB,
part of a four-gene operon for D-alanyl-lipoteichoic
acid biosynthesis that is present in the vast majority
of low-GC Gram-positive organisms. This protein may be
involved in transport of D-alanine across the plasma
membrane [Cell envelope, Biosynthesis and degradation of
murein sacculus and peptidoglycan].
Length = 380
Score = 29.0 bits (66), Expect = 4.9
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 14 EKKKKKKKKKKKKKFLQL 31
++K KK KK KK K+ +
Sbjct: 342 QRKSKKYKKNKKNKWTKA 359
>gnl|CDD|216833 pfam01991, vATP-synt_E, ATP synthase (E/31 kDa) subunit. This
family includes the vacuolar ATP synthase E subunit, as
well as the archaebacterial ATP synthase E subunit.
Length = 195
Score = 28.5 bits (64), Expect = 4.9
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 1 IISKKEQEEEEE------EEKKKKKKKKKKKKKFLQLDTNRILTRSMNA 43
I ++ E+E E E E +KK ++ +KK+K +++ I++ + N
Sbjct: 13 IRAEAEEEFEIEKAEAVEEAEKKIEEIYEKKEKQAEMEKQIIISNAKNE 61
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 29.2 bits (66), Expect = 5.0
Identities = 13/21 (61%), Positives = 17/21 (80%)
Query: 6 EQEEEEEEEKKKKKKKKKKKK 26
E +EEEEEE+K+KKKKK +
Sbjct: 366 EDDEEEEEEEKEKKKKKSAES 386
Score = 28.4 bits (64), Expect = 7.4
Identities = 13/23 (56%), Positives = 18/23 (78%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKK 27
++ EEEEEEEK+KKKKK + +
Sbjct: 366 EDDEEEEEEEKEKKKKKSAESTR 388
>gnl|CDD|187606 cd05348, BphB-like_SDR_c,
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase
(BphB)-like, classical (c) SDRs.
cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is
a classical SDR, it is of particular importance for its
role in the degradation of biphenyl/polychlorinated
biphenyls(PCBs); PCBs are a significant source of
environmental contamination. This subgroup also includes
Pseudomonas putida F1
cis-biphenyl-1,2-dihydrodiol-1,2-dehydrogenase (aka
cis-benzene glycol dehydrogenase, encoded by the bnzE
gene), which participates in benzene metabolism. In
addition it includes Pseudomonas sp. C18 putative
1,2-dihydroxy-1,2-dihydronaphthalene dehydrogenase (aka
dibenzothiophene dihydrodiol dehydrogenase, encoded by
the doxE gene) which participates in an upper
naphthalene catabolic pathway. 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 = 257
Score = 28.5 bits (64), Expect = 5.0
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 13/48 (27%)
Query: 245 YTVSK---VGVIK-LSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTG 288
YT SK VG++K L++ + P I VN V PG + TDL G
Sbjct: 154 YTASKHAVVGLVKQLAY---------ELAPHIRVNGVAPGGMVTDLRG 192
>gnl|CDD|216249 pfam01025, GrpE, GrpE.
Length = 165
Score = 27.9 bits (63), Expect = 5.2
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 12/64 (18%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARF--LRKFYQQERISQHRFL 61
+ E+E EEE ++ +++ ++ K + L+L A F RK ++ER ++
Sbjct: 10 EDEEEALEEELEELEEEIEELKDRLLRL----------LAEFENYRKRTEREREEAKKYA 59
Query: 62 IEGV 65
IE
Sbjct: 60 IEKF 63
>gnl|CDD|168204 PRK05717, PRK05717, oxidoreductase; Validated.
Length = 255
Score = 28.7 bits (64), Expect = 5.2
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 6/45 (13%)
Query: 241 PD-DPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNT 284
PD + Y SK G++ L+ +L P+I VNAV PG+++
Sbjct: 152 PDTEAYAASKGGLLALTHALAISLG-----PEIRVNAVSPGWIDA 191
>gnl|CDD|180744 PRK06914, PRK06914, short chain dehydrogenase; Provisional.
Length = 280
Score = 28.5 bits (64), Expect = 5.3
Identities = 8/30 (26%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 165 TNFFALVTVCHMLFPLLRPH--ARVVNVAS 192
TN F ++V + P +R +++N++S
Sbjct: 111 TNVFGAISVTQAVLPYMRKQKSGKIINISS 140
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 29.1 bits (66), Expect = 5.3
Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 13/77 (16%)
Query: 1 IISKKEQE----EEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRKFYQQERIS 56
+I + ++E E+E E ++ K+ KK L L + + +
Sbjct: 216 LIREIKEELEEIEKERESLLEELKELAKKYLEELLALYEYLE---IELERAEALSKFLKT 272
Query: 57 QHRFLIEGVNAGYVWAP 73
F IEG W P
Sbjct: 273 DKTFAIEG------WVP 283
>gnl|CDD|187642 cd08937, DHB_DH-like_SDR_c,
1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate
dehydrogenase (DHB DH)-like, classical (c) SDR. DHB DH
(aka 1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate
dehydrogenase) catalyzes the NAD-dependent conversion of
1,2-dihydroxycyclohexa-3,4-diene carboxylate to a
catechol. This subgroup also contains Pseudomonas putida
F1 CmtB, 2,3-dihydroxy-2,3-dihydro-p-cumate
dehydrogenase, the second enzyme in the pathway for
catabolism of p-cumate catabolism. This subgroup shares
the glycine-rich NAD-binding motif of the classical SDRs
and shares the same catalytic triad; however, the
upstream Asn implicated in cofactor binding or catalysis
in other SDRs is generally substituted by a Ser. 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 = 256
Score = 28.6 bits (64), Expect = 5.5
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNT 284
PY+ +K GV L+ A+L+ + R I VNAV PG
Sbjct: 150 PYSAAKGGVNALT----ASLAFEHARDGIRVNAVAPGGTEA 186
>gnl|CDD|182051 PRK09730, PRK09730, putative NAD(P)-binding oxidoreductase;
Provisional.
Length = 247
Score = 28.3 bits (63), Expect = 5.8
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 324 IIVNAVHPGYVNTDLTGHKGILTTEQGSVSSVKGAL 359
I VN V PG++ T++ G E G V VK +
Sbjct: 179 IRVNCVRPGFIYTEMHASGG----EPGRVDRVKSNI 210
>gnl|CDD|241471 cd13317, PH_PLEKHO1_PLEKHO2, Pleckstrin homology
domain-containing family O Pleckstrin homology domain.
The PLEKHO family members are PLEKHO1 (also called
CKIP-1/Casein kinase 2-interacting protein
1/CK2-interacting protein 1) and PLEKHO2 (PLEKHQ1/PH
domain-containing family Q member 1). They both contain
a single PH domain. PLEKHO1 acts as a scaffold protein
that functions in plasma membrane recruitment,
transcriptional activity modulation, and
posttranscriptional modification regulation. As an
adaptor protein it is involved in signaling pathways,
apoptosis, differentiation, cytoskeleton, and bone
formation. Not much is know about PLEKHO2. PH domains
have diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They
share little sequence conservation, but all have a
common fold, which is electrostatically polarized. Less
than 10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 101
Score = 27.1 bits (60), Expect = 5.9
Identities = 9/39 (23%), Positives = 19/39 (48%)
Query: 8 EEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFL 46
E E +K + KKK+K +F + + + + + +F
Sbjct: 50 ELCEYLRCQKSRSKKKRKSRFTLIRSPQPGNKVPDLKFQ 88
>gnl|CDD|212495 cd09807, retinol-DH_like_SDR_c, retinol dehydrogenases
(retinol-DHs), classical (c) SDRs. Classical SDR-like
subgroup containing retinol-DHs and related proteins.
Retinol is processed by a medium chain alcohol
dehydrogenase followed by retinol-DHs. Proteins in this
subfamily share the glycine-rich NAD-binding motif of
the classical SDRs, have a partial match to the
canonical active site tetrad, but lack the typical
active site Ser. This subgroup includes the human
proteins: retinol dehydrogenase -12, -13 ,and -14. 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 = 274
Score = 28.6 bits (64), Expect = 5.9
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 272 IIVNAVHPGYVNTDLTGHKGI 292
+ VNA+HPG V T+L H GI
Sbjct: 185 VTVNALHPGVVRTELGRHTGI 205
Score = 28.6 bits (64), Expect = 5.9
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 324 IIVNAVHPGYVNTDLTGHKGI 344
+ VNA+HPG V T+L H GI
Sbjct: 185 VTVNALHPGVVRTELGRHTGI 205
>gnl|CDD|192481 pfam10197, Cir_N, N-terminal domain of CBF1 interacting
co-repressor CIR. This is a 45 residue conserved
region at the N-terminal end of a family of proteins
referred to as CIRs (CBF1-interacting co-repressors).
CBF1 (centromere-binding factor 1) acts as a
transcription factor that causes repression by binding
specifically to GTGGGAA motifs in responsive promoters,
and it requires CIR as a co-repressor. CIR binds to
histone deacetylase and to SAP30 and serves as a linker
between CBF1 and the histone deacetylase complex.
Length = 37
Score = 25.7 bits (57), Expect = 5.9
Identities = 7/22 (31%), Positives = 16/22 (72%)
Query: 6 EQEEEEEEEKKKKKKKKKKKKK 27
E E++ EE+KK ++ +K+ ++
Sbjct: 15 EAEQKALEEQKKIEELRKEIEE 36
>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional.
Length = 80
Score = 26.7 bits (59), Expect = 6.1
Identities = 6/27 (22%), Positives = 13/27 (48%)
Query: 1 IISKKEQEEEEEEEKKKKKKKKKKKKK 27
+I +E E+++++E K K
Sbjct: 44 MIEGEEPEDDDDDEDDDDDDDKDDKDD 70
>gnl|CDD|215521 PLN02967, PLN02967, kinase.
Length = 581
Score = 28.9 bits (64), Expect = 6.4
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
+ EEE+ EKK +K++K KK
Sbjct: 123 AASSDVEEEKTEKKVRKRRKVKKMD 147
>gnl|CDD|219564 pfam07771, TSGP1, Tick salivary peptide group 1. This contains a
group of peptides derived from a salivary gland cDNA
library of the tick Ixodes scapularis. Also present are
peptides from a related tick species, Ixodes ricinus.
They are characterized by a putative signal peptide
indicative of secretion and conserved cysteine residues.
Length = 120
Score = 27.5 bits (61), Expect = 6.4
Identities = 13/25 (52%), Positives = 14/25 (56%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
S + E EK KKKKKK KK K
Sbjct: 87 SHPDDHPPEPTEKPKKKKKKSKKTK 111
Score = 27.5 bits (61), Expect = 6.4
Identities = 12/20 (60%), Positives = 13/20 (65%)
Query: 8 EEEEEEEKKKKKKKKKKKKK 27
E E+ KKKKKK KK KK
Sbjct: 94 PEPTEKPKKKKKKSKKTKKP 113
>gnl|CDD|150786 pfam10153, DUF2361, Uncharacterized conserved protein (DUF2361).
This is a region of 120 amino acids that is conserved
in a family of proteins found from plants to fungi. The
function is not known.
Length = 114
Score = 27.2 bits (61), Expect = 6.6
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFL 29
KKE E+ E +K+KK KK +F
Sbjct: 34 KKELEDAERRKKRKKMAKKYHMVRFF 59
>gnl|CDD|236278 PRK08506, PRK08506, replicative DNA helicase; Provisional.
Length = 472
Score = 28.4 bits (64), Expect = 6.6
Identities = 11/24 (45%), Positives = 20/24 (83%)
Query: 5 KEQEEEEEEEKKKKKKKKKKKKKF 28
KE+EE+E+E+K KK+ K++++ F
Sbjct: 391 KEREEKEKEKKAKKEGKEERRIHF 414
>gnl|CDD|221805 pfam12848, ABC_tran_2, ABC transporter. This domain is related
to pfam00005.
Length = 85
Score = 26.8 bits (60), Expect = 6.6
Identities = 9/27 (33%), Positives = 21/27 (77%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
K+E+ E++E+ +K++K+ KK ++F+
Sbjct: 22 KEERLEQQEKAYEKQQKEIKKLEEFID 48
>gnl|CDD|181025 PRK07544, PRK07544, branched-chain amino acid aminotransferase;
Validated.
Length = 292
Score = 28.4 bits (64), Expect = 6.7
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 368 RGQFIWYDGSIVDWN 382
R FIW DG +V W
Sbjct: 7 RDGFIWMDGELVPWR 21
>gnl|CDD|221122 pfam11490, DNA_pol3_alph_N, DNA polymerase III polC-type
N-terminus. This is an N-terminal domain of DNA
polymerase III polC subunit A that is found only in
Firmicutes. DNA polymerase polC-type III enzyme
functions as the 'replicase' in low G + C Gram-positive
bacteria. Purine asymmetry is a characteristic of
organisms with a heterodimeric DNA polymerase III
alpha-subunit constituted by polC which probably plays a
direct role in the maintenance of strand-biased gene
distribution; since, among prokaryotic genomes, the
distribution of genes on the leading and lagging strands
of the replication fork is known to be biased. The
domain is associated with DNA_pol3_alpha pfam07733.
Length = 180
Score = 28.1 bits (63), Expect = 6.8
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 5/32 (15%)
Query: 1 IISKKEQEEEE-----EEEKKKKKKKKKKKKK 27
+KE+EE + E KKK+ +KKKK+K
Sbjct: 148 FEEQKEEEEAKLAEEALEALKKKEAEKKKKEK 179
>gnl|CDD|187644 cd08940, HBDH_SDR_c, d-3-hydroxybutyrate dehydrogenase (HBDH),
classical (c) SDRs. DHBDH, an NAD+ -dependent enzyme,
catalyzes the interconversion of D-3-hydroxybutyrate and
acetoacetate. It is a classical SDR, with the canonical
NAD-binding motif and active site tetrad. 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 = 258
Score = 28.2 bits (63), Expect = 6.9
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 4/51 (7%)
Query: 324 IIVNAVHPGYVNTDLTGH--KGILTTEQGSVSSVKGALIPPDAKEPRGQFI 372
+ NA+ PG+V T L + L+ K+P QF+
Sbjct: 176 VTCNAICPGWVLTPLVEKQISALAQKNGVPQEQAARELLLE--KQPSKQFV 224
>gnl|CDD|173965 cd08045, TAF4, TATA Binding Protein (TBP) Associated Factor 4
(TAF4) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) is one of several TAFs that bind TBP and
are involved in forming the Transcription Factor IID
(TFIID) complex. TFIID is one of seven General
Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE,
TFIIF, and TFIID) that are involved in accurate
initiation of transcription by RNA polymerase II in
eukaryote. TFIID plays an important role in the
recognition of promoter DNA and assembly of the
pre-initiation complex. TFIID complex is composed of the
TBP and at least 13 TAFs. TAFs from various species were
originally named by their predicted molecular weight or
their electrophoretic mobility in polyacrylamide gels. A
new, unified nomenclature for the pol II TAFs has been
suggested to show the relationship between TAF orthologs
and paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. Each TAF, with the help of a
specific activator, is required only for the expression
of subset of genes and is not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; HFD is the interaction motif involved in
heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFS and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF4 domain interacts with TAF12 and makes
a novel histone-like heterodimer that binds DNA and has
a core promoter function of a subset of genes.
Length = 212
Score = 28.1 bits (63), Expect = 7.0
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 16/54 (29%)
Query: 6 EQEEEEEEEKK----------------KKKKKKKKKKKFLQLDTNRILTRSMNA 43
EQ E EEEEK+ ++ + K+K K+ + + + R+ NA
Sbjct: 120 EQLEREEEEKRDEEERERLLRAAKSRSEQSRLKQKAKEMQKEEDEEMRHRAANA 173
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 28.6 bits (64), Expect = 7.0
Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 5 KEQEEEEEEEKKKKKK------KKKKKKKFLQLDTNRILTRSMNARFLRKFYQQERISQH 58
++++ +++EKKKK+ K+KKK+ +++ + N + + + ERI +
Sbjct: 10 NQKDKNKKKEKKKKESPPPPHEIKRKKKRKGPDAASKLPKVTPNTKCRLRLLKLERIKDY 69
Query: 59 RFLIE 63
L E
Sbjct: 70 LLLEE 74
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 28.4 bits (64), Expect = 7.2
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTR-SMNARFLRKFYQQERISQHRFL 61
+ EEE E +KK +K ++K+K+ +L+ N I R +N++ Q+++
Sbjct: 308 EARLNEEERELKKKFTEKIREKEKRLEELEQNLIEERKELNSKLEE---IQKKLEDLEKR 364
Query: 62 IE 63
+E
Sbjct: 365 LE 366
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 28.4 bits (64), Expect = 7.3
Identities = 6/28 (21%), Positives = 18/28 (64%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKKFLQ 30
K E+ +E +K++K+ K++++++
Sbjct: 241 QKAERLRQEAAAYEKQQKELAKEQEWIR 268
>gnl|CDD|197254 cd09157, PLDc_CLS_unchar2_1, Putative catalytic domain, repeat 1,
of uncharacterized proteins similar to bacterial
cardiolipin synthase. Putative catalytic domain,
repeat 1, of uncharacterized proteins similar to
bacterial cardiolipin (CL) synthases, which catalyze
the reversible phosphatidyl group transfer between two
phosphatidylglycerol molecules to form CL and glycerol.
Members of this subfamily contain two HKD motifs
(H-x-K-x(4)-D, where x represents any amino acid
residue) that characterizes the phospholipase D (PLD)
superfamily. The two motifs may be part of the active
site and may be involved in phosphatidyl group
transfer.
Length = 155
Score = 27.5 bits (62), Expect = 7.4
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 52 QERISQHRFLIEGVNAGYVWAPLMHRLQ 79
R R LI+GV A Y + RL+
Sbjct: 45 VARGVDVRVLIDGVGARYSRPSIRRRLR 72
>gnl|CDD|180761 PRK06935, PRK06935, 2-deoxy-D-gluconate 3-dehydrogenase;
Provisional.
Length = 258
Score = 28.2 bits (63), Expect = 7.5
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTG 288
YT SK GV L+ + + +I VNA+ PGY+ T T
Sbjct: 162 AYTASKHGVAGLT----KAFANELAAYNIQVNAIAPGYIKTANTA 202
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 28.4 bits (64), Expect = 7.6
Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 12 EEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRKFYQQERISQHRF 60
KKK+K++ ++ + D + ++T S FL K + + + + +F
Sbjct: 159 YHSSLKKKEKEEFLERLKEGDFDILVTTSQ---FLSKNF--DELPKKKF 202
>gnl|CDD|180408 PRK06114, PRK06114, short chain dehydrogenase; Provisional.
Length = 254
Score = 28.2 bits (63), Expect = 7.7
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 245 YTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNT 284
Y SK GVI LS +L+ + I VN++ PGY T
Sbjct: 160 YNASKAGVIHLS----KSLAMEWVGRGIRVNSISPGYTAT 195
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 309
Score = 28.2 bits (63), Expect = 8.0
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 4 KKEQEEEEEEEKKKKKKKKKK 24
++ ++EEEE++ K+K K+
Sbjct: 161 RRLLLQKEEEEQQMNKRKNKQ 181
Score = 27.8 bits (62), Expect = 9.0
Identities = 10/60 (16%), Positives = 29/60 (48%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRKFYQQERISQHRFLIE 63
++ ++EEE+++ K+K K+ +L+T+ + + A+ + + E + +
Sbjct: 160 QRRLLLQKEEEEQQMNKRKNKQALLDELETSTLPAAELIAQHKKNSVKLEMQVEKPKPEK 219
>gnl|CDD|236596 PRK09625, porD, pyruvate flavodoxin oxidoreductase subunit delta;
Reviewed.
Length = 133
Score = 27.4 bits (61), Expect = 8.1
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 6 EQEEEEEEEKKKKKKKKKKKK 26
EQ E E + KK++KKK
Sbjct: 113 EQIENETALTQWPKKEEKKKS 133
>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional.
Length = 213
Score = 28.0 bits (63), Expect = 8.2
Identities = 6/24 (25%), Positives = 15/24 (62%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
+ ++ E E++K ++++K K K
Sbjct: 118 QAKKREAAGEKEKAPRRERKPKPK 141
>gnl|CDD|227016 COG4670, COG4670, Acyl CoA:acetate/3-ketoacid CoA transferase
[Lipid metabolism].
Length = 527
Score = 28.4 bits (64), Expect = 8.3
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 9/49 (18%)
Query: 340 GHKGILTTEQGSVSSVK------GALIPPDA--KEPRGQFIWYDGSIVD 380
LT E G V + GA + P+A P QF +Y+G +D
Sbjct: 317 HDDVTLTVESGPVGGIPLGGLDFGAAVNPEAILDMPD-QFDFYEGGGLD 364
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 27.8 bits (62), Expect = 8.5
Identities = 9/24 (37%), Positives = 19/24 (79%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKK 27
KKE+ EE+E E+++K +++K ++
Sbjct: 155 KKERAEEKEREEEEKAAEEEKARE 178
>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal
domain. This domain is found in a number of different
types of plant proteins including NAM-like proteins.
Length = 147
Score = 27.3 bits (61), Expect = 8.8
Identities = 9/33 (27%), Positives = 21/33 (63%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRI 36
K+E E+E+E+E++ K + +K+ +L+ +
Sbjct: 81 KEEAEKEKEKEERFMKALAEAEKERAELEKKKA 113
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 28.1 bits (63), Expect = 9.0
Identities = 9/25 (36%), Positives = 20/25 (80%)
Query: 3 SKKEQEEEEEEEKKKKKKKKKKKKK 27
SKK+ E++++++K+KK+ K + + K
Sbjct: 66 SKKKSEKKKKKKKEKKEPKSEGETK 90
>gnl|CDD|222863 PHA02540, 61, DNA primase; Provisional.
Length = 337
Score = 28.0 bits (63), Expect = 9.1
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDT 33
K + + E KK+KK +K +LDT
Sbjct: 94 KGRPVPKPKFEFKKEKKVIEKLPFCERLDT 123
>gnl|CDD|183832 PRK12935, PRK12935, acetoacetyl-CoA reductase; Provisional.
Length = 247
Score = 27.7 bits (61), Expect = 9.1
Identities = 12/51 (23%), Positives = 30/51 (58%), Gaps = 4/51 (7%)
Query: 236 QEAGWPDDPYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDL 286
Q G+ Y+ +K G++ + +L+ + + ++ VNA+ PG+++T++
Sbjct: 147 QAGGFGQTNYSAAKAGMLGFT----KSLALELAKTNVTVNAICPGFIDTEM 193
>gnl|CDD|192151 pfam08781, DP, Transcription factor DP. DP forms a heterodimer
with E2F and regulates genes involved in cell cycle
progression. The transcriptional activity of E2F is
inhibited by the retinoblastoma protein which binds to
the E2F-DP heterodimer and negatively regulates the
G1-S transition.
Length = 141
Score = 27.3 bits (61), Expect = 9.2
Identities = 8/22 (36%), Positives = 17/22 (77%)
Query: 9 EEEEEEKKKKKKKKKKKKKFLQ 30
E+ EEE++K+ ++ ++K+ LQ
Sbjct: 4 EKLEEERQKRIERIEQKQAQLQ 25
>gnl|CDD|223685 COG0612, PqqL, Predicted Zn-dependent peptidases [General function
prediction only].
Length = 438
Score = 28.2 bits (63), Expect = 9.5
Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 2/86 (2%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDTNRILTRSMNARFLRKFYQQERISQHRFLIE 63
KK + EE+ K+ L LD+ + + ++L + + IE
Sbjct: 345 KKGLKGPFTEEELDAAKQLLIGLLLLSLDSPSSIAELL-GQYLLLGGSLITLEELLERIE 403
Query: 64 GVNAGYVWAPLMHRLQNGEHFRVVVV 89
V V A + +L E+ +VV+
Sbjct: 404 AVTLEDVNA-VAKKLLAPENLTIVVL 428
>gnl|CDD|222812 PHA00727, PHA00727, hypothetical protein.
Length = 278
Score = 27.9 bits (62), Expect = 9.6
Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 5/42 (11%)
Query: 4 KKEQEEEEEEEKKKKKKKKKKKKKFLQLDTN-RILTRSMNAR 44
KK+Q E+ + E KKKKK KK+K +D +++ + +N+R
Sbjct: 55 KKQQFEQLKAELSKKKKKFKKEK----VDVRVKVVKKWINSR 92
>gnl|CDD|187587 cd05326, secoisolariciresinol-DH_like_SDR_c, secoisolariciresinol
dehydrogenase (secoisolariciresinol-DH)-like, classical
(c) SDRs. Podophyllum secoisolariciresinol-DH is a homo
tetrameric, classical SDR that catalyzes the
NAD-dependent conversion of (-)-secoisolariciresinol to
(-)-matairesinol via a (-)-lactol intermediate.
(-)-Matairesinol is an intermediate to various
8'-lignans, including the cancer-preventive mammalian
lignan, and those involved in vascular plant defense.
This subgroup also includes rice momilactone A synthase
which catalyzes the conversion of
3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide
into momilactone A, Arabidopsis ABA2 which during
abscisic acid (ABA) biosynthesis, catalyzes the
conversion of xanthoxin to abscisic aldehyde and, maize
Tasselseed2 which participate in the maize sex
determination pathway. 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, 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 = 27.8 bits (62), Expect = 9.6
Identities = 22/86 (25%), Positives = 32/86 (37%), Gaps = 11/86 (12%)
Query: 244 PYTVSKVGVIKLSFIQHATLSKDQTRPDIIVNAVHPGYVNTDLTGHKGILTMTIHTLKVG 303
YT SK V+ L+ + + + I VN V P V T L ++
Sbjct: 152 AYTASKHAVLGLT----RSAATELGEHGIRVNCVSPYGVATPLLTA-------GFGVEDE 200
Query: 304 VIKLSFIQHATLSKDQTRPDIIVNAV 329
I+ + A L RP+ I AV
Sbjct: 201 AIEEAVRGAANLKGTALRPEDIAAAV 226
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 28.3 bits (64), Expect = 9.9
Identities = 13/22 (59%), Positives = 18/22 (81%)
Query: 1 IISKKEQEEEEEEEKKKKKKKK 22
+IS K+++EEEEE+KK K K K
Sbjct: 274 LISGKKEKEEEEEKKKIKPKDK 295
>gnl|CDD|234533 TIGR04285, nucleoid_noc, nucleoid occlusion protein. This model
describes nucleoid occlusion protein, a close homolog to
ParB chromosome partitioning proteins including Spo0J in
Bacillus subtilis. Its gene often is located near the
gene for the Spo0J ortholog. This protein bind a
specific DNA sequence and blocks cytokinesis from
happening until chromosome segregation is complete.
Length = 255
Score = 27.9 bits (63), Expect = 9.9
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 7/35 (20%)
Query: 1 IISK----KEQEE---EEEEEKKKKKKKKKKKKKF 28
II K K+ EE + E+ +K KKKKK++K F
Sbjct: 177 IIEKGLNVKQTEELIKKLLEKPEKPKKKKKRRKGF 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
0.316 0.133 0.392
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,370,398
Number of extensions: 1862643
Number of successful extensions: 8953
Number of sequences better than 10.0: 1
Number of HSP's gapped: 7855
Number of HSP's successfully gapped: 565
Length of query: 387
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 288
Effective length of database: 6,546,556
Effective search space: 1885408128
Effective search space used: 1885408128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (27.0 bits)