RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7542
(762 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 = 334 bits (859), Expect = e-109
Identities = 126/322 (39%), Positives = 191/322 (59%), Gaps = 4/322 (1%)
Query: 62 KNIFITGASGFVGKVLLEKILRTCENV-KIYILLRPKKNKNSRERLEEIFQSPLYEALKK 120
K++ ITGA+GF+GKVLLEK+LR+C ++ KIY+L+R K +++ ERL E+ + L++ +
Sbjct: 1 KSVLITGATGFLGKVLLEKLLRSCPDIGKIYLLIRGKSGQSAEERLRELLKDKLFDRGRN 60
Query: 121 EQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQTYVFLN 180
K++PI GD++ P+LG+S ED Q L E ++I+ H AATV FD+ + + +N
Sbjct: 61 LNPLF--ESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEALSIN 118
Query: 181 TRGTRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSPHNVIEKAELLSKNE 240
GT +L L+K+ L+ FV+VSTAY + +++EEK YPPP P +I+ EL+ E
Sbjct: 119 VLGTLRLLELAKRCKKLKAFVHVSTAYVNGDRQLIEEKVYPPPADPEKLIDILELMDDLE 178
Query: 241 LELLKQELLQDFPNGYAYTKCLCEGVVTEYMEAGMPCMILRPSIIIPIWKDPLPGWTDNI 300
LE +LL PN Y +TK L E +V + +P +I+RPSI+ K+P PGW DN
Sbjct: 179 LERATPKLLGGHPNTYTFTKALAERLVLKERG-NLPLVIVRPSIVGATLKEPFPGWIDNF 237
Query: 301 NGPTGLLIGAGKGIIRTMYCDYSTCADFLPVDVLVNGVLLSTWNFLSNPGNTMRVINLTA 360
NGP GL + GKGI+RTM D + AD +PVDV+ N +L + + V + +
Sbjct: 238 NGPDGLFLAYGKGILRTMNADPNAVADIIPVDVVANALLAAAAYSGVRKPRELEVYHCGS 297
Query: 361 NKDFQITWYDIIENGKDIARNK 382
+ TW + E +
Sbjct: 298 SDVNPFTWGEAEELINQYLKKN 319
>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 = 259 bits (663), Expect = 4e-81
Identities = 103/275 (37%), Positives = 151/275 (54%), Gaps = 32/275 (11%)
Query: 66 ITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERL-EEIFQSPLYEALKKEQSE 124
+TGA+GF+GKVLLEK+LR+ VKIY L+R K +++ ERL +E+ + L++ LK
Sbjct: 1 LTGATGFLGKVLLEKLLRSTPEVKIYCLVRAKDGESALERLRQELLKYGLFDRLK----- 55
Query: 125 SAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQTYVFLNTRGT 184
E++IP+ GD++ P+LG+S ED Q L+E + ++ H AATV F + N GT
Sbjct: 56 --ALERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNFVEPYSDLRATNVLGT 113
Query: 185 RDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSPHNVIEKAELLSKNELELL 244
R++L L+KQM L F +VSTAY + + + EK L +
Sbjct: 114 REVLRLAKQMKKLP-FHHVSTAYVNGER-------------GGLLEEKPYKLDE-----D 154
Query: 245 KQELLQDFPNGYAYTKCLCEGVVTEYMEAGMPCMILRPSIIIPIWKDPLPGWTDNIN-GP 303
+ LL PNGY +K L E +V E G+P +I RPSII + GW + + GP
Sbjct: 155 EPALLGGLPNGYTQSKWLAEQLVREAAG-GLPVVIYRPSIITG---ESRTGWINGDDFGP 210
Query: 304 TGLLIGAGKGIIRTMYCDYSTCADFLPVDVLVNGV 338
GLL GAG G++ + D D +PVD + N +
Sbjct: 211 RGLLGGAGLGVLPDILGDPDARLDLVPVDYVANAI 245
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 176 bits (447), Expect = 1e-47
Identities = 100/324 (30%), Positives = 175/324 (54%), Gaps = 53/324 (16%)
Query: 59 LEHKNIFITGASGFVGKVLLEKILRTCENV-KIYILLRPKKNKNSRERL-EEIFQSPLYE 116
LE+K I +TGA+GF+ K+ +EKILR NV K+Y+LLR K++ +RL +E+ L++
Sbjct: 9 LENKTILVTGATGFLAKIFVEKILRVQPNVKKLYLLLRASDAKSATQRLHDEVIGKDLFK 68
Query: 117 ALKK---EQSESAIFEKVIPINGDVAVPDLGISAED--RQMLSETIHIVYHIAATVRFDD 171
L++ E S I EKV P+ GD++ DLG+ + +M E I IV ++AAT FD+
Sbjct: 69 VLREKLGENLNSLISEKVTPVPGDISYDDLGVKDSNLREEMWKE-IDIVVNLAATTNFDE 127
Query: 172 YMQTYVFLNTRGTRDMLNLSKQMIHLQLFVYVSTAY-CHPKEKVLEEKTYPPPVSPHNVI 230
+ +NT G ++LN +K+ + +++ ++VSTAY C K ++ EK +
Sbjct: 128 RYDVALGINTLGALNVLNFAKKCVKVKMLLHVSTAYVCGEKSGLILEKPFH--------- 178
Query: 231 EKAELLSKN-------ELELLKQEL----------------LQDF----------PNGYA 257
E L+ N E +L+K++L ++D PN Y
Sbjct: 179 -MGETLNGNRKLDINEEKKLVKEKLKELNEQDASEEEITQAMKDLGMERAKLHGWPNTYV 237
Query: 258 YTKCLCEGVVTEYMEAGMPCMILRPSIIIPIWKDPLPGWTDNINGPTGLLIGAGKGIIRT 317
+TK + E ++ + E +P +I+RP++I +K+P PGW + + +++G GKG +
Sbjct: 238 FTKAMGEMLLGNFKE-NLPLVIIRPTMITSTYKEPFPGWIEGLRTIDSVIVGYGKGKLTC 296
Query: 318 MYCDYSTCADFLPVDVLVNGVLLS 341
D ++ D +P D++VN ++++
Sbjct: 297 FLADPNSVLDVIPADMVVNAMIVA 320
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 140 bits (354), Expect = 9e-35
Identities = 100/326 (30%), Positives = 166/326 (50%), Gaps = 43/326 (13%)
Query: 55 ISATLEHKNIFITGASGFVGKVLLEKILRTCENV-KIYILLRPKKNKNSRERLE-EIFQS 112
I+ L KN ITGA+GF+ KVL+EKILRT +V KIY+L++ K + + ERL+ E+ +
Sbjct: 113 IAEFLRGKNFLITGATGFLAKVLIEKILRTNPDVGKIYLLIKAKDKEAAIERLKNEVIDA 172
Query: 113 PLYEALKK---EQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRF 169
L++ L++ + +S + K++P+ G+V +LG+ + +++ + ++ + AA F
Sbjct: 173 ELFKCLQETHGKSYQSFMLSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTF 232
Query: 170 DDYMQTYVFLNTRGTRDMLNLSKQMIHLQLFVYVSTAYCH-PKEKVLEEKTY-------- 220
D+ + +NTRG +++ +K+ L+LF+ VSTAY + ++ + EK +
Sbjct: 233 DERYDVAIDINTRGPCHLMSFAKKCKKLKLFLQVSTAYVNGQRQGRIMEKPFRMGDCIAR 292
Query: 221 ---PPPVSPHNV----IE---KAELLSKNE---------------LELLKQELLQDFPNG 255
PHN IE K L SK LE K QD
Sbjct: 293 ELGISNSLPHNRPALDIEAEIKLALDSKRHGFQSNSFAQKMKDLGLERAKLYGWQD---T 349
Query: 256 YAYTKCLCEGVVTEYMEAGMPCMILRPSIIIPIWKDPLPGWTDNINGPTGLLIGAGKGII 315
Y +TK + E V+ M +P +I+RPS+I WKDP PGW + +++ GKG +
Sbjct: 350 YVFTKAMGEMVINS-MRGDIPVVIIRPSVIESTWKDPFPGWMEGNRMMDPIVLYYGKGQL 408
Query: 316 RTMYCDYSTCADFLPVDVLVNGVLLS 341
D + D +P D++VN L +
Sbjct: 409 TGFLADPNGVLDVVPADMVVNATLAA 434
>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 = 129 bits (327), Expect = 3e-33
Identities = 75/338 (22%), Positives = 135/338 (39%), Gaps = 58/338 (17%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
+ +TGA+GF+G LL ++L+ KIY L+R K + + ERL + +
Sbjct: 1 TVLLTGATGFLGAYLLRELLKRKNVSKIYCLVRAKDEEAALERLIDNLKE-----YGLNL 55
Query: 123 SESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQTYVFLNTR 182
+ ++ + GD++ P+LG+S +D Q L+E + ++ H A V + + N
Sbjct: 56 WDELELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVNWVYPYEELKPANVL 115
Query: 183 GTRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSPHNVIEKAELLSKNELE 242
GT+++L L+ L+ +VST + AE + + E
Sbjct: 116 GTKELLKLAATG-KLKPLHFVSTLS----------------------VFSAEEYNALDDE 152
Query: 243 LLKQEL--LQDFPNGYAYTKCLCEGVVTEYMEAGMPCMILRPSIIIPIWKDPLPGWTDNI 300
L PNGY +K + E ++ E G+P I+RP I D+
Sbjct: 153 ESDDMLESQNGLPNGYIQSKWVAEKLLREAANRGLPVAIIRPGNIFG----------DSE 202
Query: 301 NGPT------GLLIGAGKGIIRT-MYCDYSTCADFLPVDVLV-NGVLLSTWNFLSNPGNT 352
G L+ KG ++ +Y D PVD + V L+ N N
Sbjct: 203 TGIGNTDDFFWRLL---KGCLQLGIYPISGAPLDLSPVDWVARAIVKLA-----LNESNE 254
Query: 353 MRVINLTANKDFQITWYDIIENGKDIARNKVPLNNVLW 390
+ +L I+ D+++ ++ + ++ W
Sbjct: 255 FSIYHLLNPP--LISLNDLLDALEEKGYSIKEVSYEEW 290
>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 = 107 bits (269), Expect = 1e-25
Identities = 74/304 (24%), Positives = 125/304 (41%), Gaps = 60/304 (19%)
Query: 64 IFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQS 123
+F+TG +GF+G+ L++++L K+ +L+R + + ER+EE
Sbjct: 1 VFVTGGTGFLGRHLVKRLLEN--GFKVLVLVRSESLGEAHERIEE--------------- 43
Query: 124 ESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRF----DDYMQTYVFL 179
++V + GD+ P+LG+SA + L+ + V H AA+ F +D +T
Sbjct: 44 AGLEADRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRT---- 99
Query: 180 NTRGTRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSPHNVIEKAELLSKN 239
N GT +L L+ + + +Q F YVSTAY +
Sbjct: 100 NIDGTEHVLELAAR-LDIQRFHYVSTAYV------------AGNREGNI----------R 136
Query: 240 ELELLKQELLQDFPNGYAYTKCLCEGVVTEYMEAGMPCMILRPSIIIPIWKDPLPGWTDN 299
E EL Q+F N Y +K E +V +P + RPSI + D G +
Sbjct: 137 ETELNPG---QNFKNPYEQSKAEAEQLVRAAATQ-IPLTVYRPSI---VVGDSKTGRIEK 189
Query: 300 INGPTGLLIG-AGKGIIRTMYCDYSTCADFLPVDVLVNGVLLSTWNFLSNPGNTMRVINL 358
I+G LL A G M + + +PVD + + ++ P ++ +L
Sbjct: 190 IDGLYELLNLLAKLGRWLPMPGNKGARLNLVPVDYVADAIVY----LSKKPEANGQIFHL 245
Query: 359 TANK 362
T
Sbjct: 246 TDPT 249
>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 = 106 bits (266), Expect = 1e-24
Identities = 61/227 (26%), Positives = 101/227 (44%), Gaps = 35/227 (15%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
+ +TGA+GF+G LLE++LR K+ L+R +++ ERL E +S L
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQAKVICLVRAASEEHAMERLREALRS---YRL---W 54
Query: 123 SESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQTYVFL--- 179
E E++ + GD++ P LG+S + + L+E + + H A V +++ Y L
Sbjct: 55 HEDLARERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALV---NWVYPYSELRGA 111
Query: 180 NTRGTRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSPHNVIEKAELLSKN 239
N GTR++L L+ + YVST V + V E ++
Sbjct: 112 NVLGTREVLRLA-ASGRAKPLHYVSTI------SVG------AAIDLSTVTEDDATVTP- 157
Query: 240 ELELLKQELLQDFPNGYAYTKCLCEGVVTEYMEAGMPCMILRPSIII 286
GYA +K + E +V E + G+P I+RP I+
Sbjct: 158 ---------PPGLAGGYAQSKWVAELLVREASDRGLPVTIVRPGRIL 195
>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 = 98.2 bits (245), Expect = 7e-22
Identities = 64/228 (28%), Positives = 105/228 (46%), Gaps = 33/228 (14%)
Query: 62 KNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKE 121
+N+ +TGA+GF+G LL ++L + K+ L+R + ++ + RLE+ F LY E
Sbjct: 1 RNVLLTGATGFLGAYLLLELLDR-SDAKVICLVRAQSDEAALARLEKTF--DLY-RHWDE 56
Query: 122 QSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQTYVFL-- 179
S ++V + GD+A PDLG+S Q L+E + ++ H AA V +++ Y L
Sbjct: 57 LSA----DRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALV---NHVFPYSELRG 109
Query: 180 -NTRGTRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSPHNVIEKAELLSK 238
N GT ++L L+ + YVS+ V E N + +S
Sbjct: 110 ANVLGTAEVLRLA-ATGKPKPLHYVSSI------SVGE------TEYYSNFTVDFDEISP 156
Query: 239 NELELLKQELLQDFPNGYAYTKCLCEGVVTEYMEAGMPCMILRPSIII 286
+ + Q GY +K + E +V E + G+P I RP I
Sbjct: 157 T------RNVGQGLAGGYGRSKWVAEKLVREAGDRGLPVTIFRPGYIT 198
>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 = 77.6 bits (192), Expect = 2e-17
Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 399 RGYEPVLKRVHNRIKKGFDIFEYYTKNSWSFKNENLHALRNMMNEKEAIRYEIAMFRDLD 458
G +P L +++ +I K D+ EY+T N W F N+N AL ++E++ + + R +D
Sbjct: 17 LGRKPRLLKLYRKIHKLLDLLEYFTTNEWRFDNDNTRALWERLSEEDRELFNFDI-RSID 75
Query: 459 EAKAYFEMCIHGARQYLL 476
YFE I G R+YLL
Sbjct: 76 WDD-YFENYIPGLRKYLL 92
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 80.0 bits (198), Expect = 2e-15
Identities = 62/251 (24%), Positives = 103/251 (41%), Gaps = 69/251 (27%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
F+TG +GF+G+ L+ ++L +++L+R + S RLE AL
Sbjct: 2 RYFVTGGTGFIGRRLVSRLLDRRREATVHVLVRRQ----SLSRLE---------ALAAYW 48
Query: 123 SESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAA----TVRFDDYMQTYVF 178
++V+P+ GD+ P LG+S D L + H V H+AA T +
Sbjct: 49 GA----DRVVPLVGDLTEPGLGLSEADIAELGDIDH-VVHLAAIYDLTADEEAQRAA--- 100
Query: 179 LNTRGTRDMLNLSKQMIHLQLFVYVST---AYCHP---KEKVLEEKTYPPPVSPHNVIEK 232
N GTR+++ L+++ + F +VS+ A + +E +E
Sbjct: 101 -NVDGTRNVVELAER-LQAATFHHVSSIAVAGDYEGVFREDDFDEG-------------- 144
Query: 233 AELLSKNELELLKQELLQDFPNGYAYTKCLCEGVVTEYMEAGMPCMILRPSIIIPIWKDP 292
Q P Y TK E +V E E G+P + RP++++ D
Sbjct: 145 -----------------QGLPTPYHRTKFEAEKLVRE--ECGLPWRVYRPAVVV---GDS 182
Query: 293 LPGWTDNINGP 303
G D I+GP
Sbjct: 183 RTGEMDKIDGP 193
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 71.5 bits (175), Expect = 2e-13
Identities = 67/336 (19%), Positives = 118/336 (35%), Gaps = 86/336 (25%)
Query: 62 KNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKE 121
I +TG +GF+G L+E++L +V+ LR +
Sbjct: 1 MRILVTGGAGFIGSHLVERLLAAGHDVRGLDRLRDGLDPLL------------------- 41
Query: 122 QSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYM----QTYV 177
V + D+ DL ++ V H+AA D ++
Sbjct: 42 -------SGVEFVVLDLTDRDL-----VDELAKGVPDAVIHLAAQSSVPDSNASDPAEFL 89
Query: 178 FLNTRGTRDMLNLSKQMIHLQLFVYVSTAYC----HPKEKVLEEKTYPPPVSPHNVIEKA 233
+N GT ++L ++ ++ FV+ S+ P + E+ P P++P
Sbjct: 90 DVNVDGTLNLLEAARAA-GVKRFVFASSVSVVYGDPPPLPIDEDLGPPRPLNP------- 141
Query: 234 ELLSKNELELLKQELLQDFPNGYAYTKCLCEGVVTEYMEA-GMPCMILRPSIIIPIWKDP 292
Y +K E ++ Y G+P +ILRP +
Sbjct: 142 ----------------------YGVSKLAAEQLLRAYARLYGLPVVILRPFNVYG----- 174
Query: 293 LPGWTDNING--PTGLLIGAGKGI-IRTMYCDYSTCADFLPVDVLVNGVLLSTWNFLSNP 349
PG +++ + + KG I + D S DF+ VD + + +LL L NP
Sbjct: 175 -PGDKPDLSSGVVSAFIRQLLKGEPIIVIGGDGSQTRDFVYVDDVADALLL----ALENP 229
Query: 350 GNTMRVINLTANKDFQITWYDIIENGKDIARNKVPL 385
V N+ + IT ++ E + +K PL
Sbjct: 230 DG--GVFNIGSGTAE-ITVRELAEAVAEAVGSKAPL 262
>gnl|CDD|132790 cd06880, PX_SNX22, The phosphoinositide binding Phox Homology
domain of Sorting Nexin 22. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions. Sorting nexins (SNXs)
make up the largest group among PX domain containing
proteins. They are involved in regulating membrane
traffic and protein sorting in the endosomal system. The
PX domain of SNXs binds PIs and targets the protein to
PI-enriched membranes. SNXs differ from each other in
PI-binding specificity and affinity, and the presence of
other protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. SNX22 may be involved in
recruiting other proteins to the membrane via
protein-protein and protein-ligand interaction. The
biological function of SNX22 is not yet known.
Length = 110
Score = 64.2 bits (157), Expect = 1e-12
Identities = 27/59 (45%), Positives = 35/59 (59%)
Query: 638 KTKFSTPSFPPKKIRSNQPKVLDERRHLLEIYLKEMFKFGPSRNQVLAFLGVNSKNSQP 696
K TP FPPK++R+ PKVL++RR LE YL+ + K Q+L FLGV S P
Sbjct: 50 KKSIKTPDFPPKRVRNWNPKVLEQRRQGLEAYLQGLLKINELPKQLLDFLGVRHFPSLP 108
Score = 43.8 bits (104), Expect = 2e-05
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 520 NCISVSGYRLI--ECEKPYYVYVIHVRMFQQHYIVEKRYSELLSWHSE 565
+S+ YRL E EKPY V+ I V + + + VEKRYSE + H +
Sbjct: 1 IEVSIPSYRLEVDESEKPYTVFTIEVLVNGRRHTVEKRYSEFHALHKK 48
>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 = 58.8 bits (143), Expect = 8e-11
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 400 GYEPVLKRVHNRIKKGFDIFEYYTKNSWSFKNENLHALRNMMNEKEAIRYEIAMFRDLDE 459
G +P L +++ +I KG ++ + ++ N W F N+N LR M+E++ + M LD
Sbjct: 18 GQKPRLVKLYRKIHKGLEVLQPFSLNEWIFDNKNTRELREKMSEEDKKLFNFDM-ESLD- 75
Query: 460 AKAYFEMCIHGARQYLLGE 478
YF I G R+YLL E
Sbjct: 76 WDEYFRNAIRGIRKYLLKE 94
>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 = 58.9 bits (143), Expect = 9e-10
Identities = 44/193 (22%), Positives = 71/193 (36%), Gaps = 51/193 (26%)
Query: 159 IVYHIAATVRFDDYMQ--TYVFL-NTRGTRDMLNLSKQMIHLQLFVYVSTA--YCHPKEK 213
+V H+AA V F N GT ++L +++ ++ FVY S+A Y P+
Sbjct: 33 VVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKA-GVKRFVYASSASVYGSPEGL 91
Query: 214 VLEEKTYPPPVSPHNVIEKAELLSKNELELLKQELLQDFPNGYAYTKCLCEGVVTEYMEA 273
EE+T P P+SP Y +K E ++ Y E+
Sbjct: 92 PEEEETPPRPLSP-----------------------------YGVSKLAAEHLLRSYGES 122
Query: 274 -GMPCMILRPSIII-----PIWKDPLPGWTDNINGPTGLLIGAGKGIIRTMYCDYSTCAD 327
G+P +ILR + + P + + L + G R D
Sbjct: 123 YGLPVVILRLANVYGPGQRPRLDGVVNDFIRRALEGKPLTVFGGGNQTR----------D 172
Query: 328 FLPVDVLVNGVLL 340
F+ VD +V +L
Sbjct: 173 FIHVDDVVRAILH 185
Score = 35.4 bits (82), Expect = 0.066
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 64 IFITGASGFVGKVLLEKILRTCENVKIY 91
I +TG +GF+G L+ ++L V +
Sbjct: 1 ILVTGGAGFIGSHLVRRLLERGHEVVVI 28
>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 = 61.6 bits (150), Expect = 1e-09
Identities = 59/253 (23%), Positives = 109/253 (43%), Gaps = 38/253 (15%)
Query: 40 IVKAIPKKFKHLPDRISATLEH-KNIFITGASGFVGKVLLEKIL--RTCENVKIYILLRP 96
+V ++PK + P R +F+TGA+GF+G +L +L R+ N K++ +R
Sbjct: 952 LVDSLPKSY---PSRKELDASTPITVFLTGATGFLGSFILRDLLTRRSNSNFKVFAHVRA 1008
Query: 97 KKNKNSRERLEEIFQSPLYEALKKEQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSET 156
K + ERL + + Y +E + ++ + GD++ G+S E L+
Sbjct: 1009 KSEEAGLERLRKTGTT--YGIWDEEWAS-----RIEVVLGDLSKEKFGLSDEKWSDLTNE 1061
Query: 157 IHIVYHIAATVRFDDYMQTYVFL---NTRGTRDMLNLSKQMIHLQLFVYVSTAYCHPKEK 213
+ ++ H A V ++ Y L N GT ++LNL + + F +VS+
Sbjct: 1062 VDVIIHNGALVH---WVYPYSKLRDANVIGTINVLNLCAEG-KAKQFSFVSST------S 1111
Query: 214 VLEEKTYPPPVSPHNVIEKAELLSKNELELLKQELLQ----DFPNGYAYTKCLCEGVVTE 269
L+ + Y V EL+ + + + L GY +K + E ++ E
Sbjct: 1112 ALDTEYY--------VNLSDELVQAGGAGIPESDDLMGSSKGLGTGYGQSKWVAEYIIRE 1163
Query: 270 YMEAGMPCMILRP 282
+ G+ I+RP
Sbjct: 1164 AGKRGLRGCIVRP 1176
>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 = 55.8 bits (135), Expect = 3e-08
Identities = 48/232 (20%), Positives = 81/232 (34%), Gaps = 73/232 (31%)
Query: 64 IFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQS 123
I +TGA+GF+G L+ +L V+ L+R + P+
Sbjct: 1 ILVTGATGFLGSNLVRALLAQGYRVR--ALVRSG------SDAVLLDGLPV--------- 43
Query: 124 ESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRF-----DDYMQTYVF 178
E V GD+ ++ M + V+H+AA + +T
Sbjct: 44 -----EVVE---GDLTDA----ASLAAAM--KGCDRVFHLAAFTSLWAKDRKELYRT--- 86
Query: 179 LNTRGTRDMLN--LSKQMIHLQLFVYVST--AYCHPKEKVLEEKTYPPPVSPHNVIEKAE 234
N GTR++L+ L ++ V+ S+ A P + ++E T
Sbjct: 87 -NVEGTRNVLDAALEAG---VRRVVHTSSIAALGGPPDGRIDETTPWNE----------- 131
Query: 235 LLSKNELELLKQELLQDFPNGYAYTKCLCEGVVTEYMEAGMPCMILRPSIII 286
+ FPN Y +K L E V E G+ +I+ PS +
Sbjct: 132 ---------------RPFPNDYYRSKLLAELEVLEAAAEGLDVVIVNPSAVF 168
>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 = 45.4 bits (108), Expect = 4e-05
Identities = 43/226 (19%), Positives = 81/226 (35%), Gaps = 66/226 (29%)
Query: 64 IFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQS 123
I +TG +GF+G L+ ++L+ E ++ +L R +++++ + L +
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQ--EGYEVIVLGRRRRSESLNTGRIRFHEGDL---TDPDAL 55
Query: 124 ESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQT---YVFLN 180
E + +V P V H+AA + ++ N
Sbjct: 56 E-RLLAEVQP------------------------DAVIHLAAQSGVGASFEDPADFIRAN 90
Query: 181 TRGTRDMLNLSKQMIHLQLFVYVSTA--YCHPKEKVLEEKTYPPPVSPHNVIEKAELLSK 238
GT +L +++ ++ FV+ S++ Y + + E T P+SP
Sbjct: 91 VLGTLRLLEAARRA-GVKRFVFASSSEVYGDVADPPITEDTPLGPLSP------------ 137
Query: 239 NELELLKQELLQDFPNGYAYTKCLCEGVVTEYMEA-GMPCMILRPS 283
YA K E +V Y A G+ +ILR
Sbjct: 138 -----------------YAAAKLAAERLVEAYARAYGLRAVILRLF 166
>gnl|CDD|187549 cd05238, Gne_like_SDR_e, Escherichia coli Gne (a
nucleoside-diphosphate-sugar 4-epimerase)-like, extended
(e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has
the characteristic active site tetrad and NAD-binding
motif of the extended SDR, and is related to more
specifically defined epimerases such as UDP-glucose 4
epimerase (aka UDP-galactose-4-epimerase), which
catalyzes the NAD-dependent conversion of UDP-galactose
to UDP-glucose, the final step in Leloir galactose
synthesis. This subgroup includes Escherichia coli
055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55
antigen synthesis. 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 = 305
Score = 43.9 bits (104), Expect = 2e-04
Identities = 47/172 (27%), Positives = 69/172 (40%), Gaps = 43/172 (25%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
+ ITGASGFVG+ L E++L N ++ IL+ SP +
Sbjct: 2 KVLITGASGFVGQRLAERLLSDVPNERL-ILID--------------VVSPKAPSGAPR- 45
Query: 123 SESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVR------FDDYMQTY 176
V I GD+AVP A + + +V+H+AA V FD +
Sbjct: 46 --------VTQIAGDLAVP-----ALIEALANGRPDVVFHLAAIVSGGAEADFDLGYRV- 91
Query: 177 VFLNTRGTRDMLN-LSKQMIHLQLFVYVST--AYCHPKEKVLEEKTYPPPVS 225
N GTR++L L K + FV+ S+ Y P + + T P S
Sbjct: 92 ---NVDGTRNLLEALRKNGPKPR-FVFTSSLAVYGLPLPNPVTDHTALDPAS 139
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 44.0 bits (104), Expect = 3e-04
Identities = 59/229 (25%), Positives = 96/229 (41%), Gaps = 49/229 (21%)
Query: 57 ATLEHKNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYE 116
AT E KNI ITGA+GF+ + +++R + KI +L + N + L SP ++
Sbjct: 2 ATYEPKNILITGAAGFIASHVANRLIRNYPDYKIVVLDKLDYCSNLKN-LNPSKSSPNFK 60
Query: 117 ALKKEQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDD-YMQT 175
+K GD+A DL + +++E I + H AA D+ + +
Sbjct: 61 FVK----------------GDIASADL----VNYLLITEGIDTIMHFAAQTHVDNSFGNS 100
Query: 176 YVFL--NTRGTRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSPHNVIEKA 233
+ F N GT +L K ++ F++VST ++V E V H E +
Sbjct: 101 FEFTKNNIYGTHVLLEACKVTGQIRRFIHVST------DEVYGETDEDADVGNH---EAS 151
Query: 234 ELLSKNELELLKQELLQDFPNGYAYTKCLCEGVVTEYMEA-GMPCMILR 281
+LL N Y+ TK E +V Y + G+P + R
Sbjct: 152 QLLPTNP---------------YSATKAGAEMLVMAYGRSYGLPVITTR 185
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase, extended
(e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was
identified in Helicobacter pylori as the hexameric flaA1
gene product (FlaA1). FlaA1 is hexameric, possesses
UDP-GlcNAc-inverting 4,6-dehydratase activity, and
catalyzes the first step in the creation of a
pseudaminic acid derivative in protein glycosylation.
Although this subgroup has the NADP-binding motif
characteristic of extended SDRs, its members tend to
have a Met substituted for the active site Tyr found in
most SDR families. 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 = 287
Score = 43.0 bits (102), Expect = 3e-04
Identities = 25/104 (24%), Positives = 42/104 (40%), Gaps = 20/104 (19%)
Query: 62 KNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKE 121
K I +TG +G +G L+ +IL+ K+ + + ++ L+E L +E
Sbjct: 3 KTILVTGGAGSIGSELVRQILKFGPK-KLIVF--------------DRDENKLHE-LVRE 46
Query: 122 QSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAA 165
+K+ I GDV + R IV+H AA
Sbjct: 47 LRSRFPHDKLRFIIGDVRDKER----LRRAFKERGPDIVFHAAA 86
>gnl|CDD|132795 cd06885, PX_SNX17_31, The phosphoinositide binding Phox Homology
domain of Sorting Nexins 17 and 31. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions. Members of this
subfamily include sorting nexin 17 (SNX17), SNX31, and
similar proteins. They contain an N-terminal PX domain
followed by a truncated FERM (4.1, ezrin, radixin, and
moesin) domain and a unique C-terminal region. SNXs make
up the largest group among PX domain containing
proteins. They are involved in regulating membrane
traffic and protein sorting in the endosomal system. The
PX domain of SNXs binds PIs and targets the protein to
PI-enriched membranes. SNXs differ from each other in
PI-binding specificity and affinity, and the presence of
other protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. SNX17 is known to regulate the
trafficking and processing of a number of proteins. It
binds some members of the low-density lipoprotein
receptor (LDLR) family such as LDLR, VLDLR, ApoER2, and
others, regulating their endocytosis. It also binds
P-selectin and may regulate its lysosomal degradation.
SNX17 is highly expressed in neurons. It binds amyloid
precursor protein (APP) and may be involved in its
intracellular trafficking and processing to amyloid beta
peptide, which plays a central role in the pathogenesis
of Alzheimer's disease. The biological function of SNX31
is unknown.
Length = 104
Score = 40.0 bits (94), Expect = 4e-04
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 636 QNKTKFS---TPSFPPKKIRSNQPKVLDERRHLLEIYLKEM 673
Q K +F P FPPKK+ P L+ERR LE YL+ +
Sbjct: 44 QLKKEFGNRKLPPFPPKKLLPLTPAQLEERRLQLEKYLQAV 84
>gnl|CDD|132768 cd06093, PX_domain, The Phox Homology domain, a phosphoinositide
binding module. The PX domain is a phosphoinositide
(PI) binding module involved in targeting proteins to
membranes. Proteins containing PX domains interact with
PIs and have been implicated in highly diverse functions
such as cell signaling, vesicular trafficking, protein
sorting, lipid modification, cell polarity and division,
activation of T and B cells, and cell survival. Many
members of this superfamily bind
phosphatidylinositol-3-phosphate (PI3P) but in some
cases, other PIs such as PI4P or PI(3,4)P2, among
others, are the preferred substrates. In addition to
protein-lipid interaction, the PX domain may also be
involved in protein-protein interaction, as in the cases
of p40phox, p47phox, and some sorting nexins (SNXs). The
PX domain is conserved from yeast to humans and is found
in more than 100 proteins. The majority of PX
domain-containing proteins are SNXs, which play
important roles in endosomal sorting.
Length = 106
Score = 38.1 bits (89), Expect = 0.002
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 644 PSFPPKKIRSNQ-PKVLDERRHLLEIYLKEMFKFGPSRN--QVLAFL 687
P PPKK+ N P+ ++ERR LE YL+ + RN ++ FL
Sbjct: 58 PPLPPKKLFGNLDPEFIEERRKQLEQYLQSLLNHPELRNSEELKEFL 104
Score = 33.5 bits (77), Expect = 0.072
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 522 ISVSGYRLIEC-EKPYYVYVIHVRM-FQQHYIVEKRYSELLSWHSE 565
+S+ Y ++ K Y VY+I V + + V +RYS+ H +
Sbjct: 2 VSIPDYEKVKDGGKKYVVYIIEVTTQGGEEWTVYRRYSDFEELHEK 47
>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 = 40.0 bits (94), Expect = 0.003
Identities = 34/146 (23%), Positives = 61/146 (41%), Gaps = 30/146 (20%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
N+ +TGA GF+G L E++LR E ++ L N + L
Sbjct: 1 NVLVTGADGFIGSHLTERLLR--EGHEVRAL--DIYNSFNSWGLL--------------- 41
Query: 123 SESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQ---TYVFL 179
++A+ ++ I+GDV L + +V+H+AA + +YV
Sbjct: 42 -DNAVHDRFHFISGDVRDASEVEY------LVKKCDVVFHLAALIAIPYSYTAPLSYVET 94
Query: 180 NTRGTRDMLNLSKQMIHLQLFVYVST 205
N GT ++L + + + + V+ ST
Sbjct: 95 NVFGTLNVLEAACVL-YRKRVVHTST 119
>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 = 38.5 bits (90), Expect = 0.004
Identities = 39/172 (22%), Positives = 74/172 (43%), Gaps = 39/172 (22%)
Query: 64 IFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQS 123
I I GA+GF+G+ L ++L + ++ +L+R + +RL + Q P+
Sbjct: 1 ILILGATGFIGRALARELLE--QGHEVTLLVR------NTKRLSKEDQEPVAV------- 45
Query: 124 ESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQTYVFLNTRG 183
+ GD+ D A +V H+A R + ++ G
Sbjct: 46 ----------VEGDLRDLDSLSDAVQGV------DVVIHLAGAPRDTRD---FCEVDVEG 86
Query: 184 TRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSPHNVIEKAEL 235
TR++L +K+ ++ F+++S+ + L E+T P P SP+ KA+
Sbjct: 87 TRNVLEAAKE-AGVKHFIFISSLG-AYGD--LHEETEPSPSSPYLA-VKAKT 133
>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 = 39.7 bits (93), Expect = 0.004
Identities = 53/224 (23%), Positives = 86/224 (38%), Gaps = 54/224 (24%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
++ +TG SGF G+ L++++L E Y+ R +I +P EAL Q
Sbjct: 1 SVLVTGGSGFFGERLVKQLL---ERGGTYV------------RSFDI--APPGEALSAWQ 43
Query: 123 SESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQTYVFLNTR 182
+ F + GD+ + A V+H AA V Y +N
Sbjct: 44 HPNIEF-----LKGDITDRNDVEQALSG------ADCVFHTAAIVPLAGPRDLYWEVNVG 92
Query: 183 GTRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSPHNVIEKAELLSKNELE 242
GT+++L+ ++ +Q FVY S++ +VI + + N E
Sbjct: 93 GTQNVLDACQRC-GVQKFVYTSSS---------------------SVIFGGQNI-HNGDE 129
Query: 243 LLKQELLQDFPNGYAYTKCLCEGVVTEYM-EAGMPCMILRPSII 285
L L YA TK + E +V E + LRP+ I
Sbjct: 130 TLPYPPLDSDM--YAETKAIAEIIVLEANGRDDLLTCALRPAGI 171
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 39.2 bits (92), Expect = 0.009
Identities = 28/117 (23%), Positives = 41/117 (35%), Gaps = 30/117 (25%)
Query: 54 RISATLEHKNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSP 113
I A L K + +TG G +G L +IL+ +I + R +
Sbjct: 243 LIGAMLTGKTVLVTGGGGSIGSELCRQILK-FNPKEIILFSRDEYK-------------- 287
Query: 114 LYEALKKEQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSE-----TIHIVYHIAA 165
LY + E E K+ GDV DR + + IV+H AA
Sbjct: 288 LYL-IDMELREKFPELKLRFYIGDVR---------DRDRVERAMEGHKVDIVFHAAA 334
>gnl|CDD|132807 cd06897, PX_SNARE, The phosphoinositide binding Phox Homology
domain of SNARE proteins from fungi. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions such as cell signaling,
vesicular trafficking, protein sorting, and lipid
modification, among others. This subfamily is composed
of fungal proteins similar to Saccharomyces cerevisiae
Vam7p. They contain an N-terminal PX domain and a
C-terminal SNARE domain. The SNARE (Soluble NSF
attachment protein receptor) family of proteins are
integral membrane proteins that serve as key factors for
vesicular trafficking. Vam7p is anchored at the vacuolar
membrane through the specific interaction of its PX
domain with phosphatidylinositol-3-phosphate (PI3P)
present in bilayers. It plays an essential role in
vacuole fusion. The PX domain is involved in targeting
of proteins to PI-enriched membranes, and may also be
involved in protein-protein interaction.
Length = 108
Score = 36.1 bits (84), Expect = 0.012
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 646 FPPKKI---RSNQPKVLDERRHLLEIYLKEMF--KFGPSRNQ--VLAFLGV 689
PPK S+ PK+++ERR LE +L+ + + RN V FL +
Sbjct: 57 LPPKSWFLSTSSNPKLVEERRVGLEAFLRALLNDEDSRWRNSPAVKEFLNL 107
Score = 29.2 bits (66), Expect = 2.4
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 522 ISVSGYRLIECEKPYYVYVIHVRMFQQHYIVEKRYSELLSWHSE 565
IS+ KPY VY I VR+ + Y V +RYSE ++ H +
Sbjct: 3 ISIPTT--SVSPKPYTVYNIQVRLPLRSYTVSRRYSEFVALHKQ 44
>gnl|CDD|200431 TIGR04180, EDH_00030, NAD dependent epimerase/dehydratase,
LLPSF_EDH_00030 family. This clade within the NAD
dependent epimerase/dehydratase superfamily (pfam01370)
is characterized by inclusion of its members within a
cassette of seven distinctive enzymes. These include
four genes homologous to the elements of the neuraminic
(sialic) acid biosynthesis cluster (NeuABCD), an
aminotransferase and a nucleotidyltransferase in
addition to the epimerase/dehydratase. Together it is
very likely that these enzymes direct the biosynthesis
of a nine-carbon sugar analagous to CMP-neuraminic acid.
These seven genes form the core of the cassette,
although they are often accompanied by additional genes
that may further modify the product sugar. Although this
cassette is widely distributed in bacteria, the family
nomenclature arises from the instance in Leptospira
interrogans serovar Lai, str. 56601, where it appears as
the 30th gene in the 91-gene lipopolysaccharide
biosynthesis cluster.
Length = 297
Score = 37.7 bits (88), Expect = 0.017
Identities = 34/128 (26%), Positives = 59/128 (46%), Gaps = 26/128 (20%)
Query: 64 IFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQS 123
+ +TGA GF+G L+E ++R V+ ++L NS F S + L + S
Sbjct: 1 VLVTGADGFIGSHLVEALVRQGYEVRAFVLY------NS-------FNS--WGWL--DTS 43
Query: 124 ESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFD-DYM--QTYVFLN 180
+ +K+ + GD+ PD A + +V+H+AA + Y+ +YV N
Sbjct: 44 PPEVKDKIEVVTGDIRDPDSVRKA------MKGCDVVFHLAALIAIPYSYIAPDSYVDTN 97
Query: 181 TRGTRDML 188
GT ++L
Sbjct: 98 VTGTLNVL 105
>gnl|CDD|216119 pfam00787, PX, PX domain. PX domains bind to phosphoinositides.
Length = 109
Score = 34.2 bits (79), Expect = 0.054
Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 644 PSFPPKKIRSNQ-PKVLDERRHLLEIYLKEMFK 675
P PPKK+ + +++RR LE YL+ + +
Sbjct: 60 PPLPPKKLFGRFSEEFIEKRRKGLEEYLQRLLQ 92
Score = 29.6 bits (67), Expect = 2.2
Identities = 9/44 (20%), Positives = 20/44 (45%)
Query: 522 ISVSGYRLIECEKPYYVYVIHVRMFQQHYIVEKRYSELLSWHSE 565
+ V + YY+Y + + + + V++RYS+ H +
Sbjct: 6 VVVVDPEKSGKKHTYYLYEVTTKTNLKEWSVKRRYSDFEELHKQ 49
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. 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 = 304
Score = 35.7 bits (83), Expect = 0.067
Identities = 40/172 (23%), Positives = 70/172 (40%), Gaps = 34/172 (19%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
+ +TG +GF+G L+E++L V + L K +E L E+
Sbjct: 1 RVLVTGGAGFIGSHLVERLLERGHEVIVLDNLSTGK----KENLPEV------------- 43
Query: 123 SESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAA---TVRFDDYMQTYVFL 179
+ F I GD+ E + E + V+H AA R + +
Sbjct: 44 KPNVKF-----IEGDIR------DDELVEFAFEGVDYVFHQAAQASVPRSIEDPIKDHEV 92
Query: 180 NTRGTRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVL--EEKTYPPPVSPHNV 229
N GT ++L +++ ++ FVY S++ + L +E P P+SP+ V
Sbjct: 93 NVLGTLNLLEAARKA-GVKRFVYASSSSVYGDPPYLPKDEDHPPNPLSPYAV 143
>gnl|CDD|132785 cd06875, PX_IRAS, The phosphoinositide binding Phox Homology domain
of the Imidazoline Receptor Antisera-Selected. The PX
domain is a phosphoinositide binding (PI) module present
in many proteins with diverse functions such as cell
signaling, vesicular trafficking, protein sorting, and
lipid modification, among others. Imidazoline Receptor
Antisera-Selected (IRAS), also called nischarin,
contains an N-terminal PX domain, leucine rich repeats,
and a predicted coiled coil domain. The PX domain of
IRAS binds to phosphatidylinositol-3-phosphate in
membranes. Together with the coiled coil domain, it is
essential for the localization of IRAS to endosomes.
IRAS has been shown to interact with integrin and
inhibit cell migration. Its interaction with alpha5
integrin causes a redistribution of the receptor from
the cell surface to endosomal structures, suggesting
that IRAS may function as a sorting nexin (SNX) which
regulates the endosomal trafficking of integrin. SNXs
make up the largest group among PX domain containing
proteins. They are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in PI-binding specificity
and affinity, and the presence of other protein-protein
interaction domains, which help determine subcellular
localization and specific function in the endocytic
pathway.
Length = 116
Score = 33.8 bits (78), Expect = 0.072
Identities = 14/31 (45%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 647 PPKKIRSNQ-PKVLDERRHLLEIYLKEMFKF 676
PPKK+ N+ P +++RR LEIYL+ + F
Sbjct: 59 PPKKLIGNKSPSFVEKRRKELEIYLQTLLSF 89
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid dehydrogenase/isomerase
family. The enzyme 3 beta-hydroxysteroid
dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD)
catalyzes the oxidation and isomerisation of 5-ene-3
beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid
precursors into the corresponding 4-ene-ketosteroids
necessary for the formation of all classes of steroid
hormones.
Length = 280
Score = 35.0 bits (81), Expect = 0.13
Identities = 32/149 (21%), Positives = 58/149 (38%), Gaps = 41/149 (27%)
Query: 66 ITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEI------FQSPLYEALK 119
+TG GF+G+ ++ +LR L+E+ F L E
Sbjct: 2 VTGGGGFLGRHIVRLLLR-------------------EGELQEVRVFDLRFSPELLEDFS 42
Query: 120 KEQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAAT--VRFDDYMQTYV 177
K + + I GDV +D + + +V H AA V Y T +
Sbjct: 43 K-------LQVITYIEGDV------TDKQDLRRALQGSDVVIHTAAIIDVFGKAYRDTIM 89
Query: 178 FLNTRGTRDMLNLSKQMIHLQLFVYVSTA 206
+N +GT+++L+ + +++ VY S+
Sbjct: 90 KVNVKGTQNVLDACVKA-GVRVLVYTSSM 117
>gnl|CDD|214610 smart00312, PX, PhoX homologous domain, present in p47phox and
p40phox. Eukaryotic domain of unknown function present
in phox proteins, PLD isoforms, a PI3K isoform.
Length = 105
Score = 32.3 bits (74), Expect = 0.21
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 644 PSFPPKKI----RSNQPKVLDERRHLLEIYLKEMFK 675
P P KK+ + + +++RR LE YL+ +
Sbjct: 54 PPLPGKKLFGRLNNFSEEFIEKRRRGLEKYLQSLLN 89
>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 = 34.0 bits (78), Expect = 0.29
Identities = 34/145 (23%), Positives = 56/145 (38%), Gaps = 31/145 (21%)
Query: 66 ITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEI--FQSPLYEALKKEQS 123
+TG GF+G + I+R +LL K E L+EI L +
Sbjct: 4 VTGGGGFLG----QHIIR--------LLLERK------EELKEIRVLDKAFGPELIEHFE 45
Query: 124 ESAIFEKVIPINGDV-AVPDLGISAEDRQMLSETIHIVYHIAATVRFDD--YMQTYVFLN 180
+S V I GD+ + L + + + +V H AA V + +N
Sbjct: 46 KSQGKTYVTDIEGDIKDLSFLFRACQG-------VSVVIHTAAIVDVFGPPNYEELEEVN 98
Query: 181 TRGTRDMLNLSKQMIHLQLFVYVST 205
GT+ +L Q +++ VY S+
Sbjct: 99 VNGTQAVLEACVQN-NVKRLVYTSS 122
>gnl|CDD|130249 TIGR01181, dTDP_gluc_dehyt, dTDP-glucose 4,6-dehydratase. This
protein is related to UDP-glucose 4-epimerase (GalE) and
likewise has an NAD cofactor [Cell envelope,
Biosynthesis and degradation of surface polysaccharides
and lipopolysaccharides].
Length = 317
Score = 33.9 bits (78), Expect = 0.29
Identities = 34/150 (22%), Positives = 56/150 (37%), Gaps = 32/150 (21%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
I +TG +GF+G + IL + ++ +L + N E L ++ +P Y
Sbjct: 1 RILVTGGAGFIGSNFVRYILNEHPDAEVIVLDKLTYAGN-LENLADLEDNPRYR------ 53
Query: 123 SESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFD-------DYMQT 175
F K GD+ +L R V H AA D +++T
Sbjct: 54 -----FVK-----GDIGDREL----VSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIET 99
Query: 176 YVFLNTRGTRDMLNLSKQMIHLQLFVYVST 205
N GT +L ++ H F ++ST
Sbjct: 100 ----NVVGTYTLLEAVRKYWHEFRFHHIST 125
>gnl|CDD|187560 cd05250, CC3_like_SDR_a, CC3(TIP30)-like, atypical (a) SDRs.
Atypical SDRs in this subgroup include CC3 (also known
as TIP30) which is implicated in tumor suppression.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine rich NAD(P)-binding
motif that resembles the extended SDRs, and have an
active site triad of the SDRs (YXXXK and upstream Ser),
although the upstream Asn of the usual SDR active site
is substituted with Asp. For CC3, the Tyr of the triad
is displaced compared to the usual SDRs and the protein
is monomeric, both these observations suggest that the
usual SDR catalytic activity is not present. NADP
appears to serve an important role as a ligand, and may
be important in the interaction with other
macromolecules. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 214
Score = 33.0 bits (76), Expect = 0.33
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 62 KNIFITGASGFVGKVLLEKILRTCENVKIYILLR 95
K + GA+G VGK LL ++L++ K+ ++R
Sbjct: 1 KTALVLGATGLVGKHLLRELLKSPYYSKVTAIVR 34
>gnl|CDD|187572 cd05262, SDR_a7, atypical (a) SDRs, subgroup 7. This subgroup
contains atypical SDRs of unknown function. Members of
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that matches the extended SDRs, TGXXGXXG, but
lacks the characteristic active site residues of the
SDRs. This subgroup has basic residues (HXXXR) in place
of the active site motif YXXXK, these may have a
catalytic role. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 291
Score = 33.5 bits (77), Expect = 0.38
Identities = 7/19 (36%), Positives = 16/19 (84%)
Query: 64 IFITGASGFVGKVLLEKIL 82
+F+TGA+GF+G ++ +++
Sbjct: 3 VFVTGATGFIGSAVVRELV 21
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 33.4 bits (76), Expect = 0.43
Identities = 46/178 (25%), Positives = 75/178 (42%), Gaps = 33/178 (18%)
Query: 52 PDRISATLEHKN--IFITGASGFVGKVLLEKIL-RTCENVKIYILLRPKKNKNSRERLEE 108
R+ + K I +TG +GFVG L++K++ R E + I +K E L
Sbjct: 109 TGRVPVGIGRKRLRIVVTGGAGFVGSHLVDKLIGRGDEVIVIDNFFTGRK-----ENLVH 163
Query: 109 IFQSPLYEALKKEQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVR 168
+F +P +E ++ + E + E V I +A P + +H Y+ T++
Sbjct: 164 LFGNPRFELIRHDVVEPILLE-VDQIY-HLACP------------ASPVHYKYNPVKTIK 209
Query: 169 FDDYMQTYVFLNTRGTRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSP 226
N GT +ML L+K++ L S Y P E +E TY V+P
Sbjct: 210 ----------TNVMGTLNMLGLAKRVGARFLLTSTSEVYGDPLEHPQKE-TYWGNVNP 256
>gnl|CDD|132784 cd06874, PX_KIF16B_SNX23, The phosphoinositide binding Phox
Homology domain of KIF16B kinesin or Sorting Nexin 23.
The PX domain is a phosphoinositide (PI) binding module
present in many proteins with diverse functions such as
cell signaling, vesicular trafficking, protein sorting,
and lipid modification, among others. KIF16B, also
called sorting nexin 23 (SNX23), is a family-3 kinesin
which harbors an N-terminal kinesin motor domain
containing ATP and microtubule binding sites, a ForkHead
Associated (FHA) domain, and a C-terminal PX domain. The
PX domain of KIF16B binds to
phosphatidylinositol-3-phosphate (PI3P) in early
endosomes and plays a role in the transport of early
endosomes to the plus end of microtubules. By regulating
early endosome plus end motility, KIF16B modulates the
balance between recycling and degradation of receptors.
SNXs make up the largest group among PX domain
containing proteins. They are involved in regulating
membrane traffic and protein sorting in the endosomal
system. The PX domain of SNXs binds PIs and targets the
protein to PI-enriched membranes. SNXs differ from each
other in PI-binding specificity and affinity, and the
presence of other protein-protein interaction domains,
which help determine subcellular localization and
specific function in the endocytic pathway.
Length = 127
Score = 32.0 bits (73), Expect = 0.45
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 646 FPPKKIRSNQ-PKVLDERRHLLEIYLKEMF 674
FPPKK+ N+ +V ERR LE YL+ F
Sbjct: 60 FPPKKLFGNKSERVAKERRRQLETYLRNFF 89
>gnl|CDD|187563 cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended (e)
SDRs. This subgroup contains UDP-D-glucuronic acid
4-epimerase, an extended SDR, which catalyzes the
conversion of UDP-alpha-D-glucuronic acid to
UDP-alpha-D-galacturonic acid. This group has the SDR's
canonical catalytic tetrad and the TGxxGxxG 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 = 332
Score = 33.1 bits (76), Expect = 0.46
Identities = 41/160 (25%), Positives = 61/160 (38%), Gaps = 49/160 (30%)
Query: 62 KNIFITGASGFVG----KVLLEKILRTC--ENVKIYILLRPKKNKNSRERLEEIFQSPLY 115
I +TGA+GF+G K LLE+ +N+ Y +R K RL
Sbjct: 1 MKILVTGAAGFIGFHVAKRLLERGDEVVGIDNLNDYYDVRLK-----EARL--------- 46
Query: 116 EALKKEQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHI-----VYHIAAT--VR 168
E L K + GD+ EDR+ L V H+AA VR
Sbjct: 47 ELLGKSGGFKF-------VKGDL---------EDREALRRLFKDHEFDAVIHLAAQAGVR 90
Query: 169 FDDYMQ---TYVFLNTRGTRDMLNLSKQMIHLQLFVYVST 205
+ ++ YV N G ++L L + ++ VY S+
Sbjct: 91 YS--LENPHAYVDSNIVGFLNLLELCRH-FGVKHLVYASS 127
>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 = 32.5 bits (74), Expect = 0.58
Identities = 25/157 (15%), Positives = 53/157 (33%), Gaps = 26/157 (16%)
Query: 59 LEHKNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEAL 118
L K +TGAS +G+ + + R E ++ + R + E E +
Sbjct: 3 LSGKVALVTGASSGIGRAIARALAR--EGARVVVAARR----SEEEAAEAL--------- 47
Query: 119 KKEQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSET--IHIVYHIAATVRF------- 169
+ A + + DV+ + + A E I I+ + A
Sbjct: 48 -AAAIKEAGGGRAAAVAADVSDDEESVEALVAAAEEEFGRIDILVNNAGIAGPDAPLEEL 106
Query: 170 -DDYMQTYVFLNTRGTRDMLNLSKQMIHLQLFVYVST 205
++ + +N G + + ++ Q V +S+
Sbjct: 107 TEEDWDRVIDVNLLGAFLLTRAALPLMKKQRIVNISS 143
>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 = 32.3 bits (74), Expect = 0.73
Identities = 49/237 (20%), Positives = 78/237 (32%), Gaps = 86/237 (36%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
+ +TGA+GF+G+ L++K+L E V+I R E S + L
Sbjct: 1 KVLVTGANGFIGRALVDKLLSRGEEVRI----------AVR-NAENAEPSVVLAELPDID 49
Query: 123 SESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATV---------RFDDYM 173
S + +F V V H+AA V DY
Sbjct: 50 SFTDLFLGVD--------------------------AVVHLAARVHVMNDQGADPLSDYR 83
Query: 174 QTYVFLNTRGTRDMLNLSKQMIH--LQLFVYVSTAYCHPKE---KVLEEKTYPPPVSPHN 228
+ +NT TR L++ ++ FV++S+ + + +E P P +
Sbjct: 84 K----VNTELTR---RLARAAARQGVKRFVFLSSVKVNGEGTVGAPFDETDPPAPQDAYG 136
Query: 229 VIEKAELLSKNELELLKQELLQDFPNGYAYTKCLCEGVVTEYMEAGMPCMILRPSII 285
SK E E EL GM +ILRP ++
Sbjct: 137 R-------SKLEAERALLEL---------------------GASDGMEVVILRPPMV 165
>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 = 32.6 bits (75), Expect = 0.74
Identities = 46/237 (19%), Positives = 79/237 (33%), Gaps = 54/237 (22%)
Query: 64 IFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQS 123
+ ITG +GF+G L L+ V + L + + + L+ + +
Sbjct: 3 VLITGGAGFIGSNLARFFLKQGWEVIGFDNLMRRGSFGNLAWLKANREDGGVRFVH---- 58
Query: 124 ESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAA----TVRFDDYMQTYVF- 178
GD+ + D + L E I ++ H AA T F
Sbjct: 59 ------------GDIR------NRNDLEDLFEDIDLIIHTAAQPSVTTSASS--PRLDFE 98
Query: 179 LNTRGTRDMLNLSKQMIHLQLFVYVSTAYCHP----KEKVLEEKTY----PPPVSPHNVI 230
N GT ++L ++Q F++ ST + + E +T P SP +
Sbjct: 99 TNALGTLNVLEAARQHAPNAPFIFTSTNKVYGDLPNYLPLEELETRYELAPEGWSPAGIS 158
Query: 231 EKAELLSKNELELLKQELLQDFPNG-YAYTKCLCEGVVTEYMEA-GMPCMILRPSII 285
E L DF + Y +K + V EY G+ ++ R +
Sbjct: 159 ESFPL---------------DFSHSLYGASKGAADQYVQEYGRIFGLKTVVFRCGCL 200
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and dehydratases
typically acting on nucleotide-sugar substrates. The
genes of the family modeled here are generally in the
same locus with genes involved in the biosynthesis and
elaboration of hopene, the cyclization product of the
polyisoprenoid squalene. This gene and its association
with hopene biosynthesis in Zymomonas mobilis has been
noted in the literature where the gene symbol hpnA was
assigned. Hopanoids are known to be components of the
plasma membrane and to have polar sugar head groups in
Z. mobilis and other species.
Length = 328
Score = 32.3 bits (74), Expect = 0.81
Identities = 29/132 (21%), Positives = 51/132 (38%), Gaps = 46/132 (34%)
Query: 65 FITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQSE 124
+TGA+GFVG ++ +L E V+ +L+RP + R LE
Sbjct: 4 LVTGATGFVGSAVVRLLLEQGEEVR--VLVRPTSD---RRNLEG---------------- 42
Query: 125 SAIFEKVIPINGDVAVPDLGISAEDRQMLSETIH---IVYHIAATVRF-----DDYMQTY 176
++ ++ DL D L + + ++H+AA R ++
Sbjct: 43 ---------LDVEIVEGDL----RDPASLRKAVAGCRALFHVAADYRLWAPDPEEMYAA- 88
Query: 177 VFLNTRGTRDML 188
N GTR++L
Sbjct: 89 ---NVEGTRNLL 97
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 32.2 bits (74), Expect = 0.88
Identities = 35/151 (23%), Positives = 55/151 (36%), Gaps = 32/151 (21%)
Query: 62 KNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKE 121
I +TG +GF+G + IL + + L + N E L ++ SP Y
Sbjct: 1 MKILVTGGAGFIGSNFVRYILNKHPDDHVVNLDKLTYAGN-LENLADVEDSPRYR----- 54
Query: 122 QSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFD-------DYMQ 174
F + GD+ +L DR V H AA D ++Q
Sbjct: 55 ------FVQ-----GDICDREL----VDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFIQ 99
Query: 175 TYVFLNTRGTRDMLNLSKQMIHLQLFVYVST 205
T N GT +L +++ F ++ST
Sbjct: 100 T----NVVGTYTLLEAARKYWGKFRFHHIST 126
>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 = 31.8 bits (73), Expect = 1.1
Identities = 40/151 (26%), Positives = 60/151 (39%), Gaps = 33/151 (21%)
Query: 62 KNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNK----NSRERLEEIFQSPLYEA 117
I +TG +GF+G + +L + KI L +K + E LE++ SP Y
Sbjct: 1 MKILVTGGAGFIGSNFVRYLLNKYPDYKIINL-----DKLTYAGNLENLEDVSSSPRYR- 54
Query: 118 LKKEQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFD-DYMQTY 176
F K GD+ +L DR E I V H AA D
Sbjct: 55 ----------FVK-----GDICDAEL----VDRLFEEEKIDAVIHFAAESHVDRSISDPE 95
Query: 177 VFL--NTRGTRDMLNLSKQMIHLQLFVYVST 205
F+ N GT +L +++ + FV++ST
Sbjct: 96 PFIRTNVLGTYTLLEAARKYGV-KRFVHIST 125
>gnl|CDD|187554 cd05243, SDR_a5, atypical (a) SDRs, subgroup 5. This subgroup
contains atypical SDRs, some of which are identified as
putative NAD(P)-dependent epimerases, one as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
have a glycine-rich NAD(P)-binding motif that is very
similar to the extended SDRs, GXXGXXG, and binds NADP.
Generally, this subgroup has poor conservation of the
active site tetrad; however, individual sequences do
contain matches to the YXXXK active site motif, the
upstream Ser, and there is a highly conserved Asp in
place of the usual active site Asn throughout the
subgroup. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 203
Score = 31.4 bits (72), Expect = 1.2
Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLE-EIFQ 111
+ + GA+G VG+ ++ ++L ++ L+R E E+
Sbjct: 1 KVLVVGATGKVGRHVVRELLD--RGYQVRALVRDPSQAEKLEAAGAEVVV 48
>gnl|CDD|132796 cd06886, PX_SNX27, The phosphoinositide binding Phox Homology
domain of Sorting Nexin 27. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions. Sorting nexins (SNXs)
make up the largest group among PX domain containing
proteins. They are involved in regulating membrane
traffic and protein sorting in the endosomal system. The
PX domain of SNXs binds PIs and targets the protein to
PI-enriched membranes. SNXs differ from each other in
PI-binding specificity and affinity, and the presence of
other protein-protein interaction domains, which help
determine subcellular localization and specific function
in the endocytic pathway. SNX27 contains an N-terminal
PDZ domain followed by a PX domain and a Ras-Associated
(RA) domain. It binds G protein-gated potassium (Kir3)
channels, which play a role in neuronal excitability
control, through its PDZ domain. SNX27 downregulates
Kir3 channels by promoting their movement in the
endosome, reducing surface expression and increasing
degradation. SNX27 also associates with
5-hydroxytryptamine type 4 receptor (5-HT4R), cytohesin
associated scaffolding protein (CASP), and
diacylglycerol kinase zeta, and may play a role in their
intracellular trafficking and endocytic recycling. The
SNX27 PX domain preferentially binds to
phosphatidylinositol-3-phosphate (PI3P) and is important
for targeting to the early endosome.
Length = 106
Score = 30.1 bits (68), Expect = 1.5
Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 4/56 (7%)
Query: 620 MTNTVNLYLYLDFGFFQNKTKFSTPSFPPKKIRSNQPKVLDERRHLLEIYLKEMFK 675
NL+ L F F P P K S + LD RR LE YL+++
Sbjct: 38 YREFANLHQNLKKEFPD----FQFPKLPGKWPFSLSEQQLDARRRGLEQYLEKVCS 89
>gnl|CDD|217199 pfam02719, Polysacc_synt_2, Polysaccharide biosynthesis protein.
This is a family of diverse bacterial polysaccharide
biosynthesis proteins including the CapD protein, WalL
protein mannosyl-transferase and several putative
epimerases (e.g. WbiI).
Length = 280
Score = 31.3 bits (72), Expect = 1.5
Identities = 27/102 (26%), Positives = 40/102 (39%), Gaps = 20/102 (19%)
Query: 64 IFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQS 123
+ +TG G +G L +IL+ N K IL R E LYE +++E
Sbjct: 1 VLVTGGGGSIGSELCRQILKF--NPKKIILF---------SRDE----FKLYE-IRQELR 44
Query: 124 ESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAA 165
+ K+ GDV + A M + V+H AA
Sbjct: 45 QEYNDPKLRFFIGDVRDRERLERA----MEQHGVDTVFHAAA 82
>gnl|CDD|187569 cd05259, PCBER_SDR_a, phenylcoumaran benzylic ether reductase
(PCBER) like, atypical (a) SDRs. PCBER and
pinoresinol-lariciresinol reductases are NADPH-dependent
aromatic alcohol reductases, and are atypical members of
the SDR family. Other proteins in this subgroup are
identified as eugenol synthase. These proteins contain
an N-terminus characteristic of NAD(P)-binding proteins
and a small C-terminal domain presumed to be involved in
substrate binding, but they do not have the conserved
active site Tyr residue typically found in SDRs.
Numerous other members have unknown functions. The
glycine rich NADP-binding motif in this subgroup is of 2
forms: GXGXXG and G[GA]XGXXG; it tends to be atypical
compared with the forms generally seen in classical or
extended SDRs. The usual SDR active site tetrad is not
present, but a critical active site Lys at the usual SDR
position has been identified in various members, though
other charged and polar residues are found at this
position in this subgroup. Atypical SDR-related proteins
retain the Rossmann fold of the SDRs, but have limited
sequence identity and generally lack the catalytic
properties of the archetypical members. Atypical SDRs
include biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 282
Score = 31.5 bits (72), Expect = 1.6
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNS 102
I I GA+G +G ++ +L + + +L RP ++
Sbjct: 1 KIAIAGATGTLGGPIVSALLAS-PGFTVTVLTRPSSTSSN 39
>gnl|CDD|235500 PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 248
Score = 30.9 bits (71), Expect = 2.1
Identities = 34/155 (21%), Positives = 53/155 (34%), Gaps = 47/155 (30%)
Query: 59 LEHKNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEAL 118
LE K +TGAS +G+ + E++ NV I N EAL
Sbjct: 3 LEGKVALVTGASRGIGRAIAERLAAQGANVVI----------NYAS------SEAGAEAL 46
Query: 119 KKEQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSET------IHIVYHIAATVR---- 168
E K + + GDV+ + S E + + E + I+ + A R
Sbjct: 47 VAEIGALGG--KALAVQGDVSDAE---SVE--RAVDEAKAEFGGVDILVNNAGITRDNLL 99
Query: 169 -------FDDYMQTYVFLNTRGTRDMLNLSKQMIH 196
+D + T N G NL+K +
Sbjct: 100 MRMKEEDWDRVIDT----NLTGV---FNLTKAVAR 127
>gnl|CDD|132810 cd07277, PX_RUN, The phosphoinositide binding Phox Homology domain
of uncharacterized proteins containing PX and RUN
domains. The PX domain is a phosphoinositide (PI)
binding module involved in targeting proteins to
PI-enriched membranes. Members in this subfamily are
uncharacterized proteins containing an N-terminal RUN
domain and a C-terminal PX domain. PX domain harboring
proteins have been implicated in highly diverse
functions such as cell signaling, vesicular trafficking,
protein sorting, lipid modification, cell polarity and
division, activation of T and B cells, and cell
survival. In addition to protein-lipid interaction, the
PX domain may also be involved in protein-protein
interaction. The RUN domain is found in GTPases in the
Rap and Rab families and may play a role in Ras-like
signaling pathways.
Length = 118
Score = 29.6 bits (67), Expect = 2.2
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 646 FPPKKIRSNQ-PKVLDERRHLLEIYLKEMF 674
FPPKK N+ K ++ERR L++YL+ +
Sbjct: 60 FPPKKAIGNKDAKFVEERRKRLQVYLRRVV 89
Score = 29.6 bits (67), Expect = 2.5
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 536 YYVYVIHVRMFQQHYIVEKRYSELLSWHSE 565
++VY +++R+ + V +RYSE H +
Sbjct: 18 HHVYQVYIRIRDDEWNVYRRYSEFYELHKK 47
>gnl|CDD|187545 cd05234, UDP_G4E_2_SDR_e, UDP-glucose 4 epimerase, subgroup 2,
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
archaeal and bacterial proteins, and 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 = 305
Score = 31.1 bits (71), Expect = 2.2
Identities = 39/168 (23%), Positives = 70/168 (41%), Gaps = 33/168 (19%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
I +TG +GF+G L++++L V + L + RE +E F++ + +K++
Sbjct: 1 RILVTGGAGFIGSHLVDRLLEEGNEVVVVDNL----SSGRRENIEPEFENKAFRFVKRDL 56
Query: 123 SESAIFEKVIPINGDV-----AVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQTYV 177
++A +KV +GD A PD+ + A D I + ++ AT + M+
Sbjct: 57 LDTA--DKVAKKDGDTVFHLAANPDVRLGATDP-----DIDLEENVLATYNVLEAMR--- 106
Query: 178 FLNTRGTRDMLNLSKQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVS 225
G + + +F ST Y K E P P+S
Sbjct: 107 ---ANGVKRI-----------VFASSSTVYGEAKVIPTPEDYPPLPIS 140
>gnl|CDD|216708 pfam01797, Y1_Tnp, Transposase IS200 like. Transposases are needed
for efficient transposition of the insertion sequence or
transposon DNA. This family includes transposases for
IS200 from E. coli.
Length = 120
Score = 29.4 bits (67), Expect = 2.5
Identities = 9/20 (45%), Positives = 9/20 (45%), Gaps = 3/20 (15%)
Query: 701 SLHHYHFVFRTKTNDYRTPV 720
YH VF TK YR V
Sbjct: 2 YNLKYHIVFVTK---YRRKV 18
>gnl|CDD|216602 pfam01609, DDE_Tnp_1, Transposase DDE domain. Transposase proteins
are necessary for efficient DNA transposition. This
domain is a member of the DDE superfamily, which contain
three carboxylate residues that are believed to be
responsible for coordinating metal ions needed for
catalysis. The catalytic activity of this enzyme
involves DNA cleavage at a specific site followed by a
strand transfer reaction. This family contains
transposases for IS4, IS421, IS5377, IS427, IS402,
IS1355, IS5, which was original isolated in
bacteriophage lambda.
Length = 194
Score = 30.3 bits (68), Expect = 2.8
Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 10/77 (12%)
Query: 30 HIFMTGASGFIVKAIPK-----KFKHLPDRISATLEHKNIFITGASGFVGKVLLEKILRT 84
HI + +G + + L + L K + +G+ G ++L
Sbjct: 38 HIVVDDTTGLPLSVVVTPANVHDRTALKQ-LLDLLRPKGRLVLADAGYAG----PELLDK 92
Query: 85 CENVKIYILLRPKKNKN 101
+ L+R KKN+
Sbjct: 93 LREKGVDFLIRLKKNQK 109
>gnl|CDD|185103 PRK15181, PRK15181, Vi polysaccharide biosynthesis protein TviC;
Provisional.
Length = 348
Score = 30.4 bits (68), Expect = 3.1
Identities = 43/183 (23%), Positives = 75/183 (40%), Gaps = 26/183 (14%)
Query: 54 RISATLEHKNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSP 113
R L K ITG +GF+G LLE++L + V + + + L+++ S
Sbjct: 8 RTKLVLAPKRWLITGVAGFIGSGLLEELLFLNQTV----IGLDNFSTGYQHNLDDVRTS- 62
Query: 114 LYEALKKEQSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYM 173
+ +EQ IF I GD+ D Q + + V H AA +
Sbjct: 63 ----VSEEQWSRFIF-----IQGDIR------KFTDCQKACKNVDYVLHQAALGSVPRSL 107
Query: 174 QTYVFLNTRGTRDMLNL--SKQMIHLQLFVYVSTAYC---HPKEKVLEEKTYPPPVSPHN 228
+ + N+ LN+ + + H+ F Y +++ HP +EE+ P+SP+
Sbjct: 108 KDPIATNSANIDGFLNMLTAARDAHVSSFTYAASSSTYGDHPDLPKIEERI-GRPLSPYA 166
Query: 229 VIE 231
V +
Sbjct: 167 VTK 169
>gnl|CDD|226706 COG4255, COG4255, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 318
Score = 30.3 bits (68), Expect = 3.2
Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 4/74 (5%)
Query: 365 QITWYDIIENGKDIARNKVPLNNV-LWYPGGAMTNRGYEPVLKRVHNRIKKGFDIFEYYT 423
Q+ N AR LN++ LW GG + V R H + D+F Y
Sbjct: 171 QMWLAAHPVNHNRKARGLPELNSLWLWGQGGTVFAD---TVWSRFHGDRRALPDLFRAYE 227
Query: 424 KNSWSFKNENLHAL 437
+ + + H L
Sbjct: 228 ETAAHLPDLTHHIL 241
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 30.3 bits (68), Expect = 3.2
Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 62 KNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQ 111
I +TGA+GFVG ++ ++L ++ +R + + E+
Sbjct: 1 MKILVTGATGFVGGAVVRELLAR--GHEVRAAVRNPEAAAALAGGVEVVL 48
>gnl|CDD|176234 cd08273, MDR8, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 331
Score = 30.3 bits (69), Expect = 3.4
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 53 DRISATLEHKNIFITGASGFVGKVLLEKILRTCENVKIY 91
R + L + + I GASG VG+ LLE L ++Y
Sbjct: 132 HRAAKVLTGQRVLIHGASGGVGQALLE--LALLAGAEVY 168
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 30.2 bits (69), Expect = 3.5
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 229 VIEKAELLSKNELELLKQELLQDF 252
VI KA+ L+ EL K+ +++D
Sbjct: 148 VIAKADTLTPEELTEFKKRIMEDI 171
>gnl|CDD|181349 PRK08278, PRK08278, short chain dehydrogenase; Provisional.
Length = 273
Score = 30.3 bits (69), Expect = 3.8
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 24 SSLKDKHIFMTGASGFIVKAIPKK 47
SL K +F+TGAS I AI +
Sbjct: 2 MSLSGKTLFITGASRGIGLAIALR 25
>gnl|CDD|187635 cd08930, SDR_c8, classical (c) SDR, subgroup 8. This subgroup has
a fairly well conserved active site tetrad and domain
size of the classical SDRs, but has an atypical
NAD-binding motif ([ST]G[GA]XGXXG). 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 = 30.0 bits (68), Expect = 3.9
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 10/85 (11%)
Query: 60 EHKNIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKN--SRERLEEIFQSPLYEA 117
E K I ITGA+G +GK + +L IL +E L ++++ + A
Sbjct: 1 EDKIILITGAAGLIGKAFCKALL---SAGARLILADINAPALEQLKEELTNLYKNRV-IA 56
Query: 118 LK----KEQSESAIFEKVIPINGDV 138
L+ ++S + E + G +
Sbjct: 57 LELDITSKESIKELIESYLEKFGRI 81
>gnl|CDD|187541 cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and
related proteins, extended (e) SDRs. UGD catalyzes the
formation of UDP-xylose from UDP-glucuronate; it is an
extended-SDR, and has the characteristic glycine-rich
NAD-binding pattern, TGXXGXXG, and 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 = 305
Score = 29.9 bits (68), Expect = 4.4
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 62 KNIFITGASGFVGKVLLEKILRTCENV 88
K I ITG +GF+G L +++L V
Sbjct: 1 KRILITGGAGFLGSHLCDRLLEDGHEV 27
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
retain the canonical active site triad (though not the
upstream Asn found in most SDRs) but have an unusual
putative glycine-rich NAD(P)-binding motif, GGXXXXG, in
the usual location. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 30.0 bits (68), Expect = 4.5
Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 2/30 (6%)
Query: 256 YAYTKCLCEGVVTEYMEAGMPCMILRPSII 285
Y K E V+ E A P I+RP I
Sbjct: 129 YGRGKRAAEDVLIEA--AAFPYTIVRPPYI 156
>gnl|CDD|213592 TIGR01179, galE, UDP-glucose-4-epimerase GalE. Alternate name:
UDPgalactose 4-epimerase This enzyme interconverts
UDP-glucose and UDP-galactose. A set of related
proteins, some of which are tentatively identified as
UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus
halodurans, and several archaea, but deeply branched
from this set and lacking experimental evidence, are
excluded from This model and described by a separate
model [Energy metabolism, Sugars].
Length = 328
Score = 30.0 bits (68), Expect = 4.6
Identities = 37/173 (21%), Positives = 65/173 (37%), Gaps = 36/173 (20%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEA-LKKE 121
I +TG +G++G + ++L + V I L ++ + R E I E L+
Sbjct: 1 KILVTGGAGYIGSHTVRQLLESGHEVVILDNL-SNGSREALPRGERITPVTFVEGDLRDR 59
Query: 122 QSESAIFEKVIPINGDVAVPDLGISAEDRQMLSETIHIVYHIAATVRFDDYMQT---YVF 178
+ +FE+ I V H A + + +Q Y
Sbjct: 60 ELLDRLFEE------------------------HKIDAVIHFAGLIAVGESVQKPLKYYR 95
Query: 179 LNTRGTRDMLNLSKQMIHLQL--FVYVSTA--YCHPKEKVLEEKTYPPPVSPH 227
N GT LNL + M + F++ S+A Y P + E + P++P+
Sbjct: 96 NNVVGT---LNLLEAMQQAGVKKFIFSSSAAVYGEPSSIPISEDSPLGPINPY 145
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A;
Provisional.
Length = 256
Score = 30.0 bits (68), Expect = 4.8
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 59 LEHKNIFITGASGFVGKVLLEKIL 82
L+ K I ITGA G +G L++ IL
Sbjct: 2 LKGKTILITGAGGLIGSALVKAIL 25
>gnl|CDD|235861 PRK06782, PRK06782, flagellar motor switch protein; Reviewed.
Length = 528
Score = 30.2 bits (68), Expect = 4.8
Identities = 34/133 (25%), Positives = 57/133 (42%), Gaps = 19/133 (14%)
Query: 125 SAIFEKVIPINGDVAVPDLGISAEDRQMLSETI--HIVYHIAATVRFDDYMQTYVFLNTR 182
S +F++ I D++ P + +ML E+I + I + D +QT ++
Sbjct: 346 SEMFQEKI----DISPPTVKFVTLKEEMLGESIEVDELVQITFNLEVGDLLQTKMY---- 397
Query: 183 GTRDMLNLS--KQMIHLQLFVYVSTAYCHPKEKVLEEKTYPPPVSPHNVIEKAELLSKNE 240
+L +S K+M+ L L+ V E++ EK P V P IE E+ E
Sbjct: 398 ---QILPISEAKEMVRLLLYPMVKEEEEIATEEIEPEKVVEPVVQP---IEFKEVKQM-E 450
Query: 241 LELLKQELLQDFP 253
+ +LQD P
Sbjct: 451 PVYMDTSILQDVP 463
>gnl|CDD|187570 cd05260, GDP_MD_SDR_e, GDP-mannose 4,6 dehydratase, extended (e)
SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR,
catalyzes the NADP(H)-dependent conversion of
GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in
the fucose biosynthesis pathway. These proteins have the
canonical active site triad and NAD-binding pattern,
however the active site Asn is often missing and may be
substituted with Asp. A Glu residue has been identified
as an important active site base. 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 = 29.9 bits (68), Expect = 5.2
Identities = 29/135 (21%), Positives = 51/135 (37%), Gaps = 37/135 (27%)
Query: 63 NIFITGASGFVGKVLLEKILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYEALKKEQ 122
ITG +G G L E +L + +++ ++R + N +R++ ++
Sbjct: 1 RALITGITGQDGSYLAEFLLE--KGYEVHGIVRRSSSFN-TDRIDHLYI----------- 46
Query: 123 SESAIFEKVIPINGDVAVPDLGISAEDRQMLSETI-----HIVYHIAA----TVRFDDYM 173
+++ GD+ D L I +YH+AA V FDD
Sbjct: 47 ----NKDRITLHYGDL---------TDSSSLRRAIEKVRPDEIYHLAAQSHVKVSFDDPE 93
Query: 174 QTYVFLNTRGTRDML 188
T N GT ++L
Sbjct: 94 YTAEV-NAVGTLNLL 107
>gnl|CDD|240341 PTZ00272, PTZ00272, heat shock protein 83 kDa (Hsp83); Provisional.
Length = 701
Score = 30.0 bits (67), Expect = 5.3
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 540 VIHVRMFQQHYIVEKRYSELLSWHSEGFGLGI 571
+H++ Q Y+ +R EL+ HSE G I
Sbjct: 172 TLHLKEDQMEYLEPRRLKELIKKHSEFIGYDI 203
>gnl|CDD|220036 pfam08837, DUF1810, Protein of unknown function (DUF1810). This is
a family of uncharacterized proteins. The structure of
one of the members in this family has been solved and it
adopts a mainly alpha helical structure.
Length = 139
Score = 28.7 bits (65), Expect = 5.3
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 446 AIRYEIAMFRDLDEAKAYFEMCIHGAR 472
A RY I LDEA+AY + G R
Sbjct: 50 ARRYAI---SSLDEARAYLAHPVLGPR 73
>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 = 29.9 bits (68), Expect = 5.5
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 13/60 (21%)
Query: 67 TGASGFVG----KVLLEK------ILRTCENVKIYILLRPKKNKNSRERLEEIFQSPLYE 116
TGASGF+G K LL++ +R + K L + + ++ERL ++F++ L +
Sbjct: 4 TGASGFIGSWLVKRLLQRGYTVRATVRDPGDEKKVAHLL--ELEGAKERL-KLFKADLLD 60
>gnl|CDD|224928 COG2017, GalM, Galactose mutarotase and related enzymes
[Carbohydrate transport and metabolism].
Length = 308
Score = 29.7 bits (67), Expect = 6.3
Identities = 15/74 (20%), Positives = 26/74 (35%), Gaps = 8/74 (10%)
Query: 350 GNTMRVINLTANKDFQITWYDIIENGKDIARNKVPLNNVLW----YPGGAMTNRGYEPVL 405
G +R++ L +T + + G + +V N+L T +L
Sbjct: 9 GQPVRLLTLGNGGGMVVT---VPDWGATLTSLRVNGRNLLLGFDDAESYPATRGYGGAIL 65
Query: 406 KRVHNRIKKG-FDI 418
NRI G F +
Sbjct: 66 GPYANRISNGRFTL 79
>gnl|CDD|240138 cd05005, SIS_PHI, Hexulose-6-phosphate isomerase (PHI). PHI is a
member of the SIS (Sugar ISomerase domain) superfamily.
In the ribulose monophosphate pathway of formaldehyde
fixation, hexulose-6-phosphate synthase catalyzes the
condensation of ribulose-5-phosphate with formadelhyde
to become hexulose-6-phosphate, which is then
isomerized to fructose-6-phosphate by PHI.
Length = 179
Score = 29.1 bits (66), Expect = 6.9
Identities = 13/23 (56%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 55 ISATLEHKNIFITGA--SGFVGK 75
ISA L K IF+ GA SG V K
Sbjct: 27 ISAILNAKRIFVYGAGRSGLVAK 49
>gnl|CDD|132805 cd06895, PX_PLD, The phosphoinositide binding Phox Homology domain
of Phospholipase D. The PX domain is a phosphoinositide
(PI) binding module present in many proteins with
diverse functions such as cell signaling, vesicular
trafficking, protein sorting, and lipid modification,
among others. Phospholipase D (PLD) catalyzes the
hydrolysis of the phosphodiester bond of
phosphatidylcholine to generate membrane-bound
phosphatidic acid and choline. Members of this subfamily
contain PX and Pleckstrin Homology (PH) domains in
addition to the catalytic domain. PLD activity has been
detected in viruses, bacteria, yeast, plants, and
mammals, but the PX domain is not present in PLDs from
viruses and bacteria. PLDs are implicated in many
cellular functions like signaling, cytoskeletal
reorganization, vesicular transport, stress responses,
and the control of differentiation, proliferation, and
survival. Vertebrates contain two PLD isozymes, PLD1 and
PLD2. PLD1 is located mainly in intracellular membranes
while PLD2 is associated with plasma membranes. The PX
domain is involved in targeting of proteins to
PI-enriched membranes, and may also be involved in
protein-protein interaction.
Length = 140
Score = 28.5 bits (64), Expect = 7.6
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 644 PSFPPKKIRSNQPKVLDERRHLLEIYLKEMFKFGPSRN--QVLAFLGV 689
PS P + LD R+ LE YL+ + K RN + L FL V
Sbjct: 92 PSLPALPDILVSEEQLDSRKKQLENYLQNLLKIPDYRNHPETLEFLEV 139
>gnl|CDD|182658 PRK10699, PRK10699, phosphatidylglycerophosphatase B; Provisional.
Length = 244
Score = 28.8 bits (65), Expect = 8.5
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 498 VITQVLLLGFFLWVLRHP 515
++T VLL G+FLW LR
Sbjct: 54 ILTHVLLCGWFLWCLRFR 71
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a
negative transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane
reductase, isoflavone reductases, and others. SDRs are
a functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. In addition to the Rossmann fold
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids, and typically have a TGXXGXXG cofactor
binding motif. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 29.1 bits (66), Expect = 8.7
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 63 NIFITGASGFVGKVL 77
I ITG +GF+G+ L
Sbjct: 1 KIVITGGTGFIGRAL 15
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.139 0.429
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 40,527,218
Number of extensions: 4112842
Number of successful extensions: 3905
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3855
Number of HSP's successfully gapped: 95
Length of query: 762
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 658
Effective length of database: 6,324,786
Effective search space: 4161709188
Effective search space used: 4161709188
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 (28.1 bits)