RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16243
(782 letters)
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 320
Score = 285 bits (732), Expect = 4e-90
Identities = 121/320 (37%), Positives = 180/320 (56%), Gaps = 40/320 (12%)
Query: 219 KVAVSINLRATKALLEMAKEMKQLKFFDPMRKRCPHYLSKMVAVTGDCLKPGVGINSEDR 278
K+ + I ++ ++ E +E+ + K FD R P + SK+V + GD +P +G++ ED
Sbjct: 29 KIYLLIRGKSGQSAEERLRELLKDKLFDRGRNLNPLFESKIVPIEGDLSEPNLGLSDEDL 88
Query: 279 QTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKALLEMAKEMKQLKSFVHVSTAYSNC 338
QTL++ ++++ HCAATV FD L A+SIN+ T LLE+AK K+LK+FVHVSTAY N
Sbjct: 89 QTLIEEVNIIIHCAATVTFDERLDEALSINVLGTLRLLELAKRCKKLKAFVHVSTAYVNG 148
Query: 339 RQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQVAEDMVRRG 398
+ +IEE+ Y PP +P LI I EL++D +++ TP ++ PNTY TK +AE +V +
Sbjct: 149 DRQLIEEKVYPPPADPEKLIDILELMDDLELERATPKLLGGHPNTYTFTKALAERLVLKE 208
Query: 399 GAGMPVAMVRPSIVIATNKEPIPGWINNHYGPTVIATNKEPIPGWINNHYGPTGIVAGAG 458
+P+ +VRPSI V AT KEP PGWI+N GP G+ G
Sbjct: 209 RGNLPLVIVRPSI--------------------VGATLKEPFPGWIDNFNGPDGLFLAYG 248
Query: 459 LGLLRSMHADPELVADMVPADNVINCIISAAWNVHQTWNEKKAAGKLVADSLDKNYPDDT 518
G+LR+M+ADP VAD++P D V N +++AA + K
Sbjct: 249 KGILRTMNADPNAVADIIPVDVVANALLAAAA---YSGVRKPR----------------- 288
Query: 519 DIEIYNYVSSTQKPIKWKEF 538
++E+Y+ SS P W E
Sbjct: 289 ELEVYHCGSSDVNPFTWGEA 308
Score = 107 bits (270), Expect = 2e-25
Identities = 36/76 (47%), Positives = 53/76 (69%)
Query: 170 PHYLSKMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRAT 229
P + SK+V + GD +P +G++ ED QTL++ ++++ HCAATV FD L A+SIN+ T
Sbjct: 63 PLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSINVLGT 122
Query: 230 KALLEMAKEMKQLKFF 245
LLE+AK K+LK F
Sbjct: 123 LRLLELAKRCKKLKAF 138
Score = 103 bits (259), Expect = 4e-24
Identities = 39/86 (45%), Positives = 58/86 (67%)
Query: 65 ESFVHVSTAYSNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYA 124
++FVHVSTAY N + +IEE+ Y PP +P LI I EL++D +++ TP ++ PNTY
Sbjct: 136 KAFVHVSTAYVNGDRQLIEEKVYPPPADPEKLIDILELMDDLELERATPKLLGGHPNTYT 195
Query: 125 LTKQVAEDMVRRGGAGMPVAMVRPSI 150
TK +AE +V + +P+ +VRPSI
Sbjct: 196 FTKALAERLVLKERGNLPLVIVRPSI 221
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 207 bits (528), Expect = 2e-61
Identities = 82/263 (31%), Positives = 125/263 (47%), Gaps = 51/263 (19%)
Query: 227 RATK---ALLEMAKEMKQLKFFDPMRKRCPHYLSKMVAVTGDCLKPGVGINSEDRQTLVD 283
RA AL + +E+ + FD ++ L +++ V GD +P +G++ ED Q L +
Sbjct: 30 RAKDGESALERLRQELLKYGLFDRLK-----ALERIIPVAGDLSEPNLGLSDEDFQELAE 84
Query: 284 NIHVVFHCAATVRFDAHLKVAVSINLRATKALLEMAKEMKQLKSFVHVSTAYSNC-RQPI 342
+ V+ H AATV F + N+ T+ +L +AK+MK+ F HVSTAY N R +
Sbjct: 85 EVDVIIHNAATVNFVEPYSDLRATNVLGTREVLRLAKQMKK-LPFHHVSTAYVNGERGGL 143
Query: 343 IEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQVAEDMVRRGGAGM 402
+EE+ +D+ P ++ PN Y +K +AE +VR G+
Sbjct: 144 LEEK-------------------PYKLDEDEPALLGGLPNGYTQSKWLAEQLVREAAGGL 184
Query: 403 PVAMVRPSIVIATNKEPIPGWINNHYGPTVIATNKEPIPGWINNHYGPTGIVAGAGLGLL 462
PV + RPSI+ E GWIN +GP G++ GAGLG+L
Sbjct: 185 PVVIYRPSIITG---ESRTGWINGDD-------------------FGPRGLLGGAGLGVL 222
Query: 463 RSMHADPELVADMVPADNVINCI 485
+ DP+ D+VP D V N I
Sbjct: 223 PDILGDPDARLDLVPVDYVANAI 245
Score = 99.6 bits (249), Expect = 2e-23
Identities = 34/124 (27%), Positives = 57/124 (45%), Gaps = 11/124 (8%)
Query: 127 KQVAEDMVRRGGAGMPVAMVRPSID------LGILFYSEQFFDPMRKRCPHYLSKMVAVT 180
K + E ++R +VR L FD ++ L +++ V
Sbjct: 10 KVLLEKLLRSTPEVKIYCLVRAKDGESALERLRQELLKYGLFDRLK-----ALERIIPVA 64
Query: 181 GDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKALLEMAKEMK 240
GD +P +G++ ED Q L + + V+ H AATV F + N+ T+ +L +AK+MK
Sbjct: 65 GDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGTREVLRLAKQMK 124
Query: 241 QLKF 244
+L F
Sbjct: 125 KLPF 128
Score = 69.2 bits (170), Expect = 5e-13
Identities = 28/86 (32%), Positives = 40/86 (46%), Gaps = 20/86 (23%)
Query: 66 SFVHVSTAYSNC-RQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYA 124
F HVSTAY N R ++EE+ +D+ P ++ PN Y
Sbjct: 127 PFHHVSTAYVNGERGGLLEEK-------------------PYKLDEDEPALLGGLPNGYT 167
Query: 125 LTKQVAEDMVRRGGAGMPVAMVRPSI 150
+K +AE +VR G+PV + RPSI
Sbjct: 168 QSKWLAEQLVREAAGGLPVVIYRPSI 193
>gnl|CDD|176924 cd09071, FAR_C, C-terminal domain of fatty acyl CoA reductases.
C-terminal domain of fatty acyl CoA reductases, a family
of SDR-like proteins. SDRs or short-chain
dehydrogenases/reductases are Rossmann-fold
NAD(P)H-binding proteins. Many proteins in this FAR_C
family may function as fatty acyl-CoA reductases (FARs),
acting on medium and long chain fatty acids, and have
been reported to be involved in diverse processes such
as the biosynthesis of insect pheromones, plant
cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. The function of this
C-terminal domain is unclear.
Length = 92
Score = 106 bits (268), Expect = 1e-27
Identities = 35/74 (47%), Positives = 56/74 (75%)
Query: 575 FLHLLPALIVDTAAKLMGRQPKLLDAYQKIHKFSEVISFFSTQQFTFTNFNTQRLYTKMT 634
FLHLLPA ++D +L+GR+P+LL Y+KIHK +++ +F+T ++ F N NT+ L+ +++
Sbjct: 1 FLHLLPAYLLDLLLRLLGRKPRLLKLYRKIHKLLDLLEYFTTNEWRFDNDNTRALWERLS 60
Query: 635 EEDRALFNFDMSQL 648
EEDR LFNFD+ +
Sbjct: 61 EEDRELFNFDIRSI 74
Score = 103 bits (259), Expect = 2e-26
Identities = 32/73 (43%), Positives = 51/73 (69%)
Query: 664 RSLKLLDAYQKIHKFSEVISFFSTQQFTFTNFNTQRLYTKMTEEDRALFNFDMSQLDWEK 723
R +LL Y+KIHK +++ +F+T ++ F N NT+ L+ +++EEDR LFNFD+ +DW+
Sbjct: 19 RKPRLLKLYRKIHKLLDLLEYFTTNEWRFDNDNTRALWERLSEEDRELFNFDIRSIDWDD 78
Query: 724 YMFWHIRGIRAYL 736
Y +I G+R YL
Sbjct: 79 YFENYIPGLRKYL 91
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 111 bits (280), Expect = 2e-25
Identities = 110/441 (24%), Positives = 176/441 (39%), Gaps = 103/441 (23%)
Query: 256 LSKMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKAL 315
LSK+V V G+ + +G+ + + + V+ + AA FD VA+ IN R L
Sbjct: 191 LSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTFDERYDVAIDINTRGPCHL 250
Query: 316 LEMAKEMKQLKSFVHVSTAYSNC-RQPIIEERFY-------------EPPVNPNHLIQIT 361
+ AK+ K+LK F+ VSTAY N RQ I E+ + + + I
Sbjct: 251 MSFAKKCKKLKLFLQVSTAYVNGQRQGRIMEKPFRMGDCIARELGISNSLPHNRPALDIE 310
Query: 362 ELLN--------DDMIDKITPGIVDY---------WPNTYALTKQVAEDMVRRGGAGMPV 404
+ + + D W +TY TK + E ++ +PV
Sbjct: 311 AEIKLALDSKRHGFQSNSFAQKMKDLGLERAKLYGWQDTYVFTKAMGEMVINSMRGDIPV 370
Query: 405 AMVRPSIVIATNKEPIPGWI--NNHYGPTVIATNKEPIPGWINNHYGPTGIVAGAGLGLL 462
++RPS++ +T K+P PGW+ N P V+ +YG G L
Sbjct: 371 VIIRPSVIESTWKDPFPGWMEGNRMMDPIVL-------------YYGK---------GQL 408
Query: 463 RSMHADPELVADMVPADNVINCIISA-AWNVHQTWNEKKAAGKLVADSLDKNYPDDTDIE 521
ADP V D+VPAD V+N ++A A + A K +I
Sbjct: 409 TGFLADPNGVLDVVPADMVVNATLAAMAKH--------GGAAK-------------PEIN 447
Query: 522 IYNYVSSTQKPIKWKEFMALNEKAVPEIPSTFAIWAYCFTLNKYKSIH----KLYI---- 573
+Y SS P+ +++ L + P + +K + IH KL+
Sbjct: 448 VYQIASSVVNPLVFQDLARLLYEHYKSSP---------YMDSKGRPIHVPPMKLFSSMED 498
Query: 574 LFLHLLPALIVDTAAKLMGRQ-PKLLDAYQKIHKFS-EVISFFST--QQFT-----FTNF 624
HL ++ + M KL + I S E + ++ + +T F N
Sbjct: 499 FSSHLWRDALLRSGLAGMSSSDRKLSQKLENICAKSVEQAKYLASIYEPYTFYGGRFDNS 558
Query: 625 NTQRLYTKMTEEDRALFNFDM 645
NTQRL +M+EE++A F FD+
Sbjct: 559 NTQRLMERMSEEEKAEFGFDV 579
Score = 50.2 bits (120), Expect = 4e-06
Identities = 24/73 (32%), Positives = 38/73 (52%)
Query: 173 LSKMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKAL 232
LSK+V V G+ + +G+ + + + V+ + AA FD VA+ IN R L
Sbjct: 191 LSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTFDERYDVAIDINTRGPCHL 250
Query: 233 LEMAKEMKQLKFF 245
+ AK+ K+LK F
Sbjct: 251 MSFAKKCKKLKLF 263
Score = 49.9 bits (119), Expect = 4e-06
Identities = 22/48 (45%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 692 FTNFNTQRLYTKMTEEDRALFNFDMSQLDWEKYMF-WHIRGIRAYLVK 738
F N NTQRL +M+EE++A F FD+ +DW Y+ HI G+R +++K
Sbjct: 555 FDNSNTQRLMERMSEEEKAEFGFDVGSIDWRDYITNVHIPGLRRHVMK 602
Score = 31.0 bits (70), Expect = 2.5
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 119 WPNTYALTKQVAEDMVRRGGAGMPVAMVRPSI 150
W +TY TK + E ++ +PV ++RPS+
Sbjct: 346 WQDTYVFTKAMGEMVINSMRGDIPVVIIRPSV 377
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 109 bits (273), Expect = 6e-25
Identities = 107/429 (24%), Positives = 175/429 (40%), Gaps = 88/429 (20%)
Query: 258 KMVAVTGDCLKPGVGINSED-RQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKALL 316
K+ V GD +G+ + R+ + I +V + AAT FD VA+ IN +L
Sbjct: 85 KVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFDERYDVALGINTLGALNVL 144
Query: 317 EMAKEMKQLKSFVHVSTAYSNCRQP--IIEERFY-EPPVNPNHLIQI-----------TE 362
AK+ ++K +HVSTAY + I+E+ F+ +N N + I E
Sbjct: 145 NFAKKCVKVKMLLHVSTAYVCGEKSGLILEKPFHMGETLNGNRKLDINEEKKLVKEKLKE 204
Query: 363 LLNDDMIDK-ITPGIVDY---------WPNTYALTKQVAEDMVRRGGAGMPVAMVRPSIV 412
L D ++ IT + D WPNTY TK + E ++ +P+ ++RP+++
Sbjct: 205 LNEQDASEEEITQAMKDLGMERAKLHGWPNTYVFTKAMGEMLLGNFKENLPLVIIRPTMI 264
Query: 413 IATNKEPIPGWINNHYGPTVIATNKEPIPGWINNHYGPTGIVAGAGLGLLRSMHADPELV 472
+T KEP PGWI + T I++ ++ G G G L ADP V
Sbjct: 265 TSTYKEPFPGWIEG------LRT--------IDS------VIVGYGKGKLTCFLADPNSV 304
Query: 473 ADMVPADNVINCIISAAWNVHQTWNEKKAAGKLVADSLDKNYPDDTDIEIYNYVSSTQKP 532
D++PAD V+N +I A + IY+ SS + P
Sbjct: 305 LDVIPADMVVNAMIVAM--AAHAGGQGSEI-------------------IYHVGSSLKNP 343
Query: 533 IKWKEFMAL-----------NEKAVPEIPSTFAIWAYCFTLNKYKSIHKLYILFLHLLPA 581
+K+ N++ P I + + + Y +I Y+L L L
Sbjct: 344 VKFSNLHDFAYRYFSKNPWINKEGSPVKVGKGTILSTMASFSLYMTIR--YLLPLKAL-Q 400
Query: 582 LIVDTAAKLMGRQPKLLDAYQKIHKFSEVISFFSTQQF---TFTNFNTQRLYTKMTEEDR 638
L+ K G + L+ +KI ++ + F F + NT++L K E +
Sbjct: 401 LVNIILPKRYGDKYTDLN--RKIKLVMRLVDLYKPYVFFKGIFDDTNTEKLRIKRKETGK 458
Query: 639 A---LFNFD 644
+F+FD
Sbjct: 459 EEADMFDFD 467
Score = 38.5 bits (90), Expect = 0.013
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 4/51 (7%)
Query: 692 FTNFNTQRLYTKMTEEDRA---LFNFDMSQLDWEKYMFW-HIRGIRAYLVK 738
F + NT++L K E + +F+FD +DWE YM HI G+ Y++K
Sbjct: 441 FDDTNTEKLRIKRKETGKEEADMFDFDPKSIDWEDYMTNVHIPGLVKYVLK 491
Score = 37.0 bits (86), Expect = 0.034
Identities = 29/107 (27%), Positives = 48/107 (44%), Gaps = 24/107 (22%)
Query: 68 VHVSTAYSNCRQP--IIEERFY-EPPVNPNHLIQI-----------TELLNDDMIDK-IT 112
+HVSTAY + I+E+ F+ +N N + I EL D ++ IT
Sbjct: 157 LHVSTAYVCGEKSGLILEKPFHMGETLNGNRKLDINEEKKLVKEKLKELNEQDASEEEIT 216
Query: 113 PGIVDY---------WPNTYALTKQVAEDMVRRGGAGMPVAMVRPSI 150
+ D WPNTY TK + E ++ +P+ ++RP++
Sbjct: 217 QAMKDLGMERAKLHGWPNTYVFTKAMGEMLLGNFKENLPLVIIRPTM 263
Score = 34.7 bits (80), Expect = 0.20
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 175 KMVAVTGDCLKPGVGINSED-RQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKALL 233
K+ V GD +G+ + R+ + I +V + AAT FD VA+ IN +L
Sbjct: 85 KVTPVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFDERYDVALGINTLGALNVL 144
Query: 234 EMAK 237
AK
Sbjct: 145 NFAK 148
>gnl|CDD|111859 pfam03015, Sterile, Male sterility protein. This family represents
the C-terminal region of the male sterility protein in a
number of arabidopsis and drosophila. A sequence-related
jojoba acyl CoA reductase is also included.
Length = 94
Score = 87.7 bits (218), Expect = 5e-21
Identities = 36/74 (48%), Positives = 49/74 (66%)
Query: 575 FLHLLPALIVDTAAKLMGRQPKLLDAYQKIHKFSEVISFFSTQQFTFTNFNTQRLYTKMT 634
F H LPA +D +L G++P+L+ Y+KIHK EV+ FS ++ F N NT+ L KM+
Sbjct: 1 FYHTLPAYFLDLLLRLYGQKPRLVKLYRKIHKGLEVLQPFSLNEWIFDNKNTRELREKMS 60
Query: 635 EEDRALFNFDMSQL 648
EED+ LFNFDM L
Sbjct: 61 EEDKKLFNFDMESL 74
Score = 87.3 bits (217), Expect = 7e-21
Identities = 39/83 (46%), Positives = 54/83 (65%)
Query: 657 LNTLVSTRSLKLLDAYQKIHKFSEVISFFSTQQFTFTNFNTQRLYTKMTEEDRALFNFDM 716
L + + +L+ Y+KIHK EV+ FS ++ F N NT+ L KM+EED+ LFNFDM
Sbjct: 12 LLLRLYGQKPRLVKLYRKIHKGLEVLQPFSLNEWIFDNKNTRELREKMSEEDKKLFNFDM 71
Query: 717 SQLDWEKYMFWHIRGIRAYLVKD 739
LDW++Y IRGIR YL+K+
Sbjct: 72 ESLDWDEYFRNAIRGIRKYLLKE 94
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR family
domains have the characteristic active site tetrad and a
well-conserved NAD(P)-binding motif. This subgroup is
not well characterized, its members are annotated as
having a variety of putative functions. One
characterized member is Pseudomonas fluorescens MupV a
protein involved in the biosynthesis of Mupirocin, a
polyketide-derived antibiotic. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 81.6 bits (202), Expect = 6e-17
Identities = 55/231 (23%), Positives = 90/231 (38%), Gaps = 52/231 (22%)
Query: 258 KMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKALLE 317
++ + GD +P +G+++ + L + V HCAA+ F A + A N+ T+ +LE
Sbjct: 50 RVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDGTEHVLE 109
Query: 318 MAKEMKQLKSFVHVSTAY-SNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGI 376
+A + + F +VSTAY + R+ I E P N
Sbjct: 110 LAARLDI-QRFHYVSTAYVAGNREGNIRETELNPGQN----------------------- 145
Query: 377 VDYWPNTYALTKQVAEDMVRRGGAGMPVAMVRPSIVIATNKEPIPGWINNHYGPTVIATN 436
+ N Y +K AE +VR +P+ + RPSIV+ G +
Sbjct: 146 ---FKNPYEQSKAEAEQLVRAAATQIPLTVYRPSIVV---------------GDSKT--- 184
Query: 437 KEPIPGWINNHYGPTG-IVAGAGLGLLRSMHADPELVADMVPADNVINCII 486
G I G + A LG M + ++VP D V + I+
Sbjct: 185 -----GRIEKIDGLYELLNLLAKLGRWLPMPGNKGARLNLVPVDYVADAIV 230
Score = 55.1 bits (133), Expect = 4e-08
Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 10/92 (10%)
Query: 175 KMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKALLE 234
++ + GD +P +G+++ + L + V HCAA+ F A + A N+ T+ +LE
Sbjct: 50 RVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDGTEHVLE 109
Query: 235 MAKEMKQLKFFDPMRKRCPHYLSKMVAVTGDC 266
+A + +F HY+S V G+
Sbjct: 110 LAARLDIQRF---------HYVST-AYVAGNR 131
Score = 31.6 bits (72), Expect = 1.5
Identities = 24/88 (27%), Positives = 34/88 (38%), Gaps = 27/88 (30%)
Query: 67 FVHVSTAY-SNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYAL 125
F +VSTAY + R+ I E P N + N Y
Sbjct: 119 FHYVSTAYVAGNREGNIRETELNPGQN--------------------------FKNPYEQ 152
Query: 126 TKQVAEDMVRRGGAGMPVAMVRPSIDLG 153
+K AE +VR +P+ + RPSI +G
Sbjct: 153 SKAEAEQLVRAAATQIPLTVYRPSIVVG 180
>gnl|CDD|187546 cd05235, SDR_e1, extended (e) SDRs, subgroup 1. This family
consists of an SDR module of multidomain proteins
identified as putative polyketide sythases fatty acid
synthases (FAS), and nonribosomal peptide synthases,
among others. However, unlike the usual ketoreductase
modules of FAS and polyketide synthase, these domains
are related to the extended SDRs, and have canonical
NAD(P)-binding motifs and an active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 290
Score = 72.7 bits (179), Expect = 7e-14
Identities = 47/186 (25%), Positives = 75/186 (40%), Gaps = 41/186 (22%)
Query: 247 PMRKRCPHY---------LSKMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRF 297
+ Y LS++ V GD KP +G++ +D Q L + + V+ H A V +
Sbjct: 43 RLIDNLKEYGLNLWDELELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNW 102
Query: 298 ---DAHLKVAVSINLRATKALLEMAKEMKQLKSFVHVSTAYSNCRQPIIEERFYEPPVNP 354
LK A N+ TK LL++A K LK VST
Sbjct: 103 VYPYEELKPA---NVLGTKELLKLAATGK-LKPLHFVSTLS------------------- 139
Query: 355 NHLIQITELLNDDMIDKITPGIV--DYWPNTYALTKQVAEDMVRRGGA-GMPVAMVRPSI 411
+ E N ++ + + PN Y +K VAE ++R G+PVA++RP
Sbjct: 140 ---VFSAEEYNALDDEESDDMLESQNGLPNGYIQSKWVAEKLLREAANRGLPVAIIRPGN 196
Query: 412 VIATNK 417
+ ++
Sbjct: 197 IFGDSE 202
Score = 49.2 bits (118), Expect = 3e-06
Identities = 29/111 (26%), Positives = 46/111 (41%), Gaps = 24/111 (21%)
Query: 159 EQFFDPMRKRCPHY---------LSKMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCA 209
E + + Y LS++ V GD KP +G++ +D Q L + + V+ H
Sbjct: 38 EAALERLIDNLKEYGLNLWDELELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNG 97
Query: 210 ATVRF---DAHLKVAVSINLRATKALLEMAKEMKQLKFFDPMRKRCPHYLS 257
A V + LK A N+ TK LL++A K H++S
Sbjct: 98 ANVNWVYPYEELKPA---NVLGTKELLKLAATGKLKPL---------HFVS 136
Score = 31.1 bits (71), Expect = 2.0
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 97 IQITELLNDDMIDKITPGIV--DYWPNTYALTKQVAEDMVRRGGA-GMPVAMVRP 148
+ E N ++ + + PN Y +K VAE ++R G+PVA++RP
Sbjct: 140 VFSAEEYNALDDEESDDMLESQNGLPNGYIQSKWVAEKLLREAANRGLPVAIIRP 194
>gnl|CDD|225857 COG3320, COG3320, Putative dehydrogenase domain of multifunctional
non-ribosomal peptide synthetases and related enzymes
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 382
Score = 56.6 bits (137), Expect = 2e-08
Identities = 41/177 (23%), Positives = 66/177 (37%), Gaps = 33/177 (18%)
Query: 249 RKRCPHYL-------SKMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRF---D 298
K Y ++ V GD +P +G++ Q L +N+ ++ H AA V
Sbjct: 45 EKTFDLYRHWDELSADRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVFPY 104
Query: 299 AHLKVAVSINLRATKALLEMAKEMKQLKSFVHVSTAYSNCRQPIIEERFYEPPVNPNHLI 358
+ L+ A N+ T +L +A K K +VS+ E N
Sbjct: 105 SELRGA---NVLGTAEVLRLAATGK-PKPLHYVSSI-----------SVGETEYYSN--- 146
Query: 359 QITELLNDDMIDKITPGIVDYWPNTYALTKQVAEDMVRR-GGAGMPVAMVRPSIVIA 414
+ D++ G Y +K VAE +VR G G+PV + RP +
Sbjct: 147 --FTVDFDEISPTRNVGQG--LAGGYGRSKWVAEKLVREAGDRGLPVTIFRPGYITG 199
Score = 37.4 bits (87), Expect = 0.024
Identities = 25/102 (24%), Positives = 41/102 (40%), Gaps = 22/102 (21%)
Query: 166 RKRCPHYL-------SKMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRF---D 215
K Y ++ V GD +P +G++ Q L +N+ ++ H AA V
Sbjct: 45 EKTFDLYRHWDELSADRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNHVFPY 104
Query: 216 AHLKVAVSINLRATKALLEMAKEMKQLKFFDPMRKRCPHYLS 257
+ L+ A N+ T +L +A K K HY+S
Sbjct: 105 SELRGA---NVLGTAEVLRLAATGK-PKPL--------HYVS 134
Score = 30.1 bits (68), Expect = 5.6
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 119 WPNTYALTKQVAEDMVRR-GGAGMPVAMVRP 148
Y +K VAE +VR G G+PV + RP
Sbjct: 164 LAGGYGRSKWVAEKLVREAGDRGLPVTIFRP 194
>gnl|CDD|212494 cd08946, SDR_e, extended (e) SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 200
Score = 54.2 bits (131), Expect = 3e-08
Identities = 39/171 (22%), Positives = 63/171 (36%), Gaps = 43/171 (25%)
Query: 280 TLVDNIHVVFHCAATVRFDA---HLKVAVSINLRATKALLEMAKEMKQLKSFVHVSTA-- 334
++D + VV H AA V A + N+ T LLE A++ +K FV+ S+A
Sbjct: 26 VVIDRLDVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKAG-VKRFVYASSASV 84
Query: 335 YSNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQVAEDM 394
Y + EE P++P Y ++K AE +
Sbjct: 85 YGSPEGLPEEEETPPRPLSP-----------------------------YGVSKLAAEHL 115
Query: 395 VRRGGA--GMPVAMVRPSIVIATNKEPIPGWINNHYGPTVI--ATNKEPIP 441
+R G G+PV ++R + V P + I A +P+
Sbjct: 116 LRSYGESYGLPVVILRLANVYG----PGQRPRLDGVVNDFIRRALEGKPLT 162
Score = 29.2 bits (66), Expect = 6.1
Identities = 19/88 (21%), Positives = 32/88 (36%), Gaps = 33/88 (37%)
Query: 67 FVHVSTA--YSNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYA 124
FV+ S+A Y + EE P++P Y
Sbjct: 76 FVYASSASVYGSPEGLPEEEETPPRPLSP-----------------------------YG 106
Query: 125 LTKQVAEDMVRRGGA--GMPVAMVRPSI 150
++K AE ++R G G+PV ++R +
Sbjct: 107 VSKLAAEHLLRSYGESYGLPVVILRLAN 134
Score = 28.8 bits (65), Expect = 9.0
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 197 TLVDNIHVVFHCAATVRFDA---HLKVAVSINLRATKALLEMAKEMKQLKFF 245
++D + VV H AA V A + N+ T LLE A++ +F
Sbjct: 26 VVIDRLDVVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKAGVKRFV 77
>gnl|CDD|233557 TIGR01746, Thioester-redct, thioester reductase domain. This model
includes the terminal domain from the fungal alpha
aminoadipate reductase enzyme (also known as
aminoadipate semialdehyde dehydrogenase) which is
involved in the biosynthesis of lysine , as well as the
reductase-containing component of the myxochelin
biosynthetic gene cluster, MxcG. The mechanism of
reduction involves activation of the substrate by
adenylation and transfer to a covalently-linked
pantetheine cofactor as a thioester. This thioester is
then reduced to give an aldehyde (thus releasing the
product) and a regenerated pantetheine thiol. (In
myxochelin biosynthesis this aldehyde is further reduced
to an alcohol or converted to an amine by an
aminotransferase.) This is a fundamentally different
reaction than beta-ketoreductase domains of polyketide
synthases which act at a carbonyl two carbons removed
from the thioester and forms an alcohol as a product.
This domain is invariably found at the C-terminus of the
proteins which contain it (presumably because it results
in the release of the product). The majority of hits to
this model are non-ribosomal peptide synthetases in
which this domain is similarly located proximal to a
thiolation domain (pfam00550). In some cases this domain
is found at the end of a polyketide synthetase enzyme,
but is unlike ketoreductase domains which are found
before the thiolase domains. Exceptions to this observed
relationship with the thiolase domain include three
proteins which consist of stand-alone reductase domains
(GP|466833 from M. leprae, GP|435954 from Anabaena and
OMNI|NTL02SC1199 from Strep. coelicolor) and one protein
(OMNI|NTL01NS2636 from Nostoc) which contains N-terminal
homology with a small group of hypothetical proteins but
no evidence of a thiolation domain next to the putative
reductase domain. Below the noise cutoff to this model
are proteins containing more distantly related
ketoreductase and dehydratase/epimerase domains. It has
been suggested that a NADP-binding motif can be found in
the N-terminal portion of this domain that may form a
Rossman-type fold.
Length = 367
Score = 54.3 bits (131), Expect = 1e-07
Identities = 41/162 (25%), Positives = 68/162 (41%), Gaps = 30/162 (18%)
Query: 257 SKMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRF---DAHLKVAVSINLRATK 313
++ V GD +P +G++ + + L +N+ + H A V + + L+ A N+ T+
Sbjct: 61 ERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSELRGA---NVLGTR 117
Query: 314 ALLEMAKEMKQLKSFVHVSTAYSNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKIT 373
+L +A + K +VST L +TE DD T
Sbjct: 118 EVLRLA-ASGRAKPLHYVSTISVG---------------AAIDLSTVTE---DDATV--T 156
Query: 374 PGIVDYWPNTYALTKQVAEDMVRRGGA-GMPVAMVRPSIVIA 414
P YA +K VAE +VR G+PV +VRP ++
Sbjct: 157 PPP--GLAGGYAQSKWVAELLVREASDRGLPVTIVRPGRILG 196
Score = 33.2 bits (76), Expect = 0.54
Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 15/93 (16%)
Query: 174 SKMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRF---DAHLKVAVSINLRATK 230
++ V GD +P +G++ + + L +N+ + H A V + + L+ A N+ T+
Sbjct: 61 ERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNWVYPYSELRGA---NVLGTR 117
Query: 231 ALLEMAKEMKQLKFFDPMRKRCPHYLSKMVAVT 263
+L +A + K HY+S +
Sbjct: 118 EVLRLA-ASGRAKPL--------HYVSTISVGA 141
Score = 31.2 bits (71), Expect = 2.0
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 118 YWPNTYALTKQVAEDMVRRGGA-GMPVAMVRP 148
YA +K VAE +VR G+PV +VRP
Sbjct: 160 GLAGGYAQSKWVAELLVREASDRGLPVTIVRP 191
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and lacks
the Asn of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 318
Score = 51.1 bits (123), Expect = 1e-06
Identities = 35/145 (24%), Positives = 48/145 (33%), Gaps = 34/145 (23%)
Query: 276 EDRQTLVD---NIHVVFHCAATVRF-DAHLKVAVSINLRATKALLEMAKEMKQLKSFVHV 331
D +L VFH AA K N+ T+ +L+ A E ++ VH
Sbjct: 51 TDAASLAAAMKGCDRVFHLAAFTSLWAKDRKELYRTNVEGTRNVLDAALE-AGVRRVVHT 109
Query: 332 ST--AYSNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQ 389
S+ A I+E P N PN Y +K
Sbjct: 110 SSIAALGGPPDGRIDETT---PWNERPF-----------------------PNDYYRSKL 143
Query: 390 VAEDMVRRGGA-GMPVAMVRPSIVI 413
+AE V A G+ V +V PS V
Sbjct: 144 LAELEVLEAAAEGLDVVIVNPSAVF 168
Score = 32.6 bits (75), Expect = 0.73
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 120 PNTYALTKQVAEDMVRRGGA-GMPVAMVRPSIDLG 153
PN Y +K +AE V A G+ V +V PS G
Sbjct: 135 PNDYYRSKLLAELEVLEAAAEGLDVVIVNPSAVFG 169
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 49.9 bits (119), Expect = 2e-06
Identities = 31/137 (22%), Positives = 47/137 (34%), Gaps = 40/137 (29%)
Query: 287 VVFHCAATVRF----DAHLKVAVSINLRATKALLEMAKEMKQLKSFVHVSTAYS----NC 338
V H AA + + +N+ T LLE A+ +K FV S+
Sbjct: 67 AVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAAG-VKRFVFASSVSVVYGDPP 125
Query: 339 RQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQVAEDMVR-- 396
PI E+ P+NP Y ++K AE ++R
Sbjct: 126 PLPIDEDLGPPRPLNP-----------------------------YGVSKLAAEQLLRAY 156
Query: 397 RGGAGMPVAMVRPSIVI 413
G+PV ++RP V
Sbjct: 157 ARLYGLPVVILRPFNVY 173
Score = 31.5 bits (71), Expect = 1.6
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 4/46 (8%)
Query: 204 VVFHCAATVRF----DAHLKVAVSINLRATKALLEMAKEMKQLKFF 245
V H AA + + +N+ T LLE A+ +F
Sbjct: 67 AVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAAGVKRFV 112
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 46.9 bits (112), Expect = 1e-05
Identities = 37/172 (21%), Positives = 51/172 (29%), Gaps = 57/172 (33%)
Query: 285 IHVVFHCAATVRFDAHLK---VAVSINLRATKALLEMAKEMKQLKSFVHVSTA--YSNCR 339
V H AA A + + N+ T LLE A+ K FV S++ Y +
Sbjct: 64 PDAVIHLAAQSGVGASFEDPADFIRANVLGTLRLLEAARRAGV-KRFVFASSSEVYGDVA 122
Query: 340 QPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQVAEDMVRRGG 399
P I E P++P YA K AE +V
Sbjct: 123 DPPITEDTPLGPLSP-----------------------------YAAAKLAAERLVEAYA 153
Query: 400 A--GMPVAMVRPSIVIATNKEPIPGWINNHYGP---TVIATNKEPIPGWINN 446
G+ ++R N YGP T+ IP I
Sbjct: 154 RAYGLRAVILRLF---------------NVYGPGNPDPFVTHV--IPALIRR 188
Score = 30.3 bits (69), Expect = 3.0
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 3/46 (6%)
Query: 202 IHVVFHCAATVRFDAHLK---VAVSINLRATKALLEMAKEMKQLKF 244
V H AA A + + N+ T LLE A+ +F
Sbjct: 64 PDAVIHLAAQSGVGASFEDPADFIRANVLGTLRLLEAARRAGVKRF 109
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 41.9 bits (99), Expect = 0.001
Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 11/91 (12%)
Query: 175 KMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKALLE 234
++V + GD +PG+G++ D L +I V H AA A + + N+ T+ ++E
Sbjct: 52 RVVPLVGDLTEPGLGLSEADIAELG-DIDHVVHLAAIYDLTADEEAQRAANVDGTRNVVE 110
Query: 235 MAKEMKQLKFFDPMRKRCPHYLSKMVAVTGD 265
+A+ ++ H++S +AV GD
Sbjct: 111 LAER---------LQAATFHHVSS-IAVAGD 131
Score = 41.9 bits (99), Expect = 0.001
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 258 KMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKALLE 317
++V + GD +PG+G++ D L +I V H AA A + + N+ T+ ++E
Sbjct: 52 RVVPLVGDLTEPGLGLSEADIAELG-DIDHVVHLAAIYDLTADEEAQRAANVDGTRNVVE 110
Query: 318 MAKEMKQLKSFVHVS 332
+A+ + Q +F HVS
Sbjct: 111 LAERL-QAATFHHVS 124
>gnl|CDD|187568 cd05258, CDP_TE_SDR_e, CDP-tyvelose 2-epimerase, extended (e) SDRs.
CDP-tyvelose 2-epimerase is a tetrameric SDR that
catalyzes the conversion of CDP-D-paratose to
CDP-D-tyvelose, the last step in tyvelose biosynthesis.
This subgroup is a member of the extended SDR subfamily,
with a characteristic active site tetrad and NAD-binding
motif. Extended SDRs are distinct from classical SDRs.
In addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 337
Score = 37.7 bits (88), Expect = 0.018
Identities = 31/149 (20%), Positives = 54/149 (36%), Gaps = 21/149 (14%)
Query: 274 NSEDRQTLVDNIHVVFHCAATVRFDAHLK---VAVSINLRATKALLEMAKEMKQLKSFVH 330
N D + L ++I ++ H AA + N T +LE A++ F+
Sbjct: 63 NRNDLEDLFEDIDLIIHTAAQPSVTTSASSPRLDFETNALGTLNVLEAARQHAPNAPFIF 122
Query: 331 VST--AYSN--CRQPIIEERF-YEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYA 385
ST Y + P+ E YE E + I + P +D+ + Y
Sbjct: 123 TSTNKVYGDLPNYLPLEELETRYELA---------PEGWSPAGISESFP--LDFSHSLYG 171
Query: 386 LTKQVAEDMVRRGGA--GMPVAMVRPSIV 412
+K A+ V+ G G+ + R +
Sbjct: 172 ASKGAADQYVQEYGRIFGLKTVVFRCGCL 200
Score = 33.0 bits (76), Expect = 0.60
Identities = 14/67 (20%), Positives = 23/67 (34%), Gaps = 15/67 (22%)
Query: 191 NSEDRQTLVDNIHVVFHCAATVRFDAHLK---VAVSINLRATKALLEMAKEMKQLKFFDP 247
N D + L ++I ++ H AA + N T +LE A
Sbjct: 63 NRNDLEDLFEDIDLIIHTAAQPSVTTSASSPRLDFETNALGTLNVLEAA----------- 111
Query: 248 MRKRCPH 254
R+ P+
Sbjct: 112 -RQHAPN 117
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 36.6 bits (85), Expect = 0.058
Identities = 40/140 (28%), Positives = 59/140 (42%), Gaps = 38/140 (27%)
Query: 308 NLRATKALLEMAKEMKQLKSFVHVSTAYSNCRQPIIEERFYEPPVNPNHLIQITELLNDD 367
N+ T LLE K Q++ F+HVST + E + V NH + ++LL
Sbjct: 107 NIYGTHVLLEACKVTGQIRRFIHVST------DEVYGETDEDADVG-NH--EASQLL--- 154
Query: 368 MIDKITPGIVDYWP-NTYALTKQVAEDMVRRGGA--GMPVAMVRPSIVIATNKEP---IP 421
P N Y+ TK AE +V G G+PV R + V N+ P IP
Sbjct: 155 -------------PTNPYSATKAGAEMLVMAYGRSYGLPVITTRGNNVYGPNQFPEKLIP 201
Query: 422 GWINNHYGPTVIATNKEPIP 441
+I ++A +P+P
Sbjct: 202 KFI-------LLAMQGKPLP 214
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended or
atypical short-chain dehydrogenases/reductases (SDRs,
aka tyrosine-dependent oxidoreductases) are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 176
Score = 34.7 bits (80), Expect = 0.091
Identities = 33/166 (19%), Positives = 53/166 (31%), Gaps = 47/166 (28%)
Query: 251 RCPHYLSKM----VAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVS 306
R LSK VAV L+ + + V + VV H A R
Sbjct: 30 RNTKRLSKEDQEPVAVVEGDLR-----DLDSLSDAVQGVDVVIHLAGAPRDTRDF---CE 81
Query: 307 INLRATKALLEMAKEMKQLKSFVHVSTAYSNCRQPIIEERFYEPPVNPNHLIQITELLND 366
+++ T+ +LE AKE +K F+ +S+ + E
Sbjct: 82 VDVEGTRNVLEAAKEAG-VKHFIFISSL--------------------GAYGDLHEETEP 120
Query: 367 DMIDKITPGIVDYWPNTYALTKQVAEDMVRRGGAGMPVAMVRPSIV 412
Y K E ++R A +P +VRP ++
Sbjct: 121 SPSSP------------YLAVKAKTEAVLRE--ASLPYTIVRPGVI 152
Score = 30.4 bits (69), Expect = 2.0
Identities = 21/82 (25%), Positives = 30/82 (36%), Gaps = 12/82 (14%)
Query: 168 RCPHYLSKM----VAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVS 223
R LSK VAV L+ + + V + VV H A R
Sbjct: 30 RNTKRLSKEDQEPVAVVEGDLR-----DLDSLSDAVQGVDVVIHLAGAPRDTRDF---CE 81
Query: 224 INLRATKALLEMAKEMKQLKFF 245
+++ T+ +LE AKE F
Sbjct: 82 VDVEGTRNVLEAAKEAGVKHFI 103
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD syndrome
(congenital hemidysplasia with ichthyosiform nevus and
limb defects), an X-linked dominant, male-lethal trait.
Mutations in the human gene encoding C(27) 3beta-HSD
underlie a rare autosomal recessive form of neonatal
cholestasis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 331
Score = 33.9 bits (78), Expect = 0.28
Identities = 27/142 (19%), Positives = 51/142 (35%), Gaps = 29/142 (20%)
Query: 274 NSEDRQTLVDNIHVVFHCAATVRFDAHLKVAVSINLRATKALLEMAKEMKQLKSFVHVST 333
+ D + + VFH AA V + +N+ T+ +L+ + ++ FV+ S+
Sbjct: 56 DRNDVEQALSGADCVFHTAAIVPLAGPRDLYWEVNVGGTQNVLDACQRCG-VQKFVYTSS 114
Query: 334 AYSNCRQPIIEERFY-EPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQVAE 392
F + N + + L +D YA TK +AE
Sbjct: 115 ---------SSVIFGGQNIHNGDETLPYPPLDSD----------------MYAETKAIAE 149
Query: 393 DMVRR--GGAGMPVAMVRPSIV 412
+V G + +RP+ +
Sbjct: 150 IIVLEANGRDDLLTCALRPAGI 171
Score = 30.9 bits (70), Expect = 2.8
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 11/56 (19%)
Query: 117 DYWPNT------YALTKQVAEDMVRR--GGAGMPVAMVRPSIDLGILFYSEQFFDP 164
+ P YA TK +AE +V G + +RP+ GI +Q P
Sbjct: 129 ETLPYPPLDSDMYAETKAIAEIIVLEANGRDDLLTCALRPA---GIFGPGDQGLVP 181
>gnl|CDD|234212 TIGR03443, alpha_am_amid, L-aminoadipate-semialdehyde dehydrogenase.
Members of this protein family are
L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31),
product of the LYS2 gene. It is also called
alpha-aminoadipate reductase. In fungi, lysine is
synthesized via aminoadipate. Currently, all members of
this family are fungal.
Length = 1389
Score = 34.3 bits (79), Expect = 0.31
Identities = 40/176 (22%), Positives = 71/176 (40%), Gaps = 36/176 (20%)
Query: 255 YLSKMVAVTGDCLKPGVGINSEDRQTLVDNIHVVFHCAATVRF---DAHLKVAVSINLRA 311
+ S++ V GD K G++ E L + + V+ H A V + + L+ A N+
Sbjct: 1032 WASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGALVHWVYPYSKLRDA---NVIG 1088
Query: 312 TKALLEMAKEMKQLKSFVHVSTAYSNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDK 371
T +L + E K K F VS+ + ++ + + L+D+++
Sbjct: 1089 TINVLNLCAEGKA-KQFSFVSSTSA---------------LDTEYYVN----LSDELVQA 1128
Query: 372 ITPGIVDYWP---------NTYALTKQVAEDMVRRGGA-GMPVAMVRPSIVIATNK 417
GI + Y +K VAE ++R G G+ +VRP V +K
Sbjct: 1129 GGAGIPESDDLMGSSKGLGTGYGQSKWVAEYIIREAGKRGLRGCIVRPGYVTGDSK 1184
>gnl|CDD|187557 cd05246, dTDP_GD_SDR_e, dTDP-D-glucose 4,6-dehydratase, extended
(e) SDRs. This subgroup contains dTDP-D-glucose
4,6-dehydratase and related proteins, members of the
extended-SDR family, with the characteristic Rossmann
fold core region, active site tetrad and NAD(P)-binding
motif. dTDP-D-glucose 4,6-dehydratase is closely related
to other sugar epimerases of the SDR family.
dTDP-D-dlucose 4,6,-dehydratase catalyzes the second of
four steps in the dTDP-L-rhamnose pathway (the
dehydration of dTDP-D-glucose to
dTDP-4-keto-6-deoxy-D-glucose) in the synthesis of
L-rhamnose, a cell wall component of some pathogenic
bacteria. In many gram negative bacteria, L-rhamnose is
an important constituent of lipopoylsaccharide
O-antigen. The larger N-terminal portion of
dTDP-D-Glucose 4,6-dehydratase forms a Rossmann fold
NAD-binding domain, while the C-terminus binds the sugar
substrate. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 315
Score = 33.3 bits (77), Expect = 0.43
Identities = 45/175 (25%), Positives = 67/175 (38%), Gaps = 60/175 (34%)
Query: 284 NIHVVFHCAATVRFDAHLKVAVSI---------NLRATKALLEMAKEMKQLKSFVHVST- 333
I V H AA ++H V SI N+ T LLE A++ K FVH+ST
Sbjct: 74 KIDAVIHFAA----ESH--VDRSISDPEPFIRTNVLGTYTLLEAARKYGV-KRFVHISTD 126
Query: 334 -AYSNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNT-YALTKQVA 391
Y +LL+D + +P P + Y+ +K A
Sbjct: 127 EVYG-------------------------DLLDDGEFTETSP----LAPTSPYSASKAAA 157
Query: 392 EDMVRRGGA--GMPVAMVRPSIVIATNKEP---IPGWINNHYGPTVIATNKEPIP 441
+ +VR G+PV + R S + P IP +I N A + +P+P
Sbjct: 158 DLLVRAYHRTYGLPVVITRCSNNYGPYQFPEKLIPLFILN-------ALDGKPLP 205
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor of
L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis. The
human gene encoding MAT2B encodes two major splicing
variants which are induced in human cell liver cancer
and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this extended
SDR domain. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 32.2 bits (74), Expect = 0.85
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 285 IHVVFHCAATVRFDA---HLKVAVSINLRATKALLEMAKEMKQLKSFVHVSTAY 335
V+ +CAA R D ++A +N+ A + L AKE+ +H+ST Y
Sbjct: 56 PDVIINCAAYTRVDKCESDPELAYRVNVLAPENLARAAKEVGAR--LIHISTDY 107
>gnl|CDD|163663 cd07420, MPP_RdgC, Drosophila melanogaster RdgC and related
proteins, metallophosphatase domain. RdgC (retinal
degeneration C) is a vertebrate serine-threonine protein
phosphatase that is required to prevent light-induced
retinal degeneration. In addition to its catalytic
domain, RdgC has two C-terminal EF hands. Homologs of
RdgC include the human phosphatases protein phosphatase
with EF hands 1 and -2 (PPEF-1 and -2). PPEF-1
transcripts are present at low levels in the retina,
PPEF-2 transcripts and PPEF-2 protein are present at
high levels in photoreceptors. The PPP (phosphoprotein
phosphatase) family, to which RdgC belongs, is one of
two known protein phosphatase families specific for
serine and threonine. The PPP family also includes:
PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1,
PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic
domain is defined by three conserved motifs (-GDXHG-,
-GDXVDRG- and -GNHE-). The PPP enzyme family is ancient
with members found in all eukaryotes, and in most
bacterial and archeal genomes. Dephosphorylation of
phosphoserines and phosphothreonines on target proteins
plays a central role in the regulation of many cellular
processes. PPPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 321
Score = 32.0 bits (73), Expect = 1.3
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 315 LLEMAKEMKQLKSFVHVSTAYSN 337
L E K +KQL + VST+ S
Sbjct: 29 LREARKVLKQLPNISRVSTSISK 51
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine. This
subgroup has the characteristic active site tetrad and
NAD-binding motif of the extended SDRs. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 303
Score = 31.2 bits (71), Expect = 2.2
Identities = 33/143 (23%), Positives = 47/143 (32%), Gaps = 42/143 (29%)
Query: 281 LVDNIHVVFHCAATV---------RFDAHLKVAVSINLRATKALLEMAKEMKQLKSFVHV 331
L + V H AA V + KV N T+ L A + +K FV +
Sbjct: 54 LFLGVDAVVHLAARVHVMNDQGADPLSDYRKV----NTELTRRLARAAAR-QGVKRFVFL 108
Query: 332 STAYSNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQVA 391
S+ N E P ++ P D Y +K A
Sbjct: 109 SSVKVN-----GEGTVGAP-------------FDETD----PPAPQDA----YGRSKLEA 142
Query: 392 EDMVRRGGA--GMPVAMVRPSIV 412
E + GA GM V ++RP +V
Sbjct: 143 ERALLELGASDGMEVVILRPPMV 165
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 30.7 bits (70), Expect = 2.5
Identities = 38/138 (27%), Positives = 52/138 (37%), Gaps = 37/138 (26%)
Query: 281 LVDNIHVVFHCAATVRFD----AHLKVAVSINLRATKALLEMAKEMKQLKSFVHVSTA-- 334
LV VVFH AA + A L V N+ T +LE A K VH ST+
Sbjct: 65 LVKKCDVVFHLAALIAIPYSYTAPLSY-VETNVFGTLNVLEAACV-LYRKRVVHTSTSEV 122
Query: 335 YSNCR-QPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQVAED 393
Y + PI E+ +P I P Y+ +KQ A+
Sbjct: 123 YGTAQDVPIDED-------HPLLYINKPR-----------------SP--YSASKQGADR 156
Query: 394 MVRRGGA--GMPVAMVRP 409
+ G G+PV ++RP
Sbjct: 157 LAYSYGRSFGLPVTIIRP 174
>gnl|CDD|132378 TIGR03335, F390_ftsA, coenzyme F390 synthetase. This enzyme,
characterized in Methanobacterium thermoautotrophicum
and found in several other methanogens, modifies
coenzyme F420 by ligation of AMP (or GMP) from ATP (or
GTP). On F420, it activates an aromatic hydroxyl group,
which is unusual chemistry for an adenylyltransferase.
This enzyme name has been attached to numbers of
uncharacterized genes likely to instead act as
phenylacetate CoA ligase, based on proximity to
predicted indolepyruvate ferredoxin oxidoreductase
(1.2.7.8) genes. The enzyme acts during transient
exposure of the organism to oxygen [Biosynthesis of
cofactors, prosthetic groups, and carriers, Other,
Energy metabolism, Methanogenesis].
Length = 445
Score = 31.0 bits (70), Expect = 2.6
Identities = 30/105 (28%), Positives = 44/105 (41%), Gaps = 23/105 (21%)
Query: 429 GPTVIATNKEPIPGWINNHYGPTGIVAGAG--LGLLRSMHADPELVADMVPADNVINCII 486
G ++I K P I Y PTGIVA L L R M A+ + PA++ I ++
Sbjct: 156 GMSIIPEGKCTFPIRIIESYRPTGIVASVFKLLRLARRMKAE-----GIDPAESSIRRLV 210
Query: 487 SAAWNVHQTWNEKKAAGKLVADSLDKNYPDDT-DIEIYNYVSSTQ 530
G+ AD +NY ++ E+YN ST+
Sbjct: 211 --------------VGGESFADE-SRNYVEELWGCEVYNTYGSTE 240
>gnl|CDD|235270 PRK04286, PRK04286, hypothetical protein; Provisional.
Length = 298
Score = 30.7 bits (70), Expect = 3.0
Identities = 11/20 (55%), Positives = 17/20 (85%)
Query: 584 VDTAAKLMGRQPKLLDAYQK 603
V TAA+ +G +P+LL+AY+K
Sbjct: 273 VLTAAEFLGLEPELLEAYRK 292
>gnl|CDD|187671 cd09811, 3b-HSD_HSDB1_like_SDR_e, human 3beta-HSD (hydroxysteroid
dehydrogenase) and HSD3B1(delta 5-delta
4-isomerase)-like, extended (e) SDRs. This extended-SDR
subgroup includes human 3 beta-HSD/HSD3B1 and C(27)
3beta-HSD/ [3beta-hydroxy-delta(5)-C(27)-steroid
oxidoreductase; HSD3B7], and related proteins. These
proteins have the characteristic active site tetrad and
NAD(P)-binding motif of extended SDRs. 3 beta-HSD
catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids. C(27)
3beta-HSD is a membrane-bound enzyme of the endoplasmic
reticulum, it catalyzes the isomerization and oxidation
of 7alpha-hydroxylated sterol intermediates, an early
step in bile acid biosynthesis. Mutations in the human
gene encoding C(27) 3beta-HSD underlie a rare autosomal
recessive form of neonatal cholestasis. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 354
Score = 30.6 bits (69), Expect = 3.4
Identities = 34/181 (18%), Positives = 63/181 (34%), Gaps = 43/181 (23%)
Query: 227 RATKALLEMAKEMKQLKFFD--PMRKRCPHYL-----SKMVAVTGDCLKPGVGINSEDRQ 279
+ LLE +E+K+++ D + H+ + + + GD +
Sbjct: 14 HIIRLLLERKEELKEIRVLDKAFGPELIEHFEKSQGKTYVTDIEGDIK------DLSFLF 67
Query: 280 TLVDNIHVVFHCAATVRFD--AHLKVAVSINLRATKALLEMAKEMKQLKSFVHVST---A 334
+ VV H AA V + + +N+ T+A+LE + +K V+ S+ A
Sbjct: 68 RACQGVSVVIHTAAIVDVFGPPNYEELEEVNVNGTQAVLEACVQ-NNVKRLVYTSSIEVA 126
Query: 335 YSNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQVAEDM 394
N + I + P D YA +K +AE++
Sbjct: 127 GPNFKGRPIFNGVEDTPYE------------------------DTSTPPYASSKLLAENI 162
Query: 395 V 395
V
Sbjct: 163 V 163
>gnl|CDD|225006 COG2095, MarC, Multiple antibiotic transporter [Intracellular
trafficking and secretion].
Length = 203
Score = 29.9 bits (68), Expect = 3.7
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 6/54 (11%)
Query: 735 YLVKDPLSTVP------DGIRLRRRLLIAHYLLIAALSVLFFFLSVRILTLIFF 782
+ + DP+ +P G+ R +A I AL +L FL + L FF
Sbjct: 15 FAIIDPIGNLPVFISLTKGLSPEERNRVALRASIIALLILLVFLLLGEGILRFF 68
>gnl|CDD|217356 pfam03078, ATHILA, ATHILA ORF-1 family. ATHILA is a group of
Arabidopsis thaliana retrotransposons belonging to the
Ty3/gypsy family of the long terminal repeat (LTR) class
of eukaryotic retrotransposons. The central region of
ATHILA retrotransposons contains two or three open
reading frames (ORFs). This family represents the ORF1
product. The function of ORF1 is unknown.
Length = 456
Score = 30.4 bits (68), Expect = 3.9
Identities = 19/104 (18%), Positives = 35/104 (33%), Gaps = 12/104 (11%)
Query: 645 MSQLGSFEVHSTLNTLVSTRSLKLLDAYQKIHKFSEVISFFSTQQFTFTNFNTQRL---- 700
M+QLG E ++ L L+ +Y E I F ST + F +
Sbjct: 71 MAQLGLLE---DVDHLFKKCHLETFMSYPYPAYKEETIEFLSTLELEFYQGSEDDEKEEE 127
Query: 701 ---YTKMTEEDRALFNFDMSQLDWEKYMFWHIRGIRAYLVKDPL 741
Y + ++ + L+ + F +G ++ L
Sbjct: 128 GLGYITFKVKGVE-YSLSIKHLE-TIFGFPSGKGTSPKFDREEL 169
>gnl|CDD|181690 PRK09195, gatY, tagatose-bisphosphate aldolase; Reviewed.
Length = 284
Score = 30.1 bits (68), Expect = 4.0
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 127 KQVAEDMVRRGGAGMPVAMVRPSIDLGI 154
+ V +V G +G+P ++ +I LGI
Sbjct: 199 QWVNIPLVLHGASGLPTKDIQQTIKLGI 226
>gnl|CDD|238643 cd01318, DHOase_IIb, Dihydroorotase (DHOase), subgroup IIb; DHOases
catalyze the reversible interconversion of carbamoyl
aspartate to dihydroorotate, a key reaction in
pyrimidine biosynthesis. This group contains the archeal
members of the DHOase family.
Length = 361
Score = 30.4 bits (69), Expect = 4.1
Identities = 13/59 (22%), Positives = 17/59 (28%), Gaps = 11/59 (18%)
Query: 287 VVFHCAATVRFDAHLKVAVSI-----------NLRATKALLEMAKEMKQLKSFVHVSTA 334
V FH R + K AT L++A+ HVST
Sbjct: 124 VTFHAEDEDRLRENRKELKGESAHPRIRDAEAAAVATARALKLARRHGARLHICHVSTP 182
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence of
some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 29.9 bits (68), Expect = 4.8
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 5/53 (9%)
Query: 286 HVVFHCAATVRFDA---HLKVAVSINLRATKALLEMAKEMKQLKSFVHVSTAY 335
VV + AA D ++A ++N L E +H+ST Y
Sbjct: 51 DVVVNAAAYTAVDKAESEPELAYAVNALGPGNLAEACAARGAP--LIHISTDY 101
>gnl|CDD|182998 PRK11150, rfaD, ADP-L-glycero-D-mannoheptose-6-epimerase;
Provisional.
Length = 308
Score = 30.1 bits (68), Expect = 5.1
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 9/74 (12%)
Query: 285 IHVVFH---CAATVRFDAHLKVAVSINLRATKALLEMAKEMKQLKSFVHVSTA--YSNCR 339
I +FH C++T +D K + N + +K LL E +++ F++ S+A Y
Sbjct: 69 IEAIFHEGACSSTTEWDG--KYMMDNNYQYSKELLHYCLE-REI-PFLYASSAATYGGRT 124
Query: 340 QPIIEERFYEPPVN 353
IEER YE P+N
Sbjct: 125 DDFIEEREYEKPLN 138
>gnl|CDD|150532 pfam09872, DUF2099, Uncharacterized protein conserved in archaea
(DUF2099). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 257
Score = 29.9 bits (68), Expect = 5.1
Identities = 31/113 (27%), Positives = 51/113 (45%), Gaps = 30/113 (26%)
Query: 219 KVAVSINLRATKALLEMAKEMKQLKFFDPMRKRCPHYLSKMVAVTGDCLKPGVGINSEDR 278
++AV++ A E AK++++L+ L V TG I+ E+
Sbjct: 165 RIAVTV------ADAEDAKKIRELEESGV------DILIFGVHTTG--------ISREEA 204
Query: 279 QTLVDNIHVVFHCAA-TVRFDAH----LKVAVSINLRA-TKA----LLEMAKE 321
+ LV +V CA+ +R A L+V S+ + A T+A +LE AKE
Sbjct: 205 ERLVKYADIVTACASKYIREIAGKKALLQVGSSVPIFALTQAGKELILERAKE 257
>gnl|CDD|187661 cd08958, FR_SDR_e, flavonoid reductase (FR), extended (e) SDRs.
This subgroup contains FRs of the extended SDR-type and
related proteins. These FRs act in the NADP-dependent
reduction of flavonoids, ketone-containing plant
secondary metabolites; they have the characteristic
active site triad of the SDRs (though not the upstream
active site Asn) and a NADP-binding motif that is very
similar to the typical extended SDR motif. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 29.5 bits (67), Expect = 6.1
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 282 VDNIHVVFHCAATVRFDAH------LKVAVSINLRATKALLEMAKEMKQLKSFVHVSTA 334
+D VFH A+ V FD+ ++ AV + T +LE + K +K V S+
Sbjct: 68 IDGCDGVFHVASPVDFDSEDPEEEMIEPAV----KGTLNVLEACAKAKSVKRVVFTSSV 122
>gnl|CDD|226509 COG4022, COG4022, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 286
Score = 29.7 bits (67), Expect = 6.2
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 10/62 (16%)
Query: 189 GINSEDRQTLVDNIHVVFHCAATV-----RFDAHLKVAVSINLRA-----TKALLEMAKE 238
GI+ E+ Q LV+N +V CA+ + L+V +I L A + L+E AK+
Sbjct: 203 GIDEEEAQGLVENSDIVTSCASKYIRELAKRRPILQVGSAIPLFALTQKGKELLIERAKD 262
Query: 239 MK 240
+K
Sbjct: 263 IK 264
Score = 29.7 bits (67), Expect = 6.2
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 10/62 (16%)
Query: 272 GINSEDRQTLVDNIHVVFHCAATV-----RFDAHLKVAVSINLRA-----TKALLEMAKE 321
GI+ E+ Q LV+N +V CA+ + L+V +I L A + L+E AK+
Sbjct: 203 GIDEEEAQGLVENSDIVTSCASKYIRELAKRRPILQVGSAIPLFALTQKGKELLIERAKD 262
Query: 322 MK 323
+K
Sbjct: 263 IK 264
>gnl|CDD|223951 COG1020, EntF, Non-ribosomal peptide synthetase modules and related
proteins [Secondary metabolites biosynthesis, transport,
and catabolism].
Length = 642
Score = 29.5 bits (66), Expect = 8.6
Identities = 33/157 (21%), Positives = 58/157 (36%), Gaps = 34/157 (21%)
Query: 352 VNPNHLIQITELLNDDMIDKITPGIVDYWPNTYALTKQVAEDMVRR---GGAGMPVAMVR 408
V+P L+++ E ++ + + A + +R+ GG +P+A+V+
Sbjct: 444 VDPAALLELLEAQGITVLLLVPLLLRLLLLAALAPDLISPCERLRQLLSGGEALPLALVQ 503
Query: 409 PSIVIATNKEPIPGWINNHYGPT----------VIATNKE------PIPGW---INNHYG 449
+ +A + + N YGPT + A + P+ I +
Sbjct: 504 RLLQLA----ALARRLLNLYGPTEATLDAPSFPISAELESRVPIGRPVANTQLYILDQGL 559
Query: 450 ---PTGIVAG----AGLGLLRSMHADPELVADMVPAD 479
P G V G AGLGL P+L A+ A
Sbjct: 560 RPLPLG-VPGELYIAGLGLALGYLNRPDLTAERFIAL 595
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 29.1 bits (66), Expect = 9.6
Identities = 41/163 (25%), Positives = 61/163 (37%), Gaps = 55/163 (33%)
Query: 281 LVDNIHVVFHCAATVRFDAHLKVAVSI---------NLRATKALLEMAKEMKQLKSFVHV 331
LVD + + A V F A V SI N+ T LLE A++ F H+
Sbjct: 65 LVDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFIQTNVVGTYTLLEAARKYWGKFRFHHI 124
Query: 332 STAYSNCRQPIIEERFYEPPVNPNHLIQITELLNDDMIDKITPGIVDYWPNT-YALTKQV 390
ST +E + + L+DD + TP Y P++ Y+ +K
Sbjct: 125 ST----------DEVYGD------------LGLDDDAFTETTP----YNPSSPYSASK-A 157
Query: 391 AEDMVRRGGA---GMPVAMVRPSIVIATNKEPIPGWINNHYGP 430
A D++ R G+P + R S N+YGP
Sbjct: 158 ASDLLVRAYVRTYGLPATITRCS---------------NNYGP 185
>gnl|CDD|224265 COG1346, LrgB, Putative effector of murein hydrolase [Cell envelope
biogenesis, outer membrane].
Length = 230
Score = 28.7 bits (65), Expect = 9.7
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 16/69 (23%)
Query: 422 GWINNHYGPTVIATNKEPIPGW-----INNHYGP--TGIVAGA------GLGLLRSMHAD 468
WIN GP +A +P + I H+ P G++ G+ G+ L +
Sbjct: 62 QWINFLLGPATVAL---AVPLYKQRHLIKRHWKPILAGVLVGSVVAIISGVLLAKLFGLS 118
Query: 469 PELVADMVP 477
PEL+ ++P
Sbjct: 119 PELILSLLP 127
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.136 0.411
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 40,439,331
Number of extensions: 4030161
Number of successful extensions: 4066
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4035
Number of HSP's successfully gapped: 91
Length of query: 782
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 677
Effective length of database: 6,280,432
Effective search space: 4251852464
Effective search space used: 4251852464
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 63 (28.0 bits)