RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11600
(277 letters)
>gnl|CDD|240303 PTZ00170, PTZ00170, D-ribulose-5-phosphate 3-epimerase;
Provisional.
Length = 228
Score = 272 bits (698), Expect = 2e-92
Identities = 106/234 (45%), Positives = 141/234 (60%), Gaps = 44/234 (18%)
Query: 1 MSHVQCMIGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRN 60
++ +I PSIL +D S L E+Q++L GAD+LH+DVMDG FVPNL+FG PVVK LR
Sbjct: 2 KQPLKAIIAPSILAADFSKLADEAQDVLSGGADWLHVDVMDGHFVPNLSFGPPVVKSLRK 61
Query: 61 KIPKAFFETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQ 120
+P F + H+MV NP++W++ A A Q+TFH+E ++ P+
Sbjct: 62 HLPNTFLDCHLMVSNPEKWVDDFAKAGASQFTFHIEATEDDPK----------------- 104
Query: 121 DWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESA-- 178
V R+I+EAGMKVG+AIKPKTPV+V+ I++
Sbjct: 105 -------------------------AVARKIREAGMKVGVAIKPKTPVEVLFPLIDTDLV 139
Query: 179 DLVLIMTVEPGFGGQKFMQDMMPKVKWLRENYPTLNIEVDGGVGPNTIDECAKC 232
D+VL+MTVEPGFGGQ FM DMMPKV+ LR+ YP LNI+VDGG+ TID A
Sbjct: 140 DMVLVMTVEPGFGGQSFMHDMMPKVRELRKRYPHLNIQVDGGINLETIDIAADA 193
>gnl|CDD|238244 cd00429, RPE, Ribulose-5-phosphate 3-epimerase (RPE). This enzyme
catalyses the interconversion of D-ribulose 5-phosphate
(Ru5P) into D-xylulose 5-phosphate, as part of the
Calvin cycle (reductive pentose phosphate pathway) in
chloroplasts and in the oxidative pentose phosphate
pathway. In the Calvin cycle Ru5P is phosphorylated by
phosphoribulose kinase to ribulose-1,5-bisphosphate,
which in turn is used by RubisCO
(ribulose-1,5-bisphosphate carboxylase/oxygenase) to
incorporate CO2 as the central step in carbohydrate
synthesis.
Length = 211
Score = 266 bits (682), Expect = 3e-90
Identities = 92/230 (40%), Positives = 126/230 (54%), Gaps = 48/230 (20%)
Query: 7 MIGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAF 66
I PSIL++D +NL E + L ++GAD++H+DVMDG FVPNLTFG PVVK LR
Sbjct: 1 KIAPSILSADFANLGEELKRLEEAGADWIHIDVMDGHFVPNLTFGPPVVKALRKHT-DLP 59
Query: 67 FETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPM 126
+ H+MV+NP+ +IE
Sbjct: 60 LDVHLMVENPE-------------------------------------------RYIEAF 76
Query: 127 ADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTV 186
A A D TFH E D++ + I+ IKE GMK G+A+ P TPV+V+ Y++ DLVL+M+V
Sbjct: 77 AKAGADIITFHAEATDHLHRTIQLIKELGMKAGVALNPGTPVEVLEPYLDEVDLVLVMSV 136
Query: 187 EPGFGGQKFMQDMMPKVKWLRENYP----TLNIEVDGGVGPNTIDECAKC 232
PGFGGQKF+ +++ K++ LRE P L IEVDGG+ TI A+
Sbjct: 137 NPGFGGQKFIPEVLEKIRKLRELIPENNLNLLIEVDGGINLETIPLLAEA 186
>gnl|CDD|215192 PLN02334, PLN02334, ribulose-phosphate 3-epimerase.
Length = 229
Score = 238 bits (610), Expect = 3e-79
Identities = 96/225 (42%), Positives = 131/225 (58%), Gaps = 44/225 (19%)
Query: 8 IGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAFF 67
I PSIL++D +NL E++ +LD+GAD+LH+DVMDG FVPNLT G PVVK LR K A
Sbjct: 10 IAPSILSADFANLAEEAKRVLDAGADWLHVDVMDGHFVPNLTIGPPVVKALR-KHTDAPL 68
Query: 68 ETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPMA 127
+ H+MV NP+ ++ A A +TFH+E
Sbjct: 69 DCHLMVTNPEDYVPDFAKAGASIFTFHIEQA----------------------------- 99
Query: 128 DANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESA--DLVLIMT 185
++ ++I+QIK AGMK G+ + P TPV+ + +E D+VL+M+
Sbjct: 100 ------------STIHLHRLIQQIKSAGMKAGVVLNPGTPVEAVEPVVEKGLVDMVLVMS 147
Query: 186 VEPGFGGQKFMQDMMPKVKWLRENYPTLNIEVDGGVGPNTIDECA 230
VEPGFGGQ F+ MM KV+ LR+ YP L+IEVDGGVGP+TID+ A
Sbjct: 148 VEPGFGGQSFIPSMMDKVRALRKKYPELDIEVDGGVGPSTIDKAA 192
>gnl|CDD|223114 COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate
transport and metabolism].
Length = 220
Score = 221 bits (565), Expect = 2e-72
Identities = 85/230 (36%), Positives = 120/230 (52%), Gaps = 49/230 (21%)
Query: 7 MIGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAF 66
I PSIL++D + L E + L +GAD +H+DVMDG FVPN+TFG PVVK LR KI
Sbjct: 5 KIAPSILSADFARLGEELKALEAAGADLIHIDVMDGHFVPNITFGPPVVKALR-KITDLP 63
Query: 67 FETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPM 126
+ H+MV+NP ++IE A A D I
Sbjct: 64 LDVHLMVENPDRYIEAFAKAGA--------------------------------DII--- 88
Query: 127 ADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTV 186
TFH E +++ + I+ IKE G+K GL + P TP++ + ++ DLVL+M+V
Sbjct: 89 --------TFHAEATEHIHRTIQLIKELGVKAGLVLNPATPLEALEPVLDDVDLVLLMSV 140
Query: 187 EPGFGGQKFMQDMMPKV----KWLRENYPTLNIEVDGGVGPNTIDECAKC 232
PGFGGQKF+ +++ K+ + E L IEVDGG+ TI + A
Sbjct: 141 NPGFGGQKFIPEVLEKIRELRAMIDERLDIL-IEVDGGINLETIKQLAAA 189
>gnl|CDD|235515 PRK05581, PRK05581, ribulose-phosphate 3-epimerase; Validated.
Length = 220
Score = 221 bits (565), Expect = 2e-72
Identities = 82/230 (35%), Positives = 126/230 (54%), Gaps = 48/230 (20%)
Query: 7 MIGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAF 66
+I PSIL++D + L E + + +GAD++H+DVMDG FVPNLT G PVV+ +R K+ K
Sbjct: 5 LIAPSILSADFARLGEEVKAVEAAGADWIHVDVMDGHFVPNLTIGPPVVEAIR-KVTKLP 63
Query: 67 FETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPM 126
+ H+MV+NP +++ A A D TFHVE ++ I
Sbjct: 64 LDVHLMVENPDRYVPDFAKAGADIITFHVEASEH-------IHR---------------- 100
Query: 127 ADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTV 186
+++ IK AG+K GL + P TP++ + + ++ DLVL+M+V
Sbjct: 101 --------------------LLQLIKSAGIKAGLVLNPATPLEPLEDVLDLLDLVLLMSV 140
Query: 187 EPGFGGQKFMQDMMPKVKWLR----ENYPTLNIEVDGGVGPNTIDECAKC 232
PGFGGQKF+ +++ K++ LR E + IEVDGG+ + I ECA+
Sbjct: 141 NPGFGGQKFIPEVLEKIRELRKLIDERGLDILIEVDGGINADNIKECAEA 190
>gnl|CDD|216142 pfam00834, Ribul_P_3_epim, Ribulose-phosphate 3 epimerase family.
This enzyme catalyzes the conversion of D-ribulose
5-phosphate into D-xylulose 5-phosphate.
Length = 201
Score = 190 bits (486), Expect = 9e-61
Identities = 81/228 (35%), Positives = 119/228 (52%), Gaps = 48/228 (21%)
Query: 8 IGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAFF 67
I PS+L++D ++L E + + ++GAD+LH+DVMDG FVPNLT G VV+ LR + +
Sbjct: 2 IAPSLLSADFAHLGEEIKAVENAGADWLHVDVMDGHFVPNLTIGPLVVEALRP-LTELPL 60
Query: 68 ETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPMA 127
+ H+MV+ P + I A+A D I
Sbjct: 61 DVHLMVEEPDRIIPDFAEAGAD--------------------------------II---- 84
Query: 128 DANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTVE 187
+FH E D+ + I+ IKEAG K GL + P TP+D I ++ DLVL+M+V
Sbjct: 85 -------SFHAEASDHPHRTIQLIKEAGAKAGLVLNPATPLDAIEYLLDDLDLVLLMSVN 137
Query: 188 PGFGGQKFMQDMMPKVKWLR----ENYPTLNIEVDGGVGPNTIDECAK 231
PGFGGQ F+ ++PK++ +R E IEVDGGV + I + A+
Sbjct: 138 PGFGGQSFIPSVLPKIRKVRKMIDEGGLDTLIEVDGGVNLDNIPQIAE 185
>gnl|CDD|130231 TIGR01163, rpe, ribulose-phosphate 3-epimerase. This family
consists of Ribulose-phosphate 3-epimerase, also known
as pentose-5-phosphate 3-epimerase (PPE). PPE converts
D-ribulose 5-phosphate into D-xylulose 5-phosphate in
Calvin's reductive pentose phosphate cycle. It has been
found in a wide range of bacteria, archebacteria, fungi
and plants [Energy metabolism, Pentose phosphate
pathway].
Length = 210
Score = 185 bits (472), Expect = 1e-58
Identities = 81/229 (35%), Positives = 122/229 (53%), Gaps = 50/229 (21%)
Query: 8 IGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAFF 67
I PSIL++D + L E + + ++GAD++H+DVMDG FVPNLTFG PV++ LR K
Sbjct: 1 IAPSILSADFARLGEEVKAVEEAGADWIHVDVMDGHFVPNLTFGPPVLEALR-KYTDLPI 59
Query: 68 ETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPMA 127
+ H+MV+NP ++IE A EAG D I
Sbjct: 60 DVHLMVENPDRYIEDFA-------------------------EAG-------ADII---- 83
Query: 128 DANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTVE 187
T H E +++ ++++ IK+ G K G+ + P TP++ + + DLVL+M+V
Sbjct: 84 -------TVHPEASEHIHRLLQLIKDLGAKAGIVLNPATPLEFLEYVLPDVDLVLLMSVN 136
Query: 188 PGFGGQKFMQDMMPKVKWLRE-----NYPTLNIEVDGGVGPNTIDECAK 231
PGFGGQKF+ D + K++ +R+ L IEVDGGV + E A+
Sbjct: 137 PGFGGQKFIPDTLEKIREVRKMIDENGLSIL-IEVDGGVNDDNARELAE 184
>gnl|CDD|236616 PRK09722, PRK09722, allulose-6-phosphate 3-epimerase; Provisional.
Length = 229
Score = 143 bits (362), Expect = 7e-42
Identities = 75/224 (33%), Positives = 105/224 (46%), Gaps = 50/224 (22%)
Query: 7 MIGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAF 66
I PS++ DL E L+S ADY H+D+MDG FVPNLT V ++ K+
Sbjct: 4 KISPSLMCMDLLKF-KEQIEFLNSKADYFHIDIMDGHFVPNLTLSPFFVSQVK-KLASKP 61
Query: 67 FETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPM 126
+ H+MV +PQ +I+ +ADA D T H E ++ Q R
Sbjct: 62 LDVHLMVTDPQDYIDQLADAGADFITLHPETING--QAFR-------------------- 99
Query: 127 ADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTV 186
+I +I+ AGMKVGL + P+TPV+ I YI D + +MTV
Sbjct: 100 --------------------LIDEIRRAGMKVGLVLNPETPVESIKYYIHLLDKITVMTV 139
Query: 187 EPGFGGQKFMQDMMPKVKWLRE-----NYPTLNIEVDGGVGPNT 225
+PGF GQ F+ +M+ K+ L+ L IEVDG T
Sbjct: 140 DPGFAGQPFIPEMLDKIAELKALRERNGLEYL-IEVDGSCNQKT 182
>gnl|CDD|136958 PRK08745, PRK08745, ribulose-phosphate 3-epimerase; Provisional.
Length = 223
Score = 132 bits (332), Expect = 1e-37
Identities = 76/229 (33%), Positives = 109/229 (47%), Gaps = 47/229 (20%)
Query: 6 CMIGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKA 65
I PSIL++D + L E N+L +GAD++H DVMD +VPNLT G V + LR A
Sbjct: 4 TAIAPSILSADFARLGEEVDNVLKAGADWVHFDVMDNHYVPNLTIGPMVCQALRKHGITA 63
Query: 66 FFETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEP 125
+ H+MV EPVD + +
Sbjct: 64 PIDVHLMV----------------------EPVDRI---------------------VPD 80
Query: 126 MADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMT 185
ADA +FH E +V + I+ IK G + GL + P TPVD++ + DLVL+M+
Sbjct: 81 FADAGATTISFHPEASRHVHRTIQLIKSHGCQAGLVLNPATPVDILDWVLPELDLVLVMS 140
Query: 186 VEPGFGGQKFMQDMMPKVKWLRENYPTLN----IEVDGGVGPNTIDECA 230
V PGFGGQ F+ + K++ +R+ L +E+DGGV + I A
Sbjct: 141 VNPGFGGQAFIPSALDKLRAIRKKIDALGKPIRLEIDGGVKADNIGAIA 189
>gnl|CDD|181575 PRK08883, PRK08883, ribulose-phosphate 3-epimerase; Provisional.
Length = 220
Score = 126 bits (318), Expect = 1e-35
Identities = 73/229 (31%), Positives = 115/229 (50%), Gaps = 47/229 (20%)
Query: 7 MIGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAF 66
+I PSIL++D + L + + +L +GAD +H DVMD +VPNLTFG P+ K LR+ A
Sbjct: 1 LIAPSILSADFARLGEDVEKVLAAGADVVHFDVMDNHYVPNLTFGAPICKALRDYGITAP 60
Query: 67 FETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPM 126
+ H+MV+ PVD + I
Sbjct: 61 IDVHLMVK----------------------PVDRI---------------------IPDF 77
Query: 127 ADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTV 186
A A TFHVE ++V + ++ IKE G + G+ + P TP+ + ++ DL+L+M+V
Sbjct: 78 AKAGASMITFHVEASEHVDRTLQLIKEHGCQAGVVLNPATPLHHLEYIMDKVDLILLMSV 137
Query: 187 EPGFGGQKFMQDMMPKVKWLRENYPT----LNIEVDGGVGPNTIDECAK 231
PGFGGQ F+ + K++ +R+ + +E+DGGV + I E A+
Sbjct: 138 NPGFGGQSFIPHTLDKLRAVRKMIDESGRDIRLEIDGGVKVDNIREIAE 186
>gnl|CDD|169179 PRK08005, PRK08005, epimerase; Validated.
Length = 210
Score = 88.9 bits (220), Expect = 2e-21
Identities = 56/212 (26%), Positives = 87/212 (41%), Gaps = 44/212 (20%)
Query: 10 PSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAFFET 69
PS+ ++D L D+ LHLD+ D +F+ N+TFG ++ + +
Sbjct: 5 PSLASADPLRYAEALTALHDAPLGSLHLDIEDTSFINNITFGMKTIQAVAQQTRHPL-SF 63
Query: 70 HMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPMADA 129
H+MV +PQ+W+ +A I+ WI
Sbjct: 64 HLMVSSPQRWLPWLA----------------------AIRPG----------WI------ 85
Query: 130 NVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTVEPG 189
H E V N +++ I+ G K GLA+ P TP+ D ++IMT EP
Sbjct: 86 -----FIHAESVQNPSEILADIRAIGAKAGLALNPATPLLPYRYLALQLDALMIMTSEPD 140
Query: 190 FGGQKFMQDMMPKVKWLRENYPTLNIEVDGGV 221
GQ+F+ M KV RE++P DGG+
Sbjct: 141 GRGQQFIAAMCEKVSQSREHFPAAECWADGGI 172
>gnl|CDD|169215 PRK08091, PRK08091, ribulose-phosphate 3-epimerase; Validated.
Length = 228
Score = 56.4 bits (136), Expect = 2e-09
Identities = 40/185 (21%), Positives = 70/185 (37%), Gaps = 46/185 (24%)
Query: 8 IGPSILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAFF 67
I IL S+ + L ++ LH D+ DG F P T G +K + P F
Sbjct: 15 ISVGILASNWLKFNETLTTLSENQLRLLHFDIADGQFSPFFTVGAIAIK----QFPTHCF 70
Query: 68 -ETHMMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPM 126
+ H+MV++ + + A D T VE ++ I + +
Sbjct: 71 KDVHLMVRDQFEVAKACVAAGADIVTLQVEQTHDLALTIEWLAK---------------- 114
Query: 127 ADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTV 186
Q T + +GL + P+TP+ ++ Y++ DL+ I+T+
Sbjct: 115 ------QKT-------------------TVLIGLCLCPETPISLLEPYLDQIDLIQILTL 149
Query: 187 EPGFG 191
+P G
Sbjct: 150 DPRTG 154
>gnl|CDD|172549 PRK14057, PRK14057, epimerase; Provisional.
Length = 254
Score = 47.0 bits (111), Expect = 4e-06
Identities = 51/196 (26%), Positives = 76/196 (38%), Gaps = 39/196 (19%)
Query: 12 ILNSDLSNLHSESQNLLDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAFF-ETH 70
IL LH Q L LHLD+MDG F P T G V ++P+ F + H
Sbjct: 26 ILAGQWIALHRYLQQLEALNQPLLHLDLMDGQFCPQFTVGPWAV----GQLPQTFIKDVH 81
Query: 71 MMVQNPQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPMADAN 130
+MV DQ+T V I E + + L W+
Sbjct: 82 LMV--------------ADQWTAAQACVKAGAHCITLQAEGDIHLHHTLS-WL------- 119
Query: 131 VDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTVEPGF 190
Q T V + VIR G+++ P TP+DVI + +++ ++ V PG+
Sbjct: 120 -GQQTVPV--IGGEMPVIR---------GISLCPATPLDVIIPILSDVEVIQLLAVNPGY 167
Query: 191 GGQKFMQDMMPKVKWL 206
G + D+ +V L
Sbjct: 168 GSKMRSSDLHERVAQL 183
>gnl|CDD|133121 cd06589, GH31, The enzymes of glycosyl hydrolase family 31 (GH31)
occur in prokaryotes, eukaryotes, and archaea with a
wide range of hydrolytic activities, including
alpha-glucosidase (glucoamylase and sucrase-isomaltase),
alpha-xylosidase, 6-alpha-glucosyltransferase,
3-alpha-isomaltosyltransferase and alpha-1,4-glucan
lyase. All GH31 enzymes cleave a terminal carbohydrate
moiety from a substrate that varies considerably in
size, depending on the enzyme, and may be either a
starch or a glycoprotein. In most cases, the pyranose
moiety recognized in subsite -1 of the substrate binding
site is an alpha-D-glucose, though some GH31 family
members show a preference for alpha-D-xylose. Several
GH31 enzymes can accommodate both glucose and xylose and
different levels of discrimination between the two have
been observed. Most characterized GH31 enzymes are
alpha-glucosidases. In mammals, GH31 members with
alpha-glucosidase activity are implicated in at least
three distinct biological processes. The lysosomal acid
alpha-glucosidase (GAA) is essential for glycogen
degradation and a deficiency or malfunction of this
enzyme causes glycogen storage disease II, also known as
pompe disease. In the endoplasmic reticulum,
alpha-glucosidase II catalyzes the second step in the
N-linked oligosaccharide processing pathway that
constitutes part of the quality control system for
glycoprotein folding and maturation. The intestinal
enzymes sucrase-isomaltase (SI) and maltase-glucoamylase
(MGAM) play key roles in the final stage of carbohydrate
digestion, making alpha-glucosidase inhibitors useful in
the treatment of type 2 diabetes. GH31
alpha-glycosidases are retaining enzymes that cleave
their substrates via an acid/base-catalyzed,
double-displacement mechanism involving a covalent
glycosyl-enzyme intermediate. Two aspartic acid residues
have been identified as the catalytic nucleophile and
the acid/base, respectively.
Length = 265
Score = 41.6 bits (98), Expect = 2e-04
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 5/75 (6%)
Query: 92 TFHVEPVDNVPQVIRQIKEAGMKV-GQVLQDWIEPMADAN-VDQYTFHVEPVDNVPQVIR 149
+ D V +VI ++E + + G VL D D + + N +I
Sbjct: 17 RYGYGDQDKVLEVIDGMRENDIPLDGFVLDDD---YTDGYGDFTFDWDAGKFPNPKSMID 73
Query: 150 QIKEAGMKVGLAIKP 164
++ + G+K+ L I P
Sbjct: 74 ELHDNGVKLVLWIDP 88
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 37.8 bits (89), Expect = 0.003
Identities = 45/204 (22%), Positives = 73/204 (35%), Gaps = 69/204 (33%)
Query: 63 PKAFFETHMMVQNPQQWIEPMADANVDQYTFHVE---PV--DNVPQ------VIRQIKEA 111
A F T ++ E + +A VD +E VPQ V+R I++
Sbjct: 12 EGATFSTEDKLE----IAEALDEAGVD----SIEVGSGASPKAVPQMEDDWEVLRAIRKL 63
Query: 112 GMKVG-QVL----QDWIEPMADANVDQYTFHV------------------EPVDNVPQVI 148
V Q L + IE +A VD + E ++N + I
Sbjct: 64 VPNVKLQALVRNREKGIERALEAGVD--EVRIFDSASETHSRKNLNKSREEDLENAEEAI 121
Query: 149 RQIKEAGMKVGLAI----KPKTPVDVIAEYIES-----ADLVLIM-TVEPGFGGQKFMQD 198
KEAG++V ++ KT + + E ++ AD + + TV G
Sbjct: 122 EAAKEAGLEVEGSLEDAFGCKTDPEYVLEVAKALEEAGADEISLKDTV----GL------ 171
Query: 199 MMPK-----VKWLRENYPTLNIEV 217
P+ VK LRE P + + +
Sbjct: 172 ATPEEVAELVKALREALPDVPLGL 195
>gnl|CDD|240283 PTZ00127, PTZ00127, cytochrome c oxidase assembly protein;
Provisional.
Length = 403
Score = 30.4 bits (69), Expect = 1.0
Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 7/47 (14%)
Query: 28 LDSGADYLHLDVMDGTFVPNLTFGHPVVKCLRNKIPKAFFETHMMVQ 74
D+G Y M G FVP+ K FFE +VQ
Sbjct: 280 NDAGLAYNTWPKMGGKFVPDDVH-------NFVPWYKNFFENTAVVQ 319
>gnl|CDD|200574 cd10950, CE4_BsYlxY_like, Putative catalytic NodB homology domain
of uncharacterized protein YlxY from Bacillus subtilis
and its bacterial homologs. The Bacillus subtilis
genome contains six polysaccharide deacetylase gene
homologs: pdaA, pdaB (previously known as ybaN), yheN,
yjeA, yxkH and ylxY. This family is represented by
Bacillus subtilis putative polysaccharide deacetylase
BsYlxY, encoded by the ylxY gene, which is a member of
the carbohydrate esterase 4 (CE4) superfamily. Although
its biological function still remains unknown, BsYlxY
shows high sequence homology to the catalytic domain of
Bacillus subtilis pdaB gene encoding a putative
polysaccharide deacetylase (BsPdaB), which is essential
for the maintenance of spores after the late stage of
sporulation and is highly conserved in spore-forming
bacteria. However, disruption of the ylxY gene in B.
subtilis did not cause any sporulation defect. Moreover,
the Asp residue in the classical His-His-Asp
zinc-binding motif of CE4 esterases is mutated to a Val
residue in this family. Other catalytically relevant
residues of CE4 esterases are also not conserved, which
suggest that members of this family may be inactive.
Length = 188
Score = 29.6 bits (67), Expect = 1.3
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 19/75 (25%)
Query: 102 PQVIRQIKEAGMKVGQVLQ-----DWIEPMADANVDQYTFHVEP------------VDNV 144
V++ E GM+ +L DW +P D VD+ + P V+ +
Sbjct: 110 DAVVKAAAELGMRT--ILWTVDTIDWKKPSPDVIVDRVLSKIHPGAIILMHPTESTVEAL 167
Query: 145 PQVIRQIKEAGMKVG 159
P++IRQ+KE G K+
Sbjct: 168 PEMIRQLKEKGYKIV 182
>gnl|CDD|182597 PRK10626, PRK10626, hypothetical protein; Provisional.
Length = 239
Score = 29.6 bits (67), Expect = 1.3
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 89 DQYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPM 126
D TFH + +D V +Q+ M G +LQD I M
Sbjct: 140 DGLTFHHQAIDQVEADGQQLVNQAM--GGILQDSINEM 175
>gnl|CDD|223235 COG0157, NadC, Nicotinate-nucleotide pyrophosphorylase [Coenzyme
metabolism].
Length = 280
Score = 29.5 bits (67), Expect = 1.6
Identities = 17/99 (17%), Positives = 40/99 (40%), Gaps = 14/99 (14%)
Query: 137 HVEPVDNVPQVIRQIKE-AGMKVGLAIKPKTPVDVIAEYIESADLVLI--MTVEPGFGGQ 193
H+ ++ + +R+ + A + ++ ++ + AD++++ M+ E
Sbjct: 167 HIAAAGSITEAVRRARAAAPFTKKIEVEVESLEEAEEALEAGADIIMLDNMSPE------ 220
Query: 194 KFMQDMMPKVKWLRENYPTLNIEVDGGVGPNTIDECAKC 232
++ VK L L +E GG+ I E A+
Sbjct: 221 ----ELKEAVKLLGLAGRAL-LEASGGITLENIREYAET 254
>gnl|CDD|169382 PRK08328, PRK08328, hypothetical protein; Provisional.
Length = 231
Score = 29.4 bits (66), Expect = 1.6
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 183 IMTVEPGFGGQKFMQDMMPKVKWLRENYPTLNIEVDGGVGPNTIDECAKCLTGFG 237
+ T+ PG K ++++ PKVK + +P L G +G E K +TG+G
Sbjct: 158 VTTIVPGK--TKRLREIFPKVKKKKGKFPILGATA-GVIGSIQAMEVIKLITGYG 209
>gnl|CDD|216667 pfam01729, QRPTase_C, Quinolinate phosphoribosyl transferase,
C-terminal domain. Quinolinate phosphoribosyl
transferase (QPRTase) or nicotinate-nucleotide
pyrophosphorylase EC:2.4.2.19 is involved in the de novo
synthesis of NAD in both prokaryotes and eukaryotes. It
catalyzes the reaction of quinolinic acid with
5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence
of Mg2+ to give rise to nicotinic acid mononucleotide
(NaMN), pyrophosphate and carbon dioxide. The QA
substrate is bound between the C-terminal domain of one
subunit, and the N-terminal domain of the other. The
C-terminal domain has a 7 beta-stranded TIM barrel-like
fold.
Length = 169
Score = 29.2 bits (66), Expect = 1.7
Identities = 18/96 (18%), Positives = 43/96 (44%), Gaps = 9/96 (9%)
Query: 137 HVEPVDNVPQVIRQIKE-AGMKVGLAIKPKTPVDVIAEYIESADLVLIMTVEPGFGGQKF 195
H+ ++ + +R+ +E A V + ++ + ++ AD++++ P
Sbjct: 59 HIAAAGSITEAVRRAREVAPFAVKIEVEVENLEELEEALEAGADIIMLDNFSPE------ 112
Query: 196 MQDMMPKVKWLRENYPTLNIEVDGGVGPNTIDECAK 231
++ V+ L E + +EV GG+ + + E AK
Sbjct: 113 --EVREAVEELDERAGRVLLEVSGGITLDNVLEYAK 146
Score = 28.8 bits (65), Expect = 2.3
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 243 QDMMPKVKWLRENYPTLNIEVDGGVGPNTIDECAK 277
+++ V+ L E + +EV GG+ + + E AK
Sbjct: 112 EEVREAVEELDERAGRVLLEVSGGITLDNVLEYAK 146
>gnl|CDD|216268 pfam01055, Glyco_hydro_31, Glycosyl hydrolases family 31. Glycosyl
hydrolases are key enzymes of carbohydrate metabolism.
Family 31 comprises of enzymes that are, or similar to,
alpha- galactosidases.
Length = 436
Score = 29.5 bits (67), Expect = 2.0
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 90 QYTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPMADANVDQYTFHVEPVDNVPQVIR 149
Q + + D V +V+ +EAG+ + + D I+ M +T+ E + +++
Sbjct: 34 QCRWGYKSEDEVREVVDGFREAGIPLDVIWLD-IDYMDGYRD--FTWDPERFPDPKEMLD 90
Query: 150 QIKEAGMKVGLAIKP 164
++ G+KV L I P
Sbjct: 91 ELHAKGIKVVLIIDP 105
>gnl|CDD|223995 COG1069, AraB, Ribulose kinase [Energy production and conversion].
Length = 544
Score = 29.2 bits (66), Expect = 2.3
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 229 CAKCLTGFGGQKFMQDMMPKVKWLRENYP 257
C L +GG+ + M+PK+ WL+ P
Sbjct: 126 CHPVLDYYGGKISPEMMIPKLMWLKREAP 154
>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 = 29.0 bits (66), Expect = 2.5
Identities = 20/69 (28%), Positives = 27/69 (39%), Gaps = 20/69 (28%)
Query: 144 VPQVIRQIKEAGMKVGLAIKPKTPVDV----IAEYI----ESADLVLIMTVEPGFGGQKF 195
+P +QI G PV V + + E+ LVL G GG+ F
Sbjct: 175 IPLFKKQIANGG-----------PVTVTHPDMTRFFMTIPEAVQLVL-QAGAMGKGGEIF 222
Query: 196 MQDMMPKVK 204
+ DM P VK
Sbjct: 223 VLDMGPPVK 231
>gnl|CDD|234323 TIGR03710, OAFO_sf, 2-oxoacid:acceptor oxidoreductase, alpha
subunit. This family of proteins contains a C-terminal
thiamine diphosphate (TPP) binding domain typical of
flavodoxin/ferredoxin oxidoreductases (pfam01855) as
well as an N-terminal domain similar to the gamma
subunit of the same group of oxidoreductases
(pfam01558). The genes represented by this model are
always found in association with a neighboring gene for
a beta subunit (TIGR02177) which also occurs in a
4-subunit (alpha/beta/gamma/ferredoxin) version of the
system. This alpha/gamma plus beta structure was used to
define the set of sequences to include in this model.
This pair of genes is not consistantly observed in
proximity to any electron acceptor genes, but is found
next to putative ferredoxins or ferredoxin-domain
proteins in Azoarcus sp. EbN1, Bradyrhizobium japonicum
USDA 110, Frankia sp. CcI3, Rhodoferax ferrireducens DSM
15236, Rhodopseudomonas palustris BisB5, Os,
Sphingomonas wittichii RW1 and Streptomyces
clavuligerus. Other potential acceptors are also
sporadically observed in close proximity including
ferritin-like proteins, reberythrin, peroxiredoxin and a
variety of other flavin and iron-sulfur
cluster-containing proteins. The phylogenetic
distribution of this family encompasses archaea, a
number of deeply-branching bacterial clades and only a
small number of firmicutes and proteobacteria. The
enzyme from Sulfolobus has been characterized with
respect to its substrate specificity which is described
as wide, encompassing various 2-oxoacids such as
2-oxoglutarate, 2-oxobutyrate and pyruvate. The enzyme
from Hydrogenobacter thermophilus has been shown to have
a high specificity towards 2-oxoglutarate and is one of
the key enzymes in the reverse TCA cycle in this
organism. Furthermore, considering its binding of
coenzyme A, it can be reasonably inferred that the
product of the reaction is succinyl-CoA. The genes for
this enzyme in Prevotella intermedia 17, Persephonella
marina EX-H1 and Picrophilus torridus DSM 9790 are in
close proximity to a variety of TCA cycle genes.
Persephonella marina and P. torridus are believed to
encode complete TCA cycles, and none of these contains
the lipoate-based 2-oxoglutarate dehydrogenase
(E1/E2/E3) system. That system is presumed to be
replaced by this one. In fact, the lipoate system is
absent in most organisms possessing a member of this
family, providing additional circumstantial evidence
that many of these enzymes are capable of acting as
2-oxoglutarate dehydrogenases and.
Length = 562
Score = 29.4 bits (67), Expect = 2.5
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 147 VIRQIKEAGMKVGLA----IKPKTPVDVIAEYIESADLVLIMTVEPGFGGQ 193
+ +++ G+KV L + P P + +AE +E A V++ VE GQ
Sbjct: 481 AVERLRAEGIKVALLHLRLLYP-FPKNELAELLEGAKKVIV--VEQNATGQ 528
>gnl|CDD|129825 TIGR00742, yjbN, tRNA dihydrouridine synthase A. This model
represents one branch of COG0042 (Predicted TIM-barrel
enzymes, possibly dehydrogenases, nifR3 family). It
represents a distinct subset by a set of shared unique
motifs, a conserved pattern of insertions/deletions
relative to other nifR3 homologs, and by subclustering
based on cross-genome bidirectional best hits. Members
are found in species as diverse as the proteobacteria, a
spirochete, a cyanobacterium, and Deinococcus
radiodurans. NifR3 itself, a protein of unknown function
associated with nitrogen regulation in Rhodobacter
capsulatus, is not a member of this branch. Members of
this family show a distant relationship to alpha/beta
(TIM) barrel enzymes such as dihydroorotate
dehydrogenase and glycolate oxidase [Protein synthesis,
tRNA and rRNA base modification].
Length = 318
Score = 29.0 bits (65), Expect = 2.6
Identities = 25/113 (22%), Positives = 51/113 (45%), Gaps = 26/113 (23%)
Query: 142 DNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIMTVEPGFGGQKF------ 195
D V ++ ++EA + + + +K + +D + Y D V I++ G G Q F
Sbjct: 109 DLVADCVKAMQEA-VNIPVTVKHRIGIDPLDSYEFLCDFVEIVS---GKGCQNFIVHARK 164
Query: 196 --MQDMMPK------------VKWLRENYPTLNIEVDGGVGPNTIDECAKCLT 234
+ + PK V L++++P L IE++GG+ ++ + L+
Sbjct: 165 AWLSGLSPKENREIPPLRYERVYQLKKDFPHLTIEINGGI--KNSEQIKQHLS 215
>gnl|CDD|235942 PRK07119, PRK07119, 2-ketoisovalerate ferredoxin reductase;
Validated.
Length = 352
Score = 29.1 bits (66), Expect = 2.7
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 7/45 (15%)
Query: 147 VIRQIKEAGMKVGLAIKPKT----PVDVIAEYIESADLVLIMTVE 187
+ +E G+KVGL +P T P + E + L +VE
Sbjct: 264 AVDMAREEGIKVGL-FRPITLWPFPEKALEELADKGKGFL--SVE 305
>gnl|CDD|181526 PRK08659, PRK08659, 2-oxoglutarate ferredoxin oxidoreductase
subunit alpha; Validated.
Length = 376
Score = 29.1 bits (66), Expect = 2.7
Identities = 10/42 (23%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 146 QVIRQIKEAGMKVGLAIKPKT----PVDVIAEYIESADLVLI 183
+ +++ +E G+KVGL + T P + I E + +++
Sbjct: 290 RAVKEAREEGIKVGL-FRLITVWPFPEEAIRELAKKVKAIVV 330
>gnl|CDD|224769 COG1856, COG1856, Uncharacterized homolog of biotin synthetase
[Function unknown].
Length = 275
Score = 28.7 bits (64), Expect = 3.1
Identities = 24/115 (20%), Positives = 48/115 (41%), Gaps = 22/115 (19%)
Query: 91 YTFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPMADANV--DQYTFHVEPVDNVPQVI 148
HV VD + ++KE + V V D++ D +V Y + V++ + +
Sbjct: 91 INAHVGFVDE--SDLEKLKEELVDV--VSLDFV---GDNDVIKRVYKLP-KSVEDYLRSL 142
Query: 149 RQIKEAGMKV------GLAIKPKT----PVDVIAEYIESADLVLIMTVEPGFGGQ 193
+KE G++V GL +D++ Y D ++++ + P G +
Sbjct: 143 LLLKENGIRVVPHITIGLDFGKIHGEFKAIDILVNY--EPDALVLVVLIPTPGTK 195
>gnl|CDD|237893 PRK15063, PRK15063, isocitrate lyase; Provisional.
Length = 428
Score = 29.1 bits (66), Expect = 3.2
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 22/63 (34%)
Query: 84 ADANV------DQ--YTFHVEPVDNVPQVIRQIKEAGMKVGQV--------LQDWIEPM- 126
ADAN+ DQ Y P ++VP V+++I A + Q+ D+ P+
Sbjct: 96 ADANLAGQMYPDQSLY-----PANSVPAVVKRINNALRRADQIQWSEGDKGYIDYFAPIV 150
Query: 127 ADA 129
ADA
Sbjct: 151 ADA 153
>gnl|CDD|225127 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 713
Score = 29.1 bits (66), Expect = 3.4
Identities = 25/108 (23%), Positives = 45/108 (41%), Gaps = 30/108 (27%)
Query: 99 DNVPQVIRQIKEAGMKVGQVLQDWIEPMADA-----NVDQYTFHVEPVDNVPQVIRQIKE 153
+ + I +K G+KV + D A+A +D+ + P D +++R+++
Sbjct: 540 PDAKEAIAALKALGIKVVMLTGD-NRRTAEAIAKELGIDEVRAELLPEDKA-EIVRELQA 597
Query: 154 AGMKV------------------GLAIKPKTPVDVIAEYIESADLVLI 183
G KV G+A+ T V IE+AD+VL+
Sbjct: 598 EGRKVAMVGDGINDAPALAAADVGIAMGSGTDVA-----IEAADVVLM 640
>gnl|CDD|184075 PRK13478, PRK13478, phosphonoacetaldehyde hydrolase; Provisional.
Length = 267
Score = 28.3 bits (64), Expect = 3.7
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 81 EPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVG 116
EP+ A + Y P+ V +VI ++ G+K+G
Sbjct: 89 EPLQIAKLADYA---TPIPGVLEVIAALRARGIKIG 121
Score = 28.3 bits (64), Expect = 3.7
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 124 EPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVG 159
EP+ A + Y P+ V +VI ++ G+K+G
Sbjct: 89 EPLQIAKLADYA---TPIPGVLEVIAALRARGIKIG 121
>gnl|CDD|219767 pfam08264, Anticodon_1, Anticodon-binding domain of tRNA. This
domain is found mainly hydrophobic tRNA synthetases. The
domain binds to the anticodon of the tRNA.
Length = 148
Score = 27.8 bits (62), Expect = 4.6
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 5/54 (9%)
Query: 118 VLQDWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVI 171
L W EP ++ E + Q IR+++ L IK P++V+
Sbjct: 99 HLAPWPEPDEVEEDEELEEEFELRQEIVQAIRKLRSE-----LKIKKSLPLEVV 147
>gnl|CDD|176681 cd07258, PpCmtC_C, C-terminal domain of
2,3-dihydroxy-p-cumate-3,4-dioxygenase (PpCmtC). This
subfamily contains the C-terminal, catalytic, domain of
PpCmtC. 2,3-dihydroxy-p-cumate-3,4-dioxygenase (CmtC of
Pseudomonas putida F1) is a dioxygenase involved in the
eight-step catabolism pathway of p-cymene. CmtC acts
upon the reaction intermediate 2,3-dihydroxy-p-cumate,
yielding
2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate. The
CmtC belongs to the type I family of extradiol
dioxygenases. Fe2+ was suggested as a cofactor, same as
for other enzymes in the family. The type I family of
extradiol dioxygenases contains two structurally
homologous barrel-shaped domains at the N- and
C-terminal. The active-site metal is located in the
C-terminal barrel and plays an essential role in the
catalytic mechanism.
Length = 141
Score = 27.5 bits (61), Expect = 5.1
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 125 PMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDVIAEYIESADLVLIM 184
P + ++ F V +D++ + + +IK +KV P D I Y D +
Sbjct: 51 PASSSHFHHVNFMVTDIDDIGKALYRIKAHDVKVVFGPGRHPPSDSIFFYFLDPDG---I 107
Query: 185 TVEPGFGGQKF 195
TVE FG ++F
Sbjct: 108 TVEYSFGMEEF 118
>gnl|CDD|234923 PRK01222, PRK01222, N-(5'-phosphoribosyl)anthranilate isomerase;
Provisional.
Length = 210
Score = 27.8 bits (63), Expect = 5.1
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 5/52 (9%)
Query: 145 PQVIRQIKEAG----MKVGLAIKPKTPVDVIAEYIESADLVLIMTVEPGFGG 192
P+ RQ+K +K L ++ ++ A Y AD +L+ GG
Sbjct: 89 PEFCRQLKRRYGLPVIKA-LRVRSAGDLEAAAAYYGDADGLLLDAYVGLPGG 139
>gnl|CDD|212663 cd07782, FGGY_YpCarbK_like, Yersinia Pseudotuberculosis
carbohydrate kinase-like subgroup; belongs to the FGGY
family of carbohydrate kinases. This subgroup is
composed of the uncharacterized Yersinia
Pseudotuberculosis carbohydrate kinase that has been
named glyerol/xylulose kinase and similar
uncharacterized proteins from bacteria and eukaryota.
Carbohydrate kinases catalyze the ATP-dependent
phosphorylation of their carbohydrate substrate to
produce phosphorylated sugar and ADP. The presence of
Mg2+ is required for catalytic activity. This subgroup
shows high homology to characterized ribulokinases and
belongs to the FGGY family of carbohydrate kinases, the
monomers of which contain two large domains, which are
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain.
Length = 536
Score = 27.9 bits (63), Expect = 6.1
Identities = 8/16 (50%), Positives = 11/16 (68%), Gaps = 2/16 (12%)
Query: 196 MQDMMPKVKWLRENYP 211
M+ PK+ WL+EN P
Sbjct: 138 ME--TPKLLWLKENLP 151
Score = 27.9 bits (63), Expect = 6.1
Identities = 8/16 (50%), Positives = 11/16 (68%), Gaps = 2/16 (12%)
Query: 242 MQDMMPKVKWLRENYP 257
M+ PK+ WL+EN P
Sbjct: 138 ME--TPKLLWLKENLP 151
>gnl|CDD|190389 pfam02679, ComA, (2R)-phospho-3-sulfolactate synthase (ComA). In
methanobacteria (2R)-phospho-3-sulfolactate synthase
(ComA) catalyzes the first step of the biosynthesis of
coenzyme M from phosphoenolpyruvate (P-enolpyruvate).
This novel enzyme catalyzes the stereospecific Michael
addition of sulfite to P-enolpyruvate, forming
L-2-phospho-3-sulfolactate (PSL). It is suggested that
the ComA-catalyzed reaction is analogous to those
reactions catalyzed by beta-elimination enzymes that
proceed through an enolate intermediate.
Length = 245
Score = 27.5 bits (62), Expect = 6.2
Identities = 33/132 (25%), Positives = 49/132 (37%), Gaps = 34/132 (25%)
Query: 92 TFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPMA--DANVDQYT-------FH-VE-- 139
T + P D + + I E G+ V + +A D+Y F +E
Sbjct: 48 TSALMPEDILKEKIDLAHEHGVYV--YTGGTLFEIAISQGKFDEYLRECKELGFDAIEIS 105
Query: 140 ------PVDNVPQVIRQIKEAGMKV--------GLAIKPKTPVDVIAEYIES-----ADL 180
P + ++IR+ K+AG KV TP ++I E IE AD
Sbjct: 106 DGTIELPEEERLRLIRKAKKAGFKVLSEVGKKDPELDSSLTPDELI-EQIERDLEAGADK 164
Query: 181 VLIMTVEPGFGG 192
V+I E G G
Sbjct: 165 VIIEARESGGVG 176
>gnl|CDD|234155 TIGR03282, methan_mark_13, putative methanogenesis marker 13
metalloprotein. Members of this protein family, to
date, are found in a completed prokaryotic genome if and
only if the species is one of the archaeal methanogens.
The exact function is unknown, but likely is linked to
methanogenesis or a process closely connected to it.
This metal cluster-binding family is related to
nitrogenase structural protein NifD and accessory
protein NifE, among others [Energy metabolism,
Methanogenesis].
Length = 352
Score = 27.8 bits (62), Expect = 6.2
Identities = 20/83 (24%), Positives = 30/83 (36%), Gaps = 18/83 (21%)
Query: 190 FGGQKFMQDMMPKVKWLRENYPTLNIEVDGGVGPNTIDECAKCLTGFGGQKFMQDMMPKV 249
FG + + VK +R E+ G VG CA + G +D+ V
Sbjct: 57 FGASEKL------VKVIRYAEEKFKPELIGVVG-----TCASMIIG-------EDLKEAV 98
Query: 250 KWLRENYPTLNIEVDGGVGPNTI 272
+ + +EV G G NT
Sbjct: 99 DEADVDAEVIAVEVHAGFGDNTE 121
>gnl|CDD|234446 TIGR04043, rSAM_MSMEG_0568, radical SAM protein, MSMEG_0568 family.
Members of this protein family are radical SAM proteins
related to MSMEG_0568 from Mycobacterium smegmatis.
Members occur within 8-gene operons in species as
diverse as M. smegmatis, Rhizobium leguminosarum,
Synechococcus elongatus, and Sorangium cellulosum. The
function of the operon is unknown, but similarity of
MSMEG_0568 to some cofactor biosynthesis radical SAM
proteins suggests a similar biosynthetic function
[Unknown function, Enzymes of unknown specificity].
Length = 354
Score = 27.7 bits (62), Expect = 6.3
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 78 QWIEPMADANVDQYTFHVEPVDNVPQVIRQI 108
W + A D H+E VD P+V R+I
Sbjct: 207 AWFTRLKAAGADSLGMHLEAVD--PEVRRRI 235
Score = 27.7 bits (62), Expect = 6.5
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 121 DWIEPMADANVDQYTFHVEPVDNVPQVIRQI 151
W + A D H+E VD P+V R+I
Sbjct: 207 AWFTRLKAAGADSLGMHLEAVD--PEVRRRI 235
>gnl|CDD|236255 PRK08385, PRK08385, nicotinate-nucleotide pyrophosphorylase;
Provisional.
Length = 278
Score = 27.8 bits (62), Expect = 6.3
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 206 LRENYPTLNIEVDGGVGPNTIDECAK 231
LRE + IEV GG+ P I+E AK
Sbjct: 228 LRER---VKIEVSGGITPENIEEYAK 250
Score = 27.8 bits (62), Expect = 6.3
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 252 LRENYPTLNIEVDGGVGPNTIDECAK 277
LRE + IEV GG+ P I+E AK
Sbjct: 228 LRER---VKIEVSGGITPENIEEYAK 250
>gnl|CDD|223576 COG0502, BioB, Biotin synthase and related enzymes [Coenzyme
metabolism].
Length = 335
Score = 27.6 bits (62), Expect = 6.6
Identities = 38/174 (21%), Positives = 68/174 (39%), Gaps = 40/174 (22%)
Query: 98 VDNVPQVIRQIKEA-GMKV----GQVLQDWIEPMADANVDQYTFHVE------------- 139
++ V + I+ +KE G++V G + ++ E +ADA VD+Y ++E
Sbjct: 117 MEEVVEAIKAVKEELGLEVCASLGMLTEEQAEKLADAGVDRYNHNLETSPEFYENIITTR 176
Query: 140 PVDNVPQVIRQIKEAGMKV------GLAIKPKTPVDVIAEYIESADL-----VLIMTVEP 188
++ + ++EAG++V GL +T D +E A+L V I + P
Sbjct: 177 TYEDRLNTLENVREAGIEVCSGGIVGL---GETVEDRAELLLELANLPTPDSVPINFLNP 233
Query: 189 --G--FGGQKFMQDMMPKVKWL---RENYPTLNIEVDGGVGPNTIDECAKCLTG 235
G K + D +K + R P I + G + A
Sbjct: 234 IPGTPLENAKPL-DPFEFLKTIAVARIIMPKSMIRLSAGRETMLPELQALAFMA 286
>gnl|CDD|238802 cd01568, QPRTase_NadC, Quinolinate phosphoribosyl transferase
(QAPRTase or QPRTase), also called nicotinate-nucleotide
pyrophosphorylase, is involved in the de novo synthesis
of NAD in both prokaryotes and eukaryotes. It catalyses
the reaction of quinolinic acid (QA) with
5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence
of Mg2+ to produce nicotinic acid mononucleotide (NAMN),
pyrophosphate and carbon dioxide. QPRTase functions as a
homodimer with two active sites, each formed by the
C-terminal region of one subunit and the N-terminal
region of the other.
Length = 269
Score = 27.8 bits (63), Expect = 6.6
Identities = 18/100 (18%), Positives = 44/100 (44%), Gaps = 16/100 (16%)
Query: 137 HVEPVDNVPQVIRQIKE-AGMKVGLAIKPKTPVDVIAEYIES-ADLVLI--MTVEPGFGG 192
H+ + + +++ + A + + ++ +T + E +E+ AD++++ M+ E
Sbjct: 160 HIAAAGGITEAVKRARAAAPFEKKIEVEVETLEEAE-EALEAGADIIMLDNMSPE----- 213
Query: 193 QKFMQDMMPKVKWLRENYPTLNIEVDGGVGPNTIDECAKC 232
++ VK L+ L +E GG+ I A+
Sbjct: 214 -----ELKEAVKLLKGLPRVL-LEASGGITLENIRAYAET 247
>gnl|CDD|239237 cd02911, arch_FMN, Archeal FMN-binding domain. This family of
archaeal proteins are part of the NAD(P)H-dependent
flavin oxidoreductase (oxidored) FMN-binding family that
reduce a range of alternative electron acceptors. Most
use FAD/FMN as a cofactor and NAD(P)H as electron donor.
Some contain 4Fe-4S cluster to transfer electron from
FAD to FMN. The specific function of this group is
unknown.
Length = 233
Score = 27.7 bits (62), Expect = 6.8
Identities = 7/18 (38%), Positives = 13/18 (72%)
Query: 24 SQNLLDSGADYLHLDVMD 41
++ + +GAD +H+D MD
Sbjct: 158 ARLIEKAGADIIHVDAMD 175
>gnl|CDD|218686 pfam05677, DUF818, Chlamydia CHLPS protein (DUF818). This family
consists of several Chlamydia CHLPS proteins, the
function of which are unknown.
Length = 364
Score = 27.4 bits (61), Expect = 8.0
Identities = 12/38 (31%), Positives = 13/38 (34%), Gaps = 5/38 (13%)
Query: 31 GADYLHLDVMDGTFVPNLTFGHPV-----VKCLRNKIP 63
G D + DG F P HP V KIP
Sbjct: 298 GTDSRRSLIGDGLFAPENCLAHPFLDPPNVPKSGKKIP 335
>gnl|CDD|238752 cd01475, vWA_Matrilin, VWA_Matrilin: In cartilaginous plate,
extracellular matrix molecules mediate cell-matrix and
matrix-matrix interactions thereby providing tissue
integrity. Some members of the matrilin family are
expressed specifically in developing cartilage
rudiments. The matrilin family consists of at least four
members. All the members of the matrilin family contain
VWA domains, EGF-like domains and a heptad repeat
coiled-coiled domain at the carboxy terminus which is
responsible for the oligomerization of the matrilins.
The VWA domains have been shown to be essential for
matrilin network formation by interacting with matrix
ligands.
Length = 224
Score = 27.3 bits (61), Expect = 8.1
Identities = 11/63 (17%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 97 PVDNVPQVIRQIKEAGMK-----VGQVLQDWIEPMADANVDQYTFHVEPVDNVPQVIRQI 151
P D+V +V + + G++ VG+ ++ + +A + + F+VE + ++ ++
Sbjct: 120 PQDDVSEVAAKARALGIEMFAVGVGRADEEELREIASEPLADHVFYVEDFSTIEELTKKF 179
Query: 152 KEA 154
+
Sbjct: 180 QGK 182
>gnl|CDD|218322 pfam04909, Amidohydro_2, Amidohydrolase. These proteins are
amidohydrolases that are related to pfam01979.
Length = 272
Score = 27.5 bits (61), Expect = 8.2
Identities = 23/156 (14%), Positives = 44/156 (28%), Gaps = 18/156 (11%)
Query: 76 PQQWIEPMADANVDQYTFHVEPVDNVPQVIRQIKEA--GMKVGQVLQDWIEPMADANVDQ 133
P + M D E V + A + + + A +
Sbjct: 13 PDPRLPLMDRRGYDPRDASPEDY-LVLGAALGVARAVIVAASCRGANNRVLAEALKRPGR 71
Query: 134 YTFHV-----EPVDNVPQVIRQIKEAGMKVGLAIKPKTPVDV---------IAEYIESAD 179
+ +P D ++ R++ E G + G+ + P I E +
Sbjct: 72 FVGGAALPPPDPEDAAAELERRLAELGFR-GVRLNPHPGGGPLLDPRLDDPIFEALAELG 130
Query: 180 LVLIMTVEPGFGGQKFMQDMMPKVKWLRENYPTLNI 215
L + + G G+ + L +P L I
Sbjct: 131 LPVDLHTGFGDAGEDLDAAQPLLLSGLARRFPDLKI 166
>gnl|CDD|238149 cd00245, Glm_e, Coenzyme B12-dependent glutamate mutase epsilon
subunit-like family; contains proteins similar to
Clostridium cochlearium glutamate mutase (Glm) and
Streptomyces tendae Tu901 NikV. Glm catalyzes a
carbon-skeleton rearrangement of L-glutamate to
L-threo-3-methylaspartate. The first step in the
catalysis is a homolytic cleavage of the Co-C bond of
the coenzyme B12 cofactor to generate a 5'-deoxyadenosyl
radical. This radical then initiates the rearrangement
reaction. C. cochlearium Glm is a sigma2epsilon2
heterotetramer. Glm plays a role in glutamate
fermentation in Clostridium sp. and in members of the
family Enterobacteriaceae, and in the synthesis of the
lipopeptide antibiotic friulimicin in Actinoplanes
friuliensis. S. tendae Tu901 glutamate mutase-like
proteins NikU and NIkV participate in the synthesis of
the peptidyl nucleoside antibiotic nikkomycin. NikU and
NikV proteins have sequence similarity to Clostridium
Glm sigma and epsilon components respectively, and may
catalyze the rearrangement of 2-oxoglutaric acid to
2-keto-3-methylsuccinic acid during nikkomycin
synthesis.
Length = 428
Score = 27.7 bits (62), Expect = 8.4
Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 12/58 (20%)
Query: 172 AEYIESADLVLIMTVEP--GFGGQKFMQDMMPKVKWLRENYPTLNIEVDGGVGPNTID 227
A+ +E AD + V+P GF +++ E TL E V P TID
Sbjct: 4 AKKLEKADKEGKLVVQPRAGFPL---LEEH-------IELLRTLQEEGAADVLPLTID 51
>gnl|CDD|163682 cd07944, DRE_TIM_HOA_like, 4-hydroxy-2-oxovalerate aldolase-like,
N-terminal catalytic TIM barrel domain. This family of
bacterial enzymes is sequence-similar to
4-hydroxy-2-oxovalerate aldolase (HOA) but its exact
function is unknown. This family includes the
Bacteroides vulgatus Bvu_2661 protein and belongs to the
DRE-TIM metallolyase superfamily. DRE-TIM metallolyases
include 2-isopropylmalate synthase (IPMS),
alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 266
Score = 27.1 bits (61), Expect = 8.4
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 8/64 (12%)
Query: 105 IRQIKEAGMK------VGQVLQDWIEPMADANVD--QYTFHVEPVDNVPQVIRQIKEAGM 156
+ + K G D +EP + + VD + FH D +I+ IKE G
Sbjct: 64 LLGDSKGNTKIAVMVDYGNDDIDLLEPASGSVVDMIRVAFHKHEFDEALPLIKAIKEKGY 123
Query: 157 KVGL 160
+V
Sbjct: 124 EVFF 127
>gnl|CDD|223479 COG0402, SsnA, Cytosine deaminase and related metal-dependent
hydrolases [Nucleotide transport and metabolism /
General function prediction only].
Length = 421
Score = 27.4 bits (61), Expect = 8.7
Identities = 20/88 (22%), Positives = 32/88 (36%), Gaps = 1/88 (1%)
Query: 92 TFHVEPVDNVPQVIRQIKEAGMKVGQVLQDWIEPMADANVDQYTFHVEPVDNVPQVIRQI 151
T VD V + EA ++VG A D E ++ +++R+
Sbjct: 118 TTARTHVDVVAESADAAFEAALEVGLRAVLGPVLQDVAFPDPGAETDEELEETEELLREA 177
Query: 152 KEAGMKVGLAIKPKTPVDVIAEYIESAD 179
G + + P P V E +ES D
Sbjct: 178 HGLGR-DVVGLAPHFPYTVSPELLESLD 204
>gnl|CDD|224011 COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 588
Score = 27.6 bits (62), Expect = 8.7
Identities = 18/69 (26%), Positives = 26/69 (37%), Gaps = 20/69 (28%)
Query: 144 VPQVIRQIKEAGMKVGLAIKPKTPVDV----IAEYI----ESADLVLIMTVEPGFGGQKF 195
+P +QI E G P+ V + + E+ LVL GG+ F
Sbjct: 427 IPLFKKQIAEGG-----------PLTVTDPDMTRFFMTIPEAVQLVL-QAGAIAKGGEIF 474
Query: 196 MQDMMPKVK 204
+ DM VK
Sbjct: 475 VLDMGEPVK 483
>gnl|CDD|133123 cd06592, GH31_glucosidase_KIAA1161, KIAA1161 is an uncharacterized
Homo sapiens protein with a glycosyl hydrolase family 31
(GH31) domain that is homologous to the Escherichia coli
YihQ glucosidase. Orthologs of KIA1161 are found in
eukaryotes and prokaryotes. In bacteria, YihQ (along
with YihO) is important for bacterial O-antigen capsule
assembly and translocation. Enzymes of the GH31 family
possess a wide range of different hydrolytic activities
including alpha-glucosidase (glucoamylase and
sucrase-isomaltase), alpha-xylosidase,
6-alpha-glucosyltransferase,
3-alpha-isomaltosyltransferase and alpha-1,4-glucan
lyase. All GH31 enzymes cleave a terminal carbohydrate
moiety from a substrate that varies considerably in
size, depending on the enzyme, and may be either a
starch or a glycoprotein.
Length = 303
Score = 27.2 bits (61), Expect = 9.9
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 7/61 (11%)
Query: 106 RQIKEAGMKVGQVLQD--WIEPMADANVDQYTFHVEPVDNVPQVIRQIKEAGMKVGLAIK 163
++I + G GQ+ D W D + D F P + +I Q+ + G +V L +
Sbjct: 37 QEIIDNGFPNGQIEIDDNWETCYGDFDFDPTKF---P--DPKGMIDQLHDLGFRVTLWVH 91
Query: 164 P 164
P
Sbjct: 92 P 92
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 0.137 0.421
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,395,308
Number of extensions: 1372920
Number of successful extensions: 1908
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1867
Number of HSP's successfully gapped: 94
Length of query: 277
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 181
Effective length of database: 6,679,618
Effective search space: 1209010858
Effective search space used: 1209010858
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 (21.7 bits)
S2: 58 (26.1 bits)