RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy705
(232 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 = 260 bits (667), Expect = 3e-87
Identities = 102/226 (45%), Positives = 154/226 (68%)
Query: 2 FERLRKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKEN 61
F+R R P S++ IEGD+ + NLG+ D DL L EEV+++ + AA++ + L E
Sbjct: 55 FDRGRNLNPLFESKIVPIEGDLSEPNLGLSDEDLQTLIEEVNIIIHCAATVTFDERLDEA 114
Query: 62 VAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWM 121
++ N GT RLL++A + KKL AF+H STA+ + D++++EEK+YP P P ++ +E M
Sbjct: 115 LSINVLGTLRLLELAKRCKKLKAFVHVSTAYVNGDRQLIEEKVYPPPADPEKLIDILELM 174
Query: 122 DDETIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVLPSFQEPVPGWV 181
DD +++ TPK+LG HPN+YTFTK L E LV + + LP+VIVRPSIV + +EP PGW+
Sbjct: 175 DDLELERATPKLLGGHPNTYTFTKALAERLVLKERGNLPLVIVRPSIVGATLKEPFPGWI 234
Query: 182 DSLNGPVGVLVASGKGVVRSMMCGAEFVAEVVPVDIAINGVILAAY 227
D+ NGP G+ +A GKG++R+M VA+++PVD+ N ++ AA
Sbjct: 235 DNFNGPDGLFLAYGKGILRTMNADPNAVADIIPVDVVANALLAAAA 280
>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 = 175 bits (447), Expect = 5e-55
Identities = 77/230 (33%), Positives = 113/230 (49%), Gaps = 33/230 (14%)
Query: 3 ERLRKECPA--------QLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKL 54
ERLR+E L R+ + GD+ + NLG+ D D L EEV V+ + AA++
Sbjct: 39 ERLRQELLKYGLFDRLKALERIIPVAGDLSEPNLGLSDEDFQELAEEVDVIIHNAATVNF 98
Query: 55 EAELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPD-QKVLEEKLYPSPVSPHD 113
+ A N GT+ +L +A +MKKL F H STA+ + + +LEEK
Sbjct: 99 VEPYSDLRATNVLGTREVLRLAKQMKKL-PFHHVSTAYVNGERGGLLEEK---------- 147
Query: 114 IMRAMEWMDDETIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVLPSF 173
+ + P +LG PN YT +K L E LV E LPVVI RPSI+
Sbjct: 148 ---------PYKLDEDEPALLGGLPNGYTQSKWLAEQLVREAAGGLPVVIYRPSIITG-- 196
Query: 174 QEPVPGWVDSLN-GPVGVLVASGKGVVRSMMCGAEFVAEVVPVDIAINGV 222
E GW++ + GP G+L +G GV+ ++ + ++VPVD N +
Sbjct: 197 -ESRTGWINGDDFGPRGLLGGAGLGVLPDILGDPDARLDLVPVDYVANAI 245
>gnl|CDD|215538 PLN02996, PLN02996, fatty acyl-CoA reductase.
Length = 491
Score = 120 bits (304), Expect = 6e-32
Identities = 69/241 (28%), Positives = 115/241 (47%), Gaps = 27/241 (11%)
Query: 18 IIEGDILQANLGIKDSDLL-MLQEEVSVVFNGAASLKLEAELKENVAANTRGTQRLLDIA 76
+ GDI +LG+KDS+L + +E+ +V N AA+ + + NT G +L+ A
Sbjct: 88 PVPGDISYDDLGVKDSNLREEMWKEIDIVVNLAATTNFDERYDVALGINTLGALNVLNFA 147
Query: 77 LKMKKLVAFIHFSTAF-CHPDQKVLEEKLYP-----SPVSPHDIMRAMEWMD-------- 122
K K+ +H STA+ C ++ EK + + DI + +
Sbjct: 148 KKCVKVKMLLHVSTAYVCGEKSGLILEKPFHMGETLNGNRKLDINEEKKLVKEKLKELNE 207
Query: 123 ----DETIKQLTPKILGPH-------PNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVLP 171
+E I Q K LG PN+Y FTK + E L+ +K LP+VI+RP+++
Sbjct: 208 QDASEEEITQ-AMKDLGMERAKLHGWPNTYVFTKAMGEMLLGNFKENLPLVIIRPTMITS 266
Query: 172 SFQEPVPGWVDSLNGPVGVLVASGKGVVRSMMCGAEFVAEVVPVDIAINGVILAAYNRDQ 231
+++EP PGW++ L V+V GKG + + V +V+P D+ +N +I+A
Sbjct: 267 TYKEPFPGWIEGLRTIDSVIVGYGKGKLTCFLADPNSVLDVIPADMVVNAMIVAMAAHAG 326
Query: 232 K 232
Sbjct: 327 G 327
>gnl|CDD|215279 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
Length = 605
Score = 88.4 bits (219), Expect = 3e-20
Identities = 65/244 (26%), Positives = 116/244 (47%), Gaps = 31/244 (12%)
Query: 13 LSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGTQRL 72
LS+L + G++ ++NLG++ + +EV V+ N AA+ + + NTRG L
Sbjct: 191 LSKLVPVVGNVCESNLGLEPDLADEIAKEVDVIINSAANTTFDERYDVAIDINTRGPCHL 250
Query: 73 LDIALKMKKLVAFIHFSTAFCHPD-QKVLEEK-----------LYPSPVSPH-----DIM 115
+ A K KKL F+ STA+ + Q + EK L S PH DI
Sbjct: 251 MSFAKKCKKLKLFLQVSTAYVNGQRQGRIMEKPFRMGDCIARELGISNSLPHNRPALDIE 310
Query: 116 RAMEWMDD------------ETIKQLTPKILGPH--PNSYTFTKRLTETLVDEYKTKLPV 161
++ D + +K L + + ++Y FTK + E +++ + +PV
Sbjct: 311 AEIKLALDSKRHGFQSNSFAQKMKDLGLERAKLYGWQDTYVFTKAMGEMVINSMRGDIPV 370
Query: 162 VIVRPSIVLPSFQEPVPGWVDSLNGPVGVLVASGKGVVRSMMCGAEFVAEVVPVDIAING 221
VI+RPS++ ++++P PGW++ +++ GKG + + V +VVP D+ +N
Sbjct: 371 VIIRPSVIESTWKDPFPGWMEGNRMMDPIVLYYGKGQLTGFLADPNGVLDVVPADMVVNA 430
Query: 222 VILA 225
+ A
Sbjct: 431 TLAA 434
>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 = 73.2 bits (180), Expect = 2e-15
Identities = 43/172 (25%), Positives = 73/172 (42%), Gaps = 32/172 (18%)
Query: 3 ERLRKECPAQLS--RLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKE 60
E + A L R+ ++EGD+ Q NLG+ + L +V V + AAS +A ++
Sbjct: 36 EAHERIEEAGLEADRVRVLEGDLTQPNLGLSAAASRELAGKVDHVIHCAASYDFQAPNED 95
Query: 61 NVAANTRGTQRLLDIA--LKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAM 118
N GT+ +L++A L +++ F + STA+ + +R
Sbjct: 96 AWRTNIDGTEHVLELAARLDIQR---FHYVSTAYV--------------AGNREGNIR-- 136
Query: 119 EWMDDETIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVL 170
E + N Y +K E LV T++P+ + RPSIV+
Sbjct: 137 ETELNPGQNF---------KNPYEQSKAEAEQLVRAAATQIPLTVYRPSIVV 179
>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 = 59.2 bits (144), Expect = 2e-10
Identities = 52/182 (28%), Positives = 74/182 (40%), Gaps = 37/182 (20%)
Query: 3 ERLRKECP---------AQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLK 53
ERL +LSR+ ++ GD+ + NLG+ D D L EEV V+ + A++
Sbjct: 42 ERLIDNLKEYGLNLWDELELSRIKVVVGDLSKPNLGLSDDDYQELAEEVDVIIHNGANVN 101
Query: 54 L---EAELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVS 110
ELK AN GT+ LL +A KL ST V + Y +
Sbjct: 102 WVYPYEELK---PANVLGTKELLKLAA-TGKLKPLHFVSTLS------VFSAEEYNAL-- 149
Query: 111 PHDIMRAMEWMDDETIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTK-LPVVIVRPSIV 169
DDE + G PN Y +K + E L+ E + LPV I+RP +
Sbjct: 150 -----------DDEESDDMLESQNG-LPNGYIQSKWVAEKLLREAANRGLPVAIIRPGNI 197
Query: 170 LP 171
Sbjct: 198 FG 199
>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 = 55.1 bits (133), Expect = 5e-09
Identities = 45/177 (25%), Positives = 69/177 (38%), Gaps = 32/177 (18%)
Query: 3 ERLRKECPAQL--------SRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKL 54
ERLR+ + R+ ++ GD+ + LG+ D++ L E V + + A +
Sbjct: 42 ERLREALRSYRLWHEDLARERIEVVAGDLSEPRLGLSDAEWERLAENVDTIVHNGALVNW 101
Query: 55 EAELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDI 114
E AN GT+ +L +A + + ST S + D+
Sbjct: 102 VYPYSELRGANVLGTREVLRLAA-SGRAKPLHYVSTI---------------SVGAAIDL 145
Query: 115 MRAMEWMDDETIKQLTPKILGPHPNSYTFTKRLTETLVDEY-KTKLPVVIVRPSIVL 170
E DD T +TP Y +K + E LV E LPV IVRP +L
Sbjct: 146 STVTE--DDAT---VTPPP--GLAGGYAQSKWVAELLVREASDRGLPVTIVRPGRIL 195
>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 = 46.9 bits (112), Expect = 1e-06
Identities = 37/158 (23%), Positives = 54/158 (34%), Gaps = 43/158 (27%)
Query: 65 NTRGTQRLLDIALKMKKLVAFIHFSTA--FCHPDQKVLEEKLYPSPVSPHDIMRAMEWMD 122
N GT LL+ A K F++ S+A + P+ EE+ P P+SP
Sbjct: 57 NVVGTLNLLEAARKAGV-KRFVYASSASVYGSPEGLPEEEETPPRPLSP----------- 104
Query: 123 DETIKQLTPKILGPHPNSYTFTKRLTETLVDEY--KTKLPVVIVRPSIVL-----PSFQE 175
Y +K E L+ Y LPVVI+R + V P
Sbjct: 105 ------------------YGVSKLAAEHLLRSYGESYGLPVVILRLANVYGPGQRPRLDG 146
Query: 176 PVPGWVDSLNGPVGVLVASGKGVVRSMMCGAEFVAEVV 213
V ++ + V G R + V +VV
Sbjct: 147 VVNDFIRRALEGKPLTVFGGGNQTRDFI----HVDDVV 180
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 45.3 bits (107), Expect = 1e-05
Identities = 48/241 (19%), Positives = 76/241 (31%), Gaps = 50/241 (20%)
Query: 1 VFERLRKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA----SLKLEA 56
+RLR LS + + D+ D + + V + AA +
Sbjct: 29 GLDRLRDGLDPLLSGVEFVVLDLTDR-----DLVDELAKGVPDAVIHLAAQSSVPDSNAS 83
Query: 57 ELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTAFC----HPDQKVLEEKLYPSPVSPH 112
+ E + N GT LL+ A F+ S+ P + E+ P P++P
Sbjct: 84 DPAEFLDVNVDGTLNLLEAARAAGV-KRFVFASSVSVVYGDPPPLPIDEDLGPPRPLNP- 141
Query: 113 DIMRAMEWMDDETIKQLTPKILGPHPNSYTFTKRLTETLVDEY--KTKLPVVIVRPSIVL 170
Y +K E L+ Y LPVVI+RP V
Sbjct: 142 ----------------------------YGVSKLAAEQLLRAYARLYGLPVVILRPFNVY 173
Query: 171 -PSFQEPVPGWVDSLNGPVGVLVASGKGVVRSMMCGAEFVAEVVPVDIAINGVILAAYNR 229
P + + V S + + +FV VD + ++LA N
Sbjct: 174 GPGDKPDLSSGVVSAFIRQLLKGEPIIVIGGDGSQTRDFVY----VDDVADALLLALENP 229
Query: 230 D 230
D
Sbjct: 230 D 230
>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 = 43.9 bits (104), Expect = 3e-05
Identities = 39/180 (21%), Positives = 65/180 (36%), Gaps = 33/180 (18%)
Query: 2 FERLRKECPAQL-------SRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA---S 51
RL K R+ ++ GD+ + +LG+ + L E V ++ + AA
Sbjct: 41 LARLEKTFDLYRHWDELSADRVEVVAGDLAEPDLGLSERTWQELAENVDLIIHNAALVNH 100
Query: 52 LKLEAELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSP 111
+ +EL+ AN GT +L +A K + S+ V E + Y
Sbjct: 101 VFPYSELRG---ANVLGTAEVLRLAA-TGKPKPLHYVSSI------SVGETEYY------ 144
Query: 112 HDIMRAMEWMDDETIKQLTPKILGPHPNSYTFTKRLTETLVDE-YKTKLPVVIVRPSIVL 170
+ + + T + Y +K + E LV E LPV I RP +
Sbjct: 145 SNFTVDFDEISP------TRNVGQGLAGGYGRSKWVAEKLVREAGDRGLPVTIFRPGYIT 198
>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 = 41.9 bits (99), Expect = 1e-04
Identities = 59/225 (26%), Positives = 79/225 (35%), Gaps = 65/225 (28%)
Query: 15 RLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA----SLKLEAELKE-NVAANTRGT 69
+ ++EGD+ A L + VF+ AA K EL NV GT
Sbjct: 42 PVEVVEGDLTDAAS------LAAAMKGCDRVFHLAAFTSLWAKDRKELYRTNVE----GT 91
Query: 70 QRLLDIALKMKKLVAFIHFSTAFC---HPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETI 126
+ +LD AL+ + +H S+ PD ++ DET
Sbjct: 92 RNVLDAALE-AGVRRVVHTSSIAALGGPPDGRI-----------------------DET- 126
Query: 127 KQLTPKILGPHPNSYTFTKRLTETLVDEYKTK-LPVVIVRPSIVL-PSFQEPVPGW---V 181
TP P PN Y +K L E V E + L VVIV PS V P + P +
Sbjct: 127 ---TPWNERPFPNDYYRSKLLAELEVLEAAAEGLDVVIVNPSAVFGPGDEGPTSTGLDVL 183
Query: 182 DSLNGPVGVLVASGKGVVRSMMCGAEFVAEVVPVDIAINGVILAA 226
D LNG + G V V +V G I A
Sbjct: 184 DYLNGKLPAYPPGGTSFV--------DVRDVA------EGHIAAM 214
>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
Length = 657
Score = 39.9 bits (94), Expect = 7e-04
Identities = 44/169 (26%), Positives = 71/169 (42%), Gaps = 30/169 (17%)
Query: 2 FERLRKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKEN 61
E L A R+ + GD+ + LG+ ++D+ L ++ V + AA L A+ +
Sbjct: 41 LEALAAYWGAD--RVVPLVGDLTEPGLGLSEADIAELG-DIDHVVHLAAIYDLTADEEAQ 97
Query: 62 VAANTRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWM 121
AAN GT+ ++++A ++L A A H + Y E
Sbjct: 98 RAANVDGTRNVVELA---ERLQA------ATFHHVSSIAVAGDYEGVFR--------EDD 140
Query: 122 DDETIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVL 170
DE + L P P Y TK E LV E + LP + RP++V+
Sbjct: 141 FDEG-QGL------PTP--YHRTKFEAEKLVRE-ECGLPWRVYRPAVVV 179
>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 = 36.8 bits (86), Expect = 0.005
Identities = 47/171 (27%), Positives = 68/171 (39%), Gaps = 42/171 (24%)
Query: 14 SRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKENVAANTR 67
R ++GDI A L D L +E++ V + AA S+ N
Sbjct: 51 PRYRFVKGDICDAEL----VDRLFEEEKIDAVIHFAAESHVDRSISDPEPFIRT---NVL 103
Query: 68 GTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIK 127
GT LL+ A K + F+H ST D+ +Y + E+ ET
Sbjct: 104 GTYTLLEAARK-YGVKRFVHIST-----DE------VYGDLLDDG------EF--TET-- 141
Query: 128 QLTPKILGPHPNSYTFTKRLTETLVDEY-KT-KLPVVIVRPSIVLPSFQEP 176
+P L P + Y+ +K + LV Y +T LPVVI R S +Q P
Sbjct: 142 --SP--LAPT-SPYSASKAAADLLVRAYHRTYGLPVVITRCSNNYGPYQFP 187
>gnl|CDD|224013 COG1088, RfbB, dTDP-D-glucose 4,6-dehydratase [Cell envelope
biogenesis, outer membrane].
Length = 340
Score = 36.8 bits (86), Expect = 0.006
Identities = 41/163 (25%), Positives = 62/163 (38%), Gaps = 42/163 (25%)
Query: 14 SRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKENVAANTR 67
R ++GDI L D L + + V + AA S+ A + N
Sbjct: 51 PRYRFVQGDICDREL----VDRLFKEYQPDAVVHFAAESHVDRSIDGPAPFIQT---NVV 103
Query: 68 GTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIK 127
GT LL+ A K F H ST +++Y +DD+
Sbjct: 104 GTYTLLEAARKYWGKFRFHHIST-----------DEVYGD-----------LGLDDDAFT 141
Query: 128 QLTPKILGPHPNS-YTFTKRLTETLVDEY-KT-KLPVVIVRPS 167
+ TP +P+S Y+ +K ++ LV Y +T LP I R S
Sbjct: 142 ETTPY----NPSSPYSASKAASDLLVRAYVRTYGLPATITRCS 180
>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 = 35.1 bits (81), Expect = 0.023
Identities = 48/217 (22%), Positives = 70/217 (32%), Gaps = 50/217 (23%)
Query: 16 LHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGTQRLLDI 75
+ ++GDI N D+ VF+ AA + L N GTQ +LD
Sbjct: 47 IEFLKGDITDRN------DVEQALSGADCVFHTAAIVPLAGPRDLYWEVNVGGTQNVLDA 100
Query: 76 --ALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIKQLTPKI 133
++K V S F Q +I DET P
Sbjct: 101 CQRCGVQKFVYTSSSSVIF--GGQ---------------NIHNG-----DET----LPY- 133
Query: 134 LGPHPNSYTFTKRLTETLVDEYKTK--LPVVIVRPSIVL-PSFQEPVPGWVDS-LNGPVG 189
+ Y TK + E +V E + L +RP+ + P Q VP + G V
Sbjct: 134 PPLDSDMYAETKAIAEIIVLEANGRDDLLTCALRPAGIFGPGDQGLVPILFEWAEKGLVK 193
Query: 190 VLVASGKGVVRSMMCGAEFVAEVVPVDIAINGVILAA 226
+ G +V + V + ILAA
Sbjct: 194 FVFGRGNNLV-----------DFTYVHNLAHAHILAA 219
>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 = 34.6 bits (80), Expect = 0.025
Identities = 29/132 (21%), Positives = 51/132 (38%), Gaps = 21/132 (15%)
Query: 1 VFERLRKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKL 54
V R R+ R+ EGD+ + + L+ + + V + AA S +
Sbjct: 27 VLGRRRRSESLNTGRIRFHEGDLTDPDALER----LLAEVQPDAVIHLAAQSGVGASFED 82
Query: 55 EAELKENVAANTRGTQRLLDIALKMKKLVAFIHFSTA----FCHPDQKVLEEKLYPSPVS 110
A+ + AN GT RLL+ A + + F+ S++ + E P+S
Sbjct: 83 PADF---IRANVLGTLRLLE-AARRAGVKRFVFASSSEVYGDVADPP--ITEDTPLGPLS 136
Query: 111 PHDIM-RAMEWM 121
P+ A E +
Sbjct: 137 PYAAAKLAAERL 148
>gnl|CDD|234212 TIGR03443, alpha_am_amid, L-aminoadipate-semialdehyde dehydrogenase.
Members of this protein family are
L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31),
product of the LYS2 gene. It is also called
alpha-aminoadipate reductase. In fungi, lysine is
synthesized via aminoadipate. Currently, all members of
this family are fungal.
Length = 1389
Score = 34.7 bits (80), Expect = 0.041
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 2 FERLRKECPAQ-------LSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVF-NGA 49
ERLRK SR+ ++ GD+ + G+ D L EV V+ NGA
Sbjct: 1015 LERLRKTGTTYGIWDEEWASRIEVVLGDLSKEKFGLSDEKWSDLTNEVDVIIHNGA 1070
>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 = 32.0 bits (73), Expect = 0.24
Identities = 36/163 (22%), Positives = 56/163 (34%), Gaps = 37/163 (22%)
Query: 11 AQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVA---ANTR 67
R ++GDI L L + + V + AA ++ + A N
Sbjct: 47 EDNPRYRFVKGDIGDREL----VSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIETNVV 102
Query: 68 GTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIK 127
GT LL+ K F H ST + D + +
Sbjct: 103 GTYTLLEAVRKYWHEFRFHHISTDEVYGDLE-----------------------KGDAFT 139
Query: 128 QLTPKILGPHPNS-YTFTKRLTETLVDEY-KT-KLPVVIVRPS 167
+ TP P+S Y+ +K ++ LV Y +T LP +I R S
Sbjct: 140 ETTPL----APSSPYSASKAASDHLVRAYHRTYGLPALITRCS 178
>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 = 30.7 bits (70), Expect = 0.54
Identities = 13/50 (26%), Positives = 17/50 (34%), Gaps = 6/50 (12%)
Query: 126 IKQLTPKILGPHPN-----SYTFTKRLTETLVDEYKTKLPVVIVRPSIVL 170
I + TP Y KR E ++ E P IVRP +
Sbjct: 109 ITESTPLREPDAVGLSDPWDYGRGKRAAEDVLIEA-AAFPYTIVRPPYIY 157
>gnl|CDD|215146 PLN02260, PLN02260, probable rhamnose biosynthetic enzyme.
Length = 668
Score = 30.9 bits (70), Expect = 0.55
Identities = 41/155 (26%), Positives = 59/155 (38%), Gaps = 39/155 (25%)
Query: 19 IEGDILQANLGIKDSDLLMLQEEVSVVFNGAA------SLKLEAELKENVAANTRGTQRL 72
++GDI A+L + L++ E + + + AA S E +N N GT L
Sbjct: 62 VKGDIASADL----VNYLLITEGIDTIMHFAAQTHVDNSFGNSFEFTKN---NIYGTHVL 114
Query: 73 LDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIKQLTPK 132
L+ ++ FIH ST +V E + V H+ QL P
Sbjct: 115 LEACKVTGQIRRFIHVST------DEVYGETDEDADVGNHE------------ASQLLPT 156
Query: 133 ILGPHPNSYTFTKRLTETLVDEYKTK--LPVVIVR 165
N Y+ TK E LV Y LPV+ R
Sbjct: 157 ------NPYSATKAGAEMLVMAYGRSYGLPVITTR 185
>gnl|CDD|187660 cd08957, WbmH_like_SDR_e, Bordetella bronchiseptica enzymes WbmH
and WbmG-like, extended (e) SDRs. Bordetella
bronchiseptica enzymes WbmH and WbmG, and related
proteins. This subgroup exhibits the active site tetrad
and NAD-binding motif of the extended SDR family. It has
been proposed that the active site in Bordetella WbmG
and WbmH cannot function as an epimerase, and that it
plays a role in O-antigen synthesis pathway from
UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid.
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 = 307
Score = 29.4 bits (66), Expect = 1.4
Identities = 24/106 (22%), Positives = 44/106 (41%), Gaps = 5/106 (4%)
Query: 6 RKECPAQLSRLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAAN 65
R+E L ++EG I A+ + D + + V + AA+ K + E+ N
Sbjct: 37 RREHLPDHPNLTVVEGSI--ADKALVDKLFGDFKPDA--VVHTAAAYKDPDDWYEDTLTN 92
Query: 66 TRGTQRLLDIALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSP 111
G ++ A K + I+F TA C+ + + + P +P
Sbjct: 93 VVGGANVVQAA-KKAGVKRLIYFQTALCYGLKPMQQPIRLDHPRAP 137
>gnl|CDD|181206 PRK08042, PRK08042, formate hydrogenlyase subunit 3; Reviewed.
Length = 593
Score = 29.8 bits (67), Expect = 1.5
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 170 LPSFQEPVPGWVDSLNGPVGVLVASGKGVVRSMMCGAEFVAEVVPV 215
L SFQ+ + GW+ + G VG L + G +++ GA V+ + +
Sbjct: 8 LFSFQKALSGWIAGIGGAVGSLYTAAAGF--TVLTGAVGVSGALSL 51
>gnl|CDD|211680 TIGR01664, DNA-3'-Pase, DNA 3'-phosphatase. This model represents
a family of proteins and protein domains which catalyze
the dephosphorylation of DNA 3'-phosphates. It is
believed that this activity is important for the repair
of single-strand breaks in DNA caused by radiation or
oxidative damage. This domain is often (TIGR01663), but
not always linked to a DNA 5'-kinase domain. The central
phosphatase domain is a member of the IIIA subfamily
(TIGR01662) of the haloacid dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases. As is
common in this superfamily, the enzyme is magnesium
dependent. A difference between this enzyme and other
HAD-superfamily phosphatases is in the third conserved
catalytic motif which usually contains two conserved
aspartate residues believed to be involved in binding
the magnesium ion. Here, the second aspartate is usually
replaced by an arginine residue which may indicate an
interaction with the phosphate backbone of the
substrate. Alternatively, there is an additional
conserved aspartate downstream of the ususal site which
may indicate slightly different fold in this region.
Length = 166
Score = 29.0 bits (65), Expect = 1.6
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 163 IVRPSIVLPSFQEPVPGWVDSLNGPVGVLVASGKGVVRSMMCGA-EFVAEVVPVDIAIN 220
I R + SF+ + +++ L P+ VL A+ G+ R M G E++ I +
Sbjct: 70 IGRGKLSAESFKNKIEAFLEKLKVPIQVLAATHAGLYRKPMTGMWEYLQSQYNSPIKMT 128
>gnl|CDD|220311 pfam09609, Cas_GSU0054, CRISPR-associated protein, GSU0054 family
(Cas_GSU0054). This entry represents a rare
CRISPR-associated protein. So far, members are found in
Geobacter sulfurreducens and in two unpublished genomes:
Gemmata obscuriglobus and Actinomyces naeslundii.
CRISPR-associated proteins typically are found near
CRISPR repeats and other CRISPR-associated proteins,
have low levels of sequence identify, have sequence
relationships that suggest lateral transfer, and show
some sequence similarity to DNA-active proteins such as
helicases and repair proteins.
Length = 519
Score = 29.6 bits (66), Expect = 1.6
Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 125 TIKQLTPKILGPHPNSYTFTKRLTETLVDEYKTKL-------PVVIVRPSIV-----LPS 172
T +TP IL +PN + ++L L L PV + SI PS
Sbjct: 396 TWASVTPVILDRYPNCAPYARKLHLMLEYGVLPDLSGMQIDGPVSQLAFSIDRAGLPQPS 455
Query: 173 FQEPVPGW 180
EP+P +
Sbjct: 456 SIEPLPAY 463
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 29.2 bits (66), Expect = 1.9
Identities = 30/171 (17%), Positives = 63/171 (36%), Gaps = 24/171 (14%)
Query: 80 KKLVAF-IHFSTAFCHPDQKV--LEEKLYPSPVSPHDIMRAMEWMDD-------ETIKQL 129
+ +V + S+ +K+ +E L PV +++R +EW D + ++
Sbjct: 40 RLVVGIVVELSSESDVDGRKLKEIERVLDTEPVLTPELLRLIEWAADYYLSPLGDVLRLA 99
Query: 130 TPKIL-------GPHPNSYTFTKRLTETLVDEYKTKLPVVIVRPSIVLPSFQEPVPGWVD 182
P +L Y T+R L D + K + + VL + +
Sbjct: 100 LPVLLRQGYAKPSLPVLFYRLTERGRAALPDLKRAK------KQARVLEALLQGGEWTRS 153
Query: 183 SLNGPVGVLVASGKGVVRSMMCGAEFVAEVVPV-DIAINGVILAAYNRDQK 232
+L GV ++ KG+ + + + + V + A N++Q+
Sbjct: 154 ALAHAAGVSLSVLKGLEKKGLIEIIELEPPLVVAPPDPSLSEWLALNQEQQ 204
>gnl|CDD|227068 COG4724, COG4724, Endo-beta-N-acetylglucosaminidase D [Carbohydrate
transport and metabolism].
Length = 553
Score = 28.7 bits (64), Expect = 3.1
Identities = 19/63 (30%), Positives = 24/63 (38%), Gaps = 12/63 (19%)
Query: 46 FNGAASLKLEAELKENVAANTRGTQRLLDIALKMKKLVAF---------IHFSTAFCHPD 96
+NG SLK +L N R L+I K K VA + FST PD
Sbjct: 438 YNGGNSLKFSGDLAGKTDQNVRLYSTKLEITEKTKLRVAHKGGKGLKVYMAFSTT---PD 494
Query: 97 QKV 99
+
Sbjct: 495 KFD 497
>gnl|CDD|114595 pfam05878, Phyto_Pns9_10, Phytoreovirus nonstructural protein
Pns9/Pns10. This family consists of the Phytoreovirus
nonstructural proteins Pns9 and Pns10. The function of
this family is unknown.
Length = 312
Score = 28.4 bits (63), Expect = 3.2
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 27 NLGIKDSDLLMLQEEVSVVFNGAASLKLEAE-LKENVAANTRGTQRLLDI-ALKMKKLVA 84
NLG D + LM+ + F+ S L+ E + V G + D L+ + +
Sbjct: 108 NLGFADDEFLMINDS----FSYMMSSFLDEEGVHSAVDMEL-GIHNIEDRYVLRTESIFY 162
Query: 85 FIH 87
FIH
Sbjct: 163 FIH 165
>gnl|CDD|181632 PRK09060, PRK09060, dihydroorotase; Validated.
Length = 444
Score = 28.3 bits (64), Expect = 3.7
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 67 RGTQRLLDIALKMKKLVAFIHFSTA 91
T+RL+ +A + + + +H STA
Sbjct: 214 LATRRLVRLARETGRRIHVLHVSTA 238
>gnl|CDD|234708 PRK00274, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1
family protein; Reviewed.
Length = 272
Score = 27.8 bits (63), Expect = 4.9
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 3 ERLRKECPAQLSRLHIIEGDILQANL 28
L + L IIEGD L+ +L
Sbjct: 78 PILAE--TFAEDNLTIIEGDALKVDL 101
>gnl|CDD|221514 pfam12297, EVC2_like, Ellis van Creveld protein 2 like protein.
This family of proteins is found in eukaryotes. Proteins
in this family are typically between 571 and 1310 amino
acids in length. There are two conserved sequence
motifs: LPA and ELH. EVC2 is implicated in Ellis van
Creveld chondrodysplastic dwarfism in humans. Mutations
in this protein can give rise to this congenital
condition. LIMBIN is a protein which shares around 80%
sequence homology with EVC2 and it is implicated in a
similar condition in bovine chondrodysplastic dwarfism.
Length = 429
Score = 27.9 bits (62), Expect = 5.7
Identities = 23/99 (23%), Positives = 35/99 (35%), Gaps = 18/99 (18%)
Query: 3 ERLRKECPAQLSRLHIIEGDILQANLGIK---DSDLLMLQEEV-------SVVFNGAASL 52
ER EC + L LH +E + LQ +L ++ D Q V S+ F S
Sbjct: 257 EREAVECSSLLDTLHGLEQEHLQRSLLLQQEEDFAKAHRQLAVFQRVELHSIFFTQLKSA 316
Query: 53 KLEAELKENVAA--------NTRGTQRLLDIALKMKKLV 83
+ ELK A + L+D ++
Sbjct: 317 TFKGELKPEEAKSLLQEYSKIQETIEELMDFFQASQRYH 355
>gnl|CDD|233909 TIGR02520, pilus_B_mal_scr, type IVB pilus formation outer membrane
protein, R64 PilN family. Several related protein
families encode outer membrane pore proteins for type II
secretion, type III secretion, and type IV pilus
formation. This protein family appears to encode a
secretin for pilus formation, although it is quite
different from PilQ. Members include the PilN
lipoprotein of the plasmid R64 thin pilus, a type IV
pilus. Scoring between the trusted and noise cutoffs are
examples of bundle-forming pilus B (bfpB) [Cell
envelope, Surface structures, Protein fate, Protein and
peptide secretion and trafficking].
Length = 497
Score = 27.9 bits (62), Expect = 5.8
Identities = 10/46 (21%), Positives = 15/46 (32%), Gaps = 1/46 (2%)
Query: 157 TKLPVVIVRPSIVLPSFQEPVPGWVDSLNGPVGVLVASGKGVVRSM 202
+PVVI P + G V + VL +G +
Sbjct: 50 CGVPVVIA-PDAMSALSGSSSQGGVGAARAIPAVLPRPDEGGRPPL 94
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially conserves
the characteristic active site tetrad and NAD-binding
motif of the extended SDRs, and has been identified as
possible UDP-glucose 4-epimerase (aka UDP-galactose
4-epimerase), a homodimeric member of the extended SDR
family. UDP-glucose 4-epimerase catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
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 = 300
Score = 27.3 bits (61), Expect = 6.2
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 2/57 (3%)
Query: 60 ENVAANTRGTQRLLD--IALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDI 114
++ N T +LL+ A + K++ T + P+Q + E P+S + I
Sbjct: 84 LDIQTNVAPTVQLLEACAAAGIGKIIFASSGGTVYGVPEQLPISESDPTLPISSYGI 140
>gnl|CDD|219952 pfam08645, PNK3P, Polynucleotide kinase 3 phosphatase.
Polynucleotide kinase 3 phosphatases play a role in the
repair of single breaks in DNA induced by DNA-damaging
agents such as gamma radiation and camptothecin.
Length = 158
Score = 26.8 bits (60), Expect = 6.4
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 170 LPSFQEPVPGWVDSLNGPVGVLVASGKGVVR 200
SF+ + + L+ P+ V A+ K R
Sbjct: 65 AESFKNKIESILKKLDVPLQVYAATKKDKYR 95
>gnl|CDD|173816 cd07491, Peptidases_S8_7, Peptidase S8 family domain,
uncharacterized subfamily 7. This family is a member of
the Peptidases S8 or Subtilases serine endo- and
exo-peptidase clan. They have an Asp/His/Ser catalytic
triad similar to that found in trypsin-like proteases,
but do not share their three-dimensional structure and
are not homologous to trypsin. The stability of
subtilases may be enhanced by calcium, some members have
been shown to bind up to 4 ions via binding sites with
different affinity. Some members of this clan contain
disulfide bonds. These enzymes can be intra- and
extracellular, some function at extreme temperatures and
pH values.
Length = 247
Score = 27.3 bits (61), Expect = 6.7
Identities = 12/44 (27%), Positives = 14/44 (31%), Gaps = 10/44 (22%)
Query: 92 FC-HPDQKVLEEKLYPSPVSPHDIMR---------AMEWMDDET 125
FC DQ YP P + I R A + DE
Sbjct: 140 FCSASDQGAFTGDTYPPPAARDRIFRIGAADEDGGADAPVGDED 183
>gnl|CDD|163642 cd07399, MPP_YvnB, Bacillus subtilis YvnB and related proteins,
metallophosphatase domain. YvnB (BSU35040) is an
uncharacterized Bacillus subtilis protein with a
metallophosphatase domain. This family includes
bacterial and eukaryotic proteins similar to YvnB. YvnB
belongs to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 214
Score = 26.9 bits (60), Expect = 7.3
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 112 HDIMRAMEW-MDDETIKQLTPKILGPHPN 139
HD++ A+E+ DE + Q ++L HP+
Sbjct: 79 HDLVLALEFGPRDEVL-QWANEVLKKHPD 106
>gnl|CDD|226727 COG4277, COG4277, Predicted DNA-binding protein with the
Helix-hairpin-helix motif [General function prediction
only].
Length = 404
Score = 27.1 bits (60), Expect = 9.4
Identities = 12/50 (24%), Positives = 22/50 (44%)
Query: 103 KLYPSPVSPHDIMRAMEWMDDETIKQLTPKILGPHPNSYTFTKRLTETLV 152
KL P DI+R+M W+ + ++ K H + + T+ +V
Sbjct: 175 KLLAPEKDPTDILRSMGWIRLKILENAEDKRRKRHTPEFAPAGQSTQMIV 224
>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 = 26.6 bits (59), Expect = 9.4
Identities = 28/157 (17%), Positives = 50/157 (31%), Gaps = 46/157 (29%)
Query: 15 RLHIIEGDILQANLGIKDSDLLMLQEEVSVVFNGAASLKLEAELKENVAANTRGTQRLLD 74
+ ++EGD+ + +Q V+ A + ++ + GT+ +L+
Sbjct: 42 PVAVVEGDLRDLDSLSDA-----VQGVDVVIHLAGAPR----DTRDFCEVDVEGTRNVLE 92
Query: 75 IALKMKKLVAFIHFSTAFCHPDQKVLEEKLYPSPVSPHDIMRAMEWMDDETIKQLTPKIL 134
A K + FI S+ Y +
Sbjct: 93 -AAKEAGVKHFIFISSLG-----------AYGDLHEETE--------------------- 119
Query: 135 GPHPNSYTF-TKRLTETLVDEYKTKLPVVIVRPSIVL 170
P P+S K TE ++ E LP IVRP ++
Sbjct: 120 -PSPSSPYLAVKAKTEAVLREAS--LPYTIVRPGVIY 153
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.394
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,109,176
Number of extensions: 1174999
Number of successful extensions: 1094
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1079
Number of HSP's successfully gapped: 54
Length of query: 232
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 138
Effective length of database: 6,768,326
Effective search space: 934028988
Effective search space used: 934028988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.5 bits)