RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7896
(718 letters)
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 472 bits (1216), Expect = e-160
Identities = 190/314 (60%), Positives = 225/314 (71%), Gaps = 23/314 (7%)
Query: 2 ADIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLE 61
DI LAE+GRK I +AENEMPGLMALR +YG K LKGARI GCLHMTVQTAVLIETL
Sbjct: 8 KDISLAEFGRKEIELAENEMPGLMALREEYGPSKPLKGARITGCLHMTVQTAVLIETLKA 67
Query: 62 LGAEVQWSSCNIFSTQDHAAAAIAARG-VAVYAWKGETDEEYVWCIEQTLVFPDGKPLNM 120
LGAEV+W SCNIFSTQDHAAAAIA G V V+AWKGET EEY WC EQ L +P+G N+
Sbjct: 68 LGAEVRWCSCNIFSTQDHAAAAIAKAGSVPVFAWKGETLEEYWWCTEQALKWPNGDGPNL 127
Query: 121 ILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSVTKP 180
I+DDGGD T LVHE GV K+++E + ++ ++ K
Sbjct: 128 IVDDGGDATLLVHE------------------GVK-AEKLYEEKGILPDPLDPSNEDEKC 168
Query: 181 LNMILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSV 240
L +L +K+ + +I G+SEETTTGVH LYKM K+ +L PAINVNDSV
Sbjct: 169 LLTVLKKLLTKNP---DKWTNLVKKIVGVSEETTTGVHRLYKMLKKGELLFPAINVNDSV 225
Query: 241 TKSKFDNLYGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEI 300
TKSKFDN+YGCR SL+DG+ RATD+M+AGK VV GYGDVGKGCAQ+LR FG+RV+VTEI
Sbjct: 226 TKSKFDNIYGCRHSLIDGIFRATDVMIAGKTVVVCGYGDVGKGCAQALRGFGARVVVTEI 285
Query: 301 DPINALQASMEGYE 314
DPI ALQA+MEGY+
Sbjct: 286 DPICALQAAMEGYQ 299
Score = 221 bits (566), Expect = 1e-64
Identities = 75/119 (63%), Positives = 93/119 (78%), Gaps = 1/119 (0%)
Query: 343 DIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAK 402
D+M+AGK VV GYGDVGKGCAQ+LR FG+RV+VTEIDPI ALQA+MEGY+V T+E+ +
Sbjct: 249 DVMIAGKTVVVCGYGDVGKGCAQALRGFGARVVVTEIDPICALQAAMEGYQVVTLEDVVE 308
Query: 403 EGGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDCEIQVSWLDK-NAVEKVNVKPQV 460
IFVT TG KDII EH +M+++AIV NIGHFD EIQV+ L+ +E V +KPQV
Sbjct: 309 TADIFVTATGNKDIITLEHMRRMKNNAIVGNIGHFDNEIQVAELEAYPGIEIVEIKPQV 367
Score = 216 bits (551), Expect = 2e-62
Identities = 85/110 (77%), Positives = 90/110 (81%), Gaps = 1/110 (0%)
Query: 503 DIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLEL 562
DI LAE+GRK I +AENEMPGLMALR +YG K LKGARI GCLHMTVQTAVLIETL L
Sbjct: 9 DISLAEFGRKEIELAENEMPGLMALREEYGPSKPLKGARITGCLHMTVQTAVLIETLKAL 68
Query: 563 GAEVQWSSCNIFSTQDHAAAAIAARG-VAVYAWKGETDEEYVWCIEQTLV 611
GAEV+W SCNIFSTQDHAAAAIA G V V+AWKGET EEY WC EQ L
Sbjct: 69 GAEVRWCSCNIFSTQDHAAAAIAKAGSVPVFAWKGETLEEYWWCTEQALK 118
Score = 215 bits (549), Expect = 4e-62
Identities = 82/110 (74%), Positives = 93/110 (84%), Gaps = 2/110 (1%)
Query: 611 VDRYTLPNGNHIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTK--HSQYPVG 668
VDRYT P+G IILLAEGRLVNLGCA GHPSFVMSNSFTNQVLAQIELW +YP G
Sbjct: 367 VDRYTFPDGKGIILLAEGRLVNLGCATGHPSFVMSNSFTNQVLAQIELWENRDTGKYPNG 426
Query: 669 VYMLPKKLDEEVAALHLEHLGVKLTKLTEDQAKYLGLPIEGPYKPDHYRY 718
VY LPK+LDE+VA LHL+ LG KLTKLT+ QA+Y+G+P++GPYK DHYRY
Sbjct: 427 VYKLPKELDEKVARLHLKKLGAKLTKLTDKQAEYIGVPVDGPYKSDHYRY 476
Score = 58.9 bits (143), Expect = 6e-09
Identities = 21/35 (60%), Positives = 28/35 (80%)
Query: 314 ELDEEVAALHLEHLGVKLTKLTEDQAKYLDIMLAG 348
ELDE+VA LHL+ LG KLTKLT+ QA+Y+ + + G
Sbjct: 433 ELDEKVARLHLKKLGAKLTKLTDKQAEYIGVPVDG 467
>gnl|CDD|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 386 bits (993), Expect = e-128
Identities = 138/178 (77%), Positives = 154/178 (86%)
Query: 2 ADIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLE 61
ADI LA+WGRK I +AE EMPGLMALR +YGA+K LKGARIAGCLHMT+QTAVLIETL+
Sbjct: 3 ADISLADWGRKEIEIAETEMPGLMALREEYGAEKPLKGARIAGCLHMTIQTAVLIETLVA 62
Query: 62 LGAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWCIEQTLVFPDGKPLNMI 121
LGAEV+W+SCNIFSTQDHAAAAIAA GV V+AWKGET EEY WCIEQTL +PDG NMI
Sbjct: 63 LGAEVRWASCNIFSTQDHAAAAIAAAGVPVFAWKGETLEEYWWCIEQTLTWPDGWGPNMI 122
Query: 122 LDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSVTK 179
LDDGGD T LVH+KYP+ L +IRG+SEETTTGVH LY+M K+ KL PAINVNDSVTK
Sbjct: 123 LDDGGDATLLVHKKYPRMLKKIRGVSEETTTGVHRLYQMAKKGKLLFPAINVNDSVTK 180
Score = 304 bits (782), Expect = 2e-96
Identities = 111/145 (76%), Positives = 125/145 (86%), Gaps = 2/145 (1%)
Query: 179 KPLNMILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVND 238
NMILDDGGD T LVH+KYP+ L +IRG+SEETTTGVH LY+M K+ KL PAINVND
Sbjct: 117 WGPNMILDDGGDATLLVHKKYPRMLKKIRGVSEETTTGVHRLYQMAKKGKLLFPAINVND 176
Query: 239 SVTKSKFDNLYGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVT 298
SVTKSKFDNLYGCRESLVDG+KRATD+M+AGKVAVV GYGDVGKGCAQSLR G+RVIVT
Sbjct: 177 SVTKSKFDNLYGCRESLVDGIKRATDVMIAGKVAVVCGYGDVGKGCAQSLRGQGARVIVT 236
Query: 299 EIDPINALQASMEGYELD--EEVAA 321
EIDPI ALQA+M+G+E+ EEVA
Sbjct: 237 EIDPICALQAAMDGFEVVTMEEVAP 261
Score = 245 bits (629), Expect = 4e-74
Identities = 88/108 (81%), Positives = 97/108 (89%)
Query: 503 DIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLEL 562
DI LA+WGRK I +AE EMPGLMALR +YGA+K LKGARIAGCLHMT+QTAVLIETL+ L
Sbjct: 4 DISLADWGRKEIEIAETEMPGLMALREEYGAEKPLKGARIAGCLHMTIQTAVLIETLVAL 63
Query: 563 GAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWCIEQTL 610
GAEV+W+SCNIFSTQDHAAAAIAA GV V+AWKGET EEY WCIEQTL
Sbjct: 64 GAEVRWASCNIFSTQDHAAAAIAAAGVPVFAWKGETLEEYWWCIEQTL 111
Score = 239 bits (612), Expect = 1e-71
Identities = 82/107 (76%), Positives = 93/107 (86%)
Query: 611 VDRYTLPNGNHIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTKHSQYPVGVY 670
VD T P+G IILLAEGRLVNLGCA GHPSFVMSNSFTNQVLAQIEL+TK +Y GVY
Sbjct: 320 VDHITFPDGKRIILLAEGRLVNLGCATGHPSFVMSNSFTNQVLAQIELFTKPGKYKNGVY 379
Query: 671 MLPKKLDEEVAALHLEHLGVKLTKLTEDQAKYLGLPIEGPYKPDHYR 717
+LPKKLDE+VA LHLE LG KLTKLT++QA Y+G+P+EGP+KPDHYR
Sbjct: 380 VLPKKLDEKVARLHLEKLGAKLTKLTKEQADYIGVPVEGPFKPDHYR 426
Score = 238 bits (611), Expect = 1e-71
Identities = 81/119 (68%), Positives = 94/119 (78%), Gaps = 1/119 (0%)
Query: 343 DIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAK 402
D+M+AGKVAVV GYGDVGKGCAQSLR G+RVIVTEIDPI ALQA+M+G+EV TMEE A
Sbjct: 202 DVMIAGKVAVVCGYGDVGKGCAQSLRGQGARVIVTEIDPICALQAAMDGFEVVTMEEVAP 261
Query: 403 EGGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDCEIQVSWLDKNA-VEKVNVKPQV 460
+ IFVTTTG KD+I EH M+D AIVCNIGHFD EI V+ L N ++ N+KPQV
Sbjct: 262 QADIFVTTTGNKDVITREHMRAMKDGAIVCNIGHFDNEIDVASLRNNPGLKWENIKPQV 320
Score = 61.4 bits (150), Expect = 7e-10
Identities = 21/35 (60%), Positives = 28/35 (80%)
Query: 314 ELDEEVAALHLEHLGVKLTKLTEDQAKYLDIMLAG 348
+LDE+VA LHLE LG KLTKLT++QA Y+ + + G
Sbjct: 384 KLDEKVARLHLEKLGAKLTKLTKEQADYIGVPVEG 418
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 367 bits (943), Expect = e-120
Identities = 173/315 (54%), Positives = 209/315 (66%), Gaps = 22/315 (6%)
Query: 1 MADIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLL 60
+ D+ A++GR I +AE EMPGLMA R ++G + KGARI G LHMT+QTAVLIETL
Sbjct: 8 VKDMSQADFGRLEIELAEVEMPGLMACRTEFGPSQPFKGARITGSLHMTIQTAVLIETLT 67
Query: 61 ELGAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWCIEQTLVFPDGKPLNM 120
LGAEV+W SCNIFSTQDHAAAAIA AV+AWKGET +EY WC E+ L + G ++
Sbjct: 68 ALGAEVRWCSCNIFSTQDHAAAAIARDSAAVFAWKGETLQEYWWCTERALDWGPGGGPDL 127
Query: 121 ILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSVTKP 180
I+DDGGD T L+HE GV + K+ L P N
Sbjct: 128 IVDDGGDATLLIHE------------------GVKAEEEFEKDGTLPDPTSTDNAEFKIV 169
Query: 181 LNMILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSV 240
L +I D + +KY + + G+SEETTTGV LY+M K L PAINVNDSV
Sbjct: 170 LTII----KDGLKVDPKKYHKMKERLVGVSEETTTGVKRLYQMQKNGTLLFPAINVNDSV 225
Query: 241 TKSKFDNLYGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEI 300
TKSKFDNLYGCR SL DGL RATD+M+AGKVAV+ GYGDVGKGCA +++ G+RVIVTEI
Sbjct: 226 TKSKFDNLYGCRHSLPDGLMRATDVMIAGKVAVICGYGDVGKGCAAAMKAAGARVIVTEI 285
Query: 301 DPINALQASMEGYEL 315
DPI ALQA MEGY++
Sbjct: 286 DPICALQALMEGYQV 300
Score = 179 bits (455), Expect = 5e-49
Identities = 72/111 (64%), Positives = 87/111 (78%), Gaps = 3/111 (2%)
Query: 611 VDRYTLPNGNH-IILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTKHS--QYPV 667
DR+ P+ II+LAEGRL+NLGCA GHPSFVMS SFTNQV+AQ+ELW + +Y
Sbjct: 367 TDRWVFPDTGSGIIVLAEGRLMNLGCATGHPSFVMSCSFTNQVIAQLELWNEKKSGKYEK 426
Query: 668 GVYMLPKKLDEEVAALHLEHLGVKLTKLTEDQAKYLGLPIEGPYKPDHYRY 718
VY+LPK LDE+VAALHL LG KLTKL++DQA Y+ +P+EGPYKP HYRY
Sbjct: 427 KVYVLPKHLDEKVAALHLGKLGAKLTKLSKDQADYINVPVEGPYKPAHYRY 477
Score = 170 bits (433), Expect = 4e-46
Identities = 71/108 (65%), Positives = 83/108 (76%)
Query: 503 DIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLEL 562
D+ A++GR I +AE EMPGLMA R ++G + KGARI G LHMT+QTAVLIETL L
Sbjct: 10 DMSQADFGRLEIELAEVEMPGLMACRTEFGPSQPFKGARITGSLHMTIQTAVLIETLTAL 69
Query: 563 GAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWCIEQTL 610
GAEV+W SCNIFSTQDHAAAAIA AV+AWKGET +EY WC E+ L
Sbjct: 70 GAEVRWCSCNIFSTQDHAAAAIARDSAAVFAWKGETLQEYWWCTERAL 117
Score = 168 bits (426), Expect = 4e-45
Identities = 71/119 (59%), Positives = 92/119 (77%), Gaps = 1/119 (0%)
Query: 343 DIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAK 402
D+M+AGKVAV+ GYGDVGKGCA +++ G+RVIVTEIDPI ALQA MEGY+V T+E+
Sbjct: 249 DVMIAGKVAVICGYGDVGKGCAAAMKAAGARVIVTEIDPICALQALMEGYQVLTLEDVVS 308
Query: 403 EGGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDCEIQVSWLDK-NAVEKVNVKPQV 460
E IFVTTTG KDII +H +M+++AIVCNIGHFD EI + L+ V+++ +KPQ
Sbjct: 309 EADIFVTTTGNKDIIMVDHMRKMKNNAIVCNIGHFDNEIDMLGLETYPGVKRITIKPQT 367
Score = 51.4 bits (123), Expect = 1e-06
Identities = 21/34 (61%), Positives = 28/34 (82%)
Query: 315 LDEEVAALHLEHLGVKLTKLTEDQAKYLDIMLAG 348
LDE+VAALHL LG KLTKL++DQA Y+++ + G
Sbjct: 435 LDEKVAALHLGKLGAKLTKLSKDQADYINVPVEG 468
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 350 bits (899), Expect = e-114
Identities = 135/178 (75%), Positives = 151/178 (84%)
Query: 2 ADIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLE 61
DI LA +GRK I +AENEMPGLMALR +YG + LKGARIAGCLHMTVQTAVLIETL+
Sbjct: 6 KDISLAAFGRKEIELAENEMPGLMALREEYGPSQPLKGARIAGCLHMTVQTAVLIETLVA 65
Query: 62 LGAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWCIEQTLVFPDGKPLNMI 121
LGAEV+W+SCNIFSTQDHAAAAIAA GV V+AWKGET EEY WCIE+ L F DG+ NMI
Sbjct: 66 LGAEVRWASCNIFSTQDHAAAAIAAAGVPVFAWKGETLEEYWWCIERALTFKDGQGPNMI 125
Query: 122 LDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSVTK 179
LDDGGD T L+H+KYPQ+L+ IRG+SEETTTGVH LYKM K+ KL PAINVNDSVTK
Sbjct: 126 LDDGGDATLLIHKKYPQYLAGIRGVSEETTTGVHRLYKMLKKGKLLFPAINVNDSVTK 183
Score = 283 bits (726), Expect = 2e-88
Identities = 110/145 (75%), Positives = 124/145 (85%), Gaps = 3/145 (2%)
Query: 179 KPLNMILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVND 238
+ NMILDDGGD T L+H+KYPQ+L+ IRG+SEETTTGVH LYKM K+ KL PAINVND
Sbjct: 120 QGPNMILDDGGDATLLIHKKYPQYLAGIRGVSEETTTGVHRLYKMLKKGKLLFPAINVND 179
Query: 239 SVTKSKFDNLYGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVT 298
SVTKSKFDNLYGCRESL DG+KRATD+M+AGKVAVV GYGDVGKGCA SLR G+RVIVT
Sbjct: 180 SVTKSKFDNLYGCRESLPDGIKRATDVMIAGKVAVVCGYGDVGKGCAASLRGQGARVIVT 239
Query: 299 EIDPINALQASMEGYE---LDEEVA 320
EIDPI ALQA+MEGY+ L+E V
Sbjct: 240 EIDPICALQAAMEGYQVVTLEEVVK 264
Score = 218 bits (558), Expect = 6e-64
Identities = 85/109 (77%), Positives = 94/109 (86%)
Query: 503 DIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLEL 562
DI LA +GRK I +AENEMPGLMALR +YG + LKGARIAGCLHMTVQTAVLIETL+ L
Sbjct: 7 DISLAAFGRKEIELAENEMPGLMALREEYGPSQPLKGARIAGCLHMTVQTAVLIETLVAL 66
Query: 563 GAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWCIEQTLV 611
GAEV+W+SCNIFSTQDHAAAAIAA GV V+AWKGET EEY WCIE+ L
Sbjct: 67 GAEVRWASCNIFSTQDHAAAAIAAAGVPVFAWKGETLEEYWWCIERALT 115
Score = 210 bits (537), Expect = 4e-61
Identities = 85/118 (72%), Positives = 97/118 (82%)
Query: 343 DIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAK 402
D+M+AGKVAVV GYGDVGKGCA SLR G+RVIVTEIDPI ALQA+MEGY+V T+EE K
Sbjct: 205 DVMIAGKVAVVCGYGDVGKGCAASLRGQGARVIVTEIDPICALQAAMEGYQVVTLEEVVK 264
Query: 403 EGGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDCEIQVSWLDKNAVEKVNVKPQV 460
+ IFVTTTGC DII G HF+ M+ DAIVCNIGHFDCEI V WL+ NA + N+KPQV
Sbjct: 265 DADIFVTTTGCVDIIVGRHFMNMKKDAIVCNIGHFDCEIDVGWLNYNAKKITNIKPQV 322
Score = 210 bits (536), Expect = 8e-61
Identities = 86/109 (78%), Positives = 96/109 (88%), Gaps = 2/109 (1%)
Query: 611 VDRYTLPNGNHIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTK--HSQYPVG 668
VDRYTLPNG IILLAEGRL+NLGCA GHPSFVMSNSFTNQVLAQIELWTK +Y VG
Sbjct: 322 VDRYTLPNGRRIILLAEGRLLNLGCATGHPSFVMSNSFTNQVLAQIELWTKRDTGKYEVG 381
Query: 669 VYMLPKKLDEEVAALHLEHLGVKLTKLTEDQAKYLGLPIEGPYKPDHYR 717
VY+LPK LDE+VA LHL LGVKLTKLT+ QA+Y+G+P+EGP+KPDHYR
Sbjct: 382 VYVLPKHLDEKVARLHLGKLGVKLTKLTDKQAEYIGVPVEGPFKPDHYR 430
Score = 56.3 bits (136), Expect = 3e-08
Identities = 21/34 (61%), Positives = 27/34 (79%)
Query: 315 LDEEVAALHLEHLGVKLTKLTEDQAKYLDIMLAG 348
LDE+VA LHL LGVKLTKLT+ QA+Y+ + + G
Sbjct: 389 LDEKVARLHLGKLGVKLTKLTDKQAEYIGVPVEG 422
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 333 bits (857), Expect = e-107
Identities = 122/179 (68%), Positives = 142/179 (79%), Gaps = 3/179 (1%)
Query: 1 MADIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLL 60
+ADI LA+WGRK I AE EMPGLMA+R ++ A+K LKGARIAGCLHMT+QTAVLIETL
Sbjct: 10 VADISLADWGRKEIEWAETEMPGLMAIREEFAAEKPLKGARIAGCLHMTIQTAVLIETLK 69
Query: 61 ELGAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWCIEQTLVFPDGKPLNM 120
LGAEV+W+SCN FSTQD AAA+AA G+ V+AWKGET EEY CIE+ L DG NM
Sbjct: 70 ALGAEVRWASCNPFSTQDDVAAALAAAGIPVFAWKGETLEEYWECIERAL---DGHGPNM 126
Query: 121 ILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSVTK 179
ILDDGGDLT LVH + P+ L+ I+G++EETTTGVH LY M K+ L PAINVNDSVTK
Sbjct: 127 ILDDGGDLTLLVHTERPELLANIKGVTEETTTGVHRLYAMAKDGALKFPAINVNDSVTK 185
Score = 275 bits (706), Expect = 2e-85
Identities = 94/133 (70%), Positives = 112/133 (84%)
Query: 182 NMILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSVT 241
NMILDDGGDLT LVH + P+ L+ I+G++EETTTGVH LY M K+ L PAINVNDSVT
Sbjct: 125 NMILDDGGDLTLLVHTERPELLANIKGVTEETTTGVHRLYAMAKDGALKFPAINVNDSVT 184
Query: 242 KSKFDNLYGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEID 301
KSKFDN YG ESL+DG+KRAT++++AGKV VVAGYGDVGKGCAQ LR G+RVIVTE+D
Sbjct: 185 KSKFDNRYGTGESLLDGIKRATNVLIAGKVVVVAGYGDVGKGCAQRLRGLGARVIVTEVD 244
Query: 302 PINALQASMEGYE 314
PI ALQA+M+G+
Sbjct: 245 PICALQAAMDGFR 257
Score = 233 bits (598), Expect = 1e-69
Identities = 75/118 (63%), Positives = 93/118 (78%)
Query: 343 DIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAK 402
++++AGKV VVAGYGDVGKGCAQ LR G+RVIVTE+DPI ALQA+M+G+ V TMEEAA+
Sbjct: 207 NVLIAGKVVVVAGYGDVGKGCAQRLRGLGARVIVTEVDPICALQAAMDGFRVMTMEEAAE 266
Query: 403 EGGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDCEIQVSWLDKNAVEKVNVKPQV 460
G IFVT TG KD+I EH M+D AI+ NIGHFD EI V+ L++ AV+ +KPQV
Sbjct: 267 LGDIFVTATGNKDVITAEHMEAMKDGAILANIGHFDNEIDVAALEELAVKWREIKPQV 324
Score = 218 bits (559), Expect = 4e-64
Identities = 81/122 (66%), Positives = 94/122 (77%), Gaps = 5/122 (4%)
Query: 503 DIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLEL 562
DI LA+WGRK I AE EMPGLMA+R ++ A+K LKGARIAGCLHMT+QTAVLIETL L
Sbjct: 12 DISLADWGRKEIEWAETEMPGLMAIREEFAAEKPLKGARIAGCLHMTIQTAVLIETLKAL 71
Query: 563 GAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWCIEQTLVDRYTLPNGNHI 622
GAEV+W+SCN FSTQD AAA+AA G+ V+AWKGET EEY CIE+ L PN +
Sbjct: 72 GAEVRWASCNPFSTQDDVAAALAAAGIPVFAWKGETLEEYWECIERALDGHG--PN---M 126
Query: 623 IL 624
IL
Sbjct: 127 IL 128
Score = 203 bits (520), Expect = 1e-58
Identities = 68/102 (66%), Positives = 81/102 (79%)
Query: 611 VDRYTLPNGNHIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTKHSQYPVGVY 670
VD YTLP+G IILLAEGRLVNLG A GHPS VM SF NQ LAQIEL+T + GVY
Sbjct: 324 VDEYTLPDGKRIILLAEGRLVNLGAATGHPSEVMDMSFANQALAQIELFTNRGKLEPGVY 383
Query: 671 MLPKKLDEEVAALHLEHLGVKLTKLTEDQAKYLGLPIEGPYK 712
+LPK+LDEEVA L L+ LGVKL +LTE+QA+Y+G+ +EGP+K
Sbjct: 384 VLPKELDEEVARLKLKALGVKLDELTEEQAEYIGVWVEGPFK 425
Score = 58.2 bits (142), Expect = 7e-09
Identities = 20/29 (68%), Positives = 25/29 (86%)
Query: 314 ELDEEVAALHLEHLGVKLTKLTEDQAKYL 342
ELDEEVA L L+ LGVKL +LTE+QA+Y+
Sbjct: 388 ELDEEVARLKLKALGVKLDELTEEQAEYI 416
>gnl|CDD|240619 cd00401, SAHH, S-Adenosylhomocysteine Hydrolase, NAD-binding and
catalytic domains. S-adenosyl-L-homocysteine hydrolase
(SAHH, AdoHycase) catalyzes the hydrolysis of
S-adenosyl-L-homocysteine (AdoHyc) to form adenosine
(Ado) and homocysteine (Hcy). The equilibrium lies far
on the side of AdoHyc synthesis, but in nature the
removal of Ado and Hyc is sufficiently fast, so that the
net reaction is in the direction of hydrolysis. Since
AdoHyc is a potent inhibitor of S-adenosyl-L-methionine
dependent methyltransferases, AdoHycase plays a critical
role in the modulation of the activity of various
methyltransferases. The enzyme forms homotetramers, with
each monomer binding one molecule of NAD+.
Length = 402
Score = 326 bits (838), Expect = e-105
Identities = 113/172 (65%), Positives = 127/172 (73%), Gaps = 4/172 (2%)
Query: 8 EWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLELGAEVQ 67
E+GRK I AE EMP LMALR +Y +K LKGARIAGCLHMT QTAVLIETL LGAEV+
Sbjct: 1 EFGRKEIEWAEQEMPVLMALRERYAKEKPLKGARIAGCLHMTAQTAVLIETLKALGAEVR 60
Query: 68 WSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWCIEQTLVFPDGKPLNMILDDGGD 127
W SCN STQD AAA+A G+ V+AWKGET+EEY WCIEQ L N+I+DDGGD
Sbjct: 61 WCSCNPLSTQDDVAAALAEAGIPVFAWKGETEEEYWWCIEQAL----DHGPNLIIDDGGD 116
Query: 128 LTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSVTK 179
LT+L+H K P L +I G SEETTTGVH L M KE KL PAI VND+VTK
Sbjct: 117 LTHLLHTKRPDLLKKIIGGSEETTTGVHRLRAMEKEGKLLFPAIAVNDAVTK 168
Score = 278 bits (713), Expect = 1e-86
Identities = 87/136 (63%), Positives = 105/136 (77%)
Query: 179 KPLNMILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVND 238
N+I+DDGGDLT+L+H K P L +I G SEETTTGVH L M KE KL PAI VND
Sbjct: 105 HGPNLIIDDGGDLTHLLHTKRPDLLKKIIGGSEETTTGVHRLRAMEKEGKLLFPAIAVND 164
Query: 239 SVTKSKFDNLYGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVT 298
+VTK KFDN YG +S +DG+KRAT++++AGKV VVAGYG VGKGCA R G+RVIVT
Sbjct: 165 AVTKHKFDNRYGTGQSTIDGIKRATNVLIAGKVVVVAGYGWVGKGCAMRARGLGARVIVT 224
Query: 299 EIDPINALQASMEGYE 314
E+DPI ALQA+M+G+E
Sbjct: 225 EVDPICALQAAMDGFE 240
Score = 240 bits (614), Expect = 3e-72
Identities = 77/118 (65%), Positives = 95/118 (80%)
Query: 343 DIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAK 402
++++AGKV VVAGYG VGKGCA R G+RVIVTE+DPI ALQA+M+G+EV MEEAAK
Sbjct: 190 NVLIAGKVVVVAGYGWVGKGCAMRARGLGARVIVTEVDPICALQAAMDGFEVMPMEEAAK 249
Query: 403 EGGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDCEIQVSWLDKNAVEKVNVKPQV 460
G IFVT TG KD+IRGEHF +M+D AI+CN GHFD EI V+ L++ AVEK ++PQV
Sbjct: 250 IGDIFVTATGNKDVIRGEHFEKMKDGAILCNAGHFDVEIDVAALEELAVEKREIRPQV 307
Score = 211 bits (539), Expect = 2e-61
Identities = 73/103 (70%), Positives = 81/103 (78%)
Query: 508 EWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLELGAEVQ 567
E+GRK I AE EMP LMALR +Y +K LKGARIAGCLHMT QTAVLIETL LGAEV+
Sbjct: 1 EFGRKEIEWAEQEMPVLMALRERYAKEKPLKGARIAGCLHMTAQTAVLIETLKALGAEVR 60
Query: 568 WSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWCIEQTL 610
W SCN STQD AAA+A G+ V+AWKGET+EEY WCIEQ L
Sbjct: 61 WCSCNPLSTQDDVAAALAEAGIPVFAWKGETEEEYWWCIEQAL 103
Score = 194 bits (497), Expect = 1e-55
Identities = 67/96 (69%), Positives = 74/96 (77%)
Query: 611 VDRYTLPNGNHIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTKHSQYPVGVY 670
VD YTLP+G IILLAEGRLVNL CA GHPSFVM SF NQ LAQIELW + GVY
Sbjct: 307 VDEYTLPDGRRIILLAEGRLVNLACATGHPSFVMDMSFANQALAQIELWKNRDKLEPGVY 366
Query: 671 MLPKKLDEEVAALHLEHLGVKLTKLTEDQAKYLGLP 706
+LPK+LDEEVA L LE LG+KL KLTE+QA+YLG
Sbjct: 367 VLPKELDEEVARLKLEALGIKLDKLTEEQAEYLGSW 402
Score = 60.9 bits (149), Expect = 8e-10
Identities = 22/31 (70%), Positives = 25/31 (80%)
Query: 314 ELDEEVAALHLEHLGVKLTKLTEDQAKYLDI 344
ELDEEVA L LE LG+KL KLTE+QA+YL
Sbjct: 371 ELDEEVARLKLEALGIKLDKLTEEQAEYLGS 401
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 286 bits (733), Expect = 2e-89
Identities = 109/179 (60%), Positives = 129/179 (72%), Gaps = 5/179 (2%)
Query: 2 ADIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLE 61
DI LA+ GRK I AE EMP LMA+R ++ +K LKGARIAGCLHMT +TAVLIETL
Sbjct: 8 KDISLADEGRKEIEWAEREMPVLMAIREEFAEEKPLKGARIAGCLHMTAKTAVLIETLKA 67
Query: 62 LGAEVQWSSCNIFSTQDHAAAAIAAR-GVAVYAWKGETDEEYVWCIEQTLVFPDGKPLNM 120
GAEV+W+SCN STQD AAA+AA+ G+ V+AWKGET EEY I+Q L N+
Sbjct: 68 GGAEVRWASCNPLSTQDDVAAALAAKEGIPVFAWKGETLEEYYEAIDQVL----DWEPNI 123
Query: 121 ILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSVTK 179
I+DDGGDLT LVH + P+ L I+G +EETTTGVH L M K+ L PAINVNDSVTK
Sbjct: 124 IIDDGGDLTKLVHLERPELLDAIKGGTEETTTGVHRLRAMEKDGVLKFPAINVNDSVTK 182
Score = 244 bits (624), Expect = 1e-73
Identities = 83/137 (60%), Positives = 103/137 (75%)
Query: 178 TKPLNMILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVN 237
N+I+DDGGDLT LVH + P+ L I+G +EETTTGVH L M K+ L PAINVN
Sbjct: 118 DWEPNIIIDDGGDLTKLVHLERPELLDAIKGGTEETTTGVHRLRAMEKDGVLKFPAINVN 177
Query: 238 DSVTKSKFDNLYGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIV 297
DSVTKS FDN YG +SL+DG+ RAT+++LAGK VVAGYG VG+G A LR G+RVIV
Sbjct: 178 DSVTKSLFDNRYGTGQSLLDGILRATNVLLAGKNVVVAGYGWVGRGIAMRLRGMGARVIV 237
Query: 298 TEIDPINALQASMEGYE 314
TE+DPI AL+A+M+G+
Sbjct: 238 TEVDPIRALEAAMDGFR 254
Score = 210 bits (537), Expect = 5e-61
Identities = 74/119 (62%), Positives = 92/119 (77%)
Query: 342 LDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAA 401
+++LAGK VVAGYG VG+G A LR G+RVIVTE+DPI AL+A+M+G+ V TMEEAA
Sbjct: 203 TNVLLAGKNVVVAGYGWVGRGIAMRLRGMGARVIVTEVDPIRALEAAMDGFRVMTMEEAA 262
Query: 402 KEGGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDCEIQVSWLDKNAVEKVNVKPQV 460
K G IFVT TG KD+IR EHF +M+D AI+ N GHFD EI V+ L++ AVEK V+PQV
Sbjct: 263 KTGDIFVTATGNKDVIRKEHFEKMKDGAILANAGHFDVEIDVAGLEELAVEKREVRPQV 321
Score = 187 bits (477), Expect = 1e-52
Identities = 70/109 (64%), Positives = 83/109 (76%), Gaps = 1/109 (0%)
Query: 503 DIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLEL 562
DI LA+ GRK I AE EMP LMA+R ++ +K LKGARIAGCLHMT +TAVLIETL
Sbjct: 9 DISLADEGRKEIEWAEREMPVLMAIREEFAEEKPLKGARIAGCLHMTAKTAVLIETLKAG 68
Query: 563 GAEVQWSSCNIFSTQDHAAAAIAAR-GVAVYAWKGETDEEYVWCIEQTL 610
GAEV+W+SCN STQD AAA+AA+ G+ V+AWKGET EEY I+Q L
Sbjct: 69 GAEVRWASCNPLSTQDDVAAALAAKEGIPVFAWKGETLEEYYEAIDQVL 117
Score = 174 bits (443), Expect = 8e-48
Identities = 62/101 (61%), Positives = 71/101 (70%)
Query: 610 LVDRYTLPNGNHIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTKHSQYPVGV 669
VD Y LP+G IILLAEGRLVNL A GHPS VM SF NQ LAQI L H + GV
Sbjct: 320 QVDEYELPDGKRIILLAEGRLVNLAAATGHPSEVMDMSFANQALAQIYLVKNHGKLEPGV 379
Query: 670 YMLPKKLDEEVAALHLEHLGVKLTKLTEDQAKYLGLPIEGP 710
Y LPK+LDEEVA L LE +G++L +LTE+QA+YLG EG
Sbjct: 380 YRLPKELDEEVARLKLEAMGIELDELTEEQAEYLGSWEEGT 420
Score = 51.9 bits (125), Expect = 7e-07
Identities = 20/35 (57%), Positives = 26/35 (74%)
Query: 314 ELDEEVAALHLEHLGVKLTKLTEDQAKYLDIMLAG 348
ELDEEVA L LE +G++L +LTE+QA+YL G
Sbjct: 385 ELDEEVARLKLEAMGIELDELTEEQAEYLGSWEEG 419
>gnl|CDD|213572 TIGR00936, ahcY, adenosylhomocysteinase. This enzyme hydrolyzes
adenosylhomocysteine as part of a cycle for the
regeneration of the methyl donor S-adenosylmethionine.
Species that lack this enzyme are likely to have
adenosylhomocysteine nucleosidase (EC 3.2.2.9), an
enzyme which also acts as 5'-methyladenosine
nucleosidase (see TIGR01704) [Energy metabolism, Amino
acids and amines].
Length = 407
Score = 270 bits (691), Expect = 2e-83
Identities = 98/173 (56%), Positives = 118/173 (68%), Gaps = 5/173 (2%)
Query: 8 EWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLELGAEVQ 67
GRK I AE EMP LM +R ++ +K LKGARIA CLH+TV+TAVLIETL+ GAEV
Sbjct: 1 AEGRKKIEWAEREMPVLMRIRERFSEEKPLKGARIAACLHVTVETAVLIETLVAGGAEVA 60
Query: 68 WSSCNIFSTQDHAAAAIAA-RGVAVYAWKGETDEEYVWCIEQTLVFPDGKPLNMILDDGG 126
W+SCN STQD AAA+A G+ V+AW+GET+EEY W IEQ L N+I+DDG
Sbjct: 61 WTSCNPLSTQDDVAAALAKGAGIPVFAWRGETNEEYYWAIEQVL----DHEPNIIIDDGA 116
Query: 127 DLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDSVTK 179
DL L+H + P+ L +I G SEETTTGV L M E L PAINVND+ TK
Sbjct: 117 DLIFLLHTERPELLEKIIGGSEETTTGVIRLRAMEAEGVLKFPAINVNDAYTK 169
Score = 239 bits (611), Expect = 6e-72
Identities = 75/143 (52%), Positives = 97/143 (67%)
Query: 172 NVNDSVTKPLNMILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGV 231
+ + N+I+DDG DL L+H + P+ L +I G SEETTTGV L M E L
Sbjct: 99 AIEQVLDHEPNIIIDDGADLIFLLHTERPELLEKIIGGSEETTTGVIRLRAMEAEGVLKF 158
Query: 232 PAINVNDSVTKSKFDNLYGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLF 291
PAINVND+ TKS FDN YG +S +DG+ RAT++++AGK VVAGYG GKG A R
Sbjct: 159 PAINVNDAYTKSLFDNRYGTGQSTIDGILRATNLLIAGKTVVVAGYGWCGKGIAMRARGM 218
Query: 292 GSRVIVTEIDPINALQASMEGYE 314
G+RVIVTE+DPI AL+A+M+G+
Sbjct: 219 GARVIVTEVDPIRALEAAMDGFR 241
Score = 211 bits (538), Expect = 2e-61
Identities = 76/118 (64%), Positives = 92/118 (77%)
Query: 343 DIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAK 402
++++AGK VVAGYG GKG A R G+RVIVTE+DPI AL+A+M+G+ V TMEEAAK
Sbjct: 191 NLLIAGKTVVVAGYGWCGKGIAMRARGMGARVIVTEVDPIRALEAAMDGFRVMTMEEAAK 250
Query: 403 EGGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDCEIQVSWLDKNAVEKVNVKPQV 460
G IF+T TG KD+IRGEHF M+D AIV NIGHFD EI V L++ AVEKVNV+PQV
Sbjct: 251 IGDIFITATGNKDVIRGEHFENMKDGAIVANIGHFDVEIDVKALEELAVEKVNVRPQV 308
Score = 171 bits (434), Expect = 7e-47
Identities = 64/104 (61%), Positives = 77/104 (74%), Gaps = 1/104 (0%)
Query: 508 EWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAGCLHMTVQTAVLIETLLELGAEVQ 567
GRK I AE EMP LM +R ++ +K LKGARIA CLH+TV+TAVLIETL+ GAEV
Sbjct: 1 AEGRKKIEWAEREMPVLMRIRERFSEEKPLKGARIAACLHVTVETAVLIETLVAGGAEVA 60
Query: 568 WSSCNIFSTQDHAAAAIAA-RGVAVYAWKGETDEEYVWCIEQTL 610
W+SCN STQD AAA+A G+ V+AW+GET+EEY W IEQ L
Sbjct: 61 WTSCNPLSTQDDVAAALAKGAGIPVFAWRGETNEEYYWAIEQVL 104
Score = 167 bits (426), Expect = 1e-45
Identities = 56/100 (56%), Positives = 66/100 (66%)
Query: 611 VDRYTLPNGNHIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTKHSQYPVGVY 670
VD Y L +G I LLAEGRLVNL A GHPS VM SF NQ LA LW H + GVY
Sbjct: 308 VDEYILKDGRRIYLLAEGRLVNLAAAEGHPSEVMDMSFANQALAAEYLWKNHDKLEPGVY 367
Query: 671 MLPKKLDEEVAALHLEHLGVKLTKLTEDQAKYLGLPIEGP 710
LPK+LDE VA L LE +G+++ +LTE+Q +YLG EG
Sbjct: 368 RLPKELDEMVARLKLEAMGIEIDELTEEQKEYLGSWEEGT 407
Score = 48.9 bits (117), Expect = 5e-06
Identities = 16/32 (50%), Positives = 23/32 (71%)
Query: 313 YELDEEVAALHLEHLGVKLTKLTEDQAKYLDI 344
ELDE VA L LE +G+++ +LTE+Q +YL
Sbjct: 371 KELDEMVARLKLEAMGIEIDELTEEQKEYLGS 402
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 234 bits (598), Expect = 3e-73
Identities = 81/118 (68%), Positives = 97/118 (82%)
Query: 343 DIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAK 402
D+M+AGKVAVV GYGDVGKGCA SL+ G+RVIVTEIDPI ALQA+MEG++V T+EE K
Sbjct: 18 DVMIAGKVAVVCGYGDVGKGCAASLKGQGARVIVTEIDPICALQAAMEGFQVVTLEEVVK 77
Query: 403 EGGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDCEIQVSWLDKNAVEKVNVKPQV 460
+ IFVTTTG KDII GEH +M++DAIVCNIGHFD EI V+WL+ N + N+KPQV
Sbjct: 78 KADIFVTTTGNKDIITGEHMAKMKNDAIVCNIGHFDNEIDVAWLNTNGKKWENIKPQV 135
Score = 150 bits (381), Expect = 2e-42
Identities = 57/77 (74%), Positives = 67/77 (87%), Gaps = 2/77 (2%)
Query: 247 NLYGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINAL 306
NLYGCRESL+DG+KRATD+M+AGKVAVV GYGDVGKGCA SL+ G+RVIVTEIDPI AL
Sbjct: 1 NLYGCRESLIDGIKRATDVMIAGKVAVVCGYGDVGKGCAASLKGQGARVIVTEIDPICAL 60
Query: 307 QASMEGYELD--EEVAA 321
QA+MEG+++ EEV
Sbjct: 61 QAAMEGFQVVTLEEVVK 77
Score = 63.1 bits (154), Expect = 1e-11
Identities = 25/28 (89%), Positives = 26/28 (92%)
Query: 611 VDRYTLPNGNHIILLAEGRLVNLGCAMG 638
VDRYTLP+G HIILLAEGRLVNLGCA G
Sbjct: 135 VDRYTLPDGKHIILLAEGRLVNLGCATG 162
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 219 bits (561), Expect = 7e-68
Identities = 75/119 (63%), Positives = 90/119 (75%)
Query: 342 LDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAA 401
+++LAGK VVAGYGDVGKG A LR G+RVIVTEIDPI AL+A+M+G+EV MEEAA
Sbjct: 17 TNVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVTEIDPIRALEAAMDGFEVMKMEEAA 76
Query: 402 KEGGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDCEIQVSWLDKNAVEKVNVKPQV 460
K IFVT TG KD+I EHF M+D AI+ N GHFD EI V+ L++ AVEK V+PQV
Sbjct: 77 KRADIFVTATGNKDVITREHFRAMKDGAILANAGHFDVEIDVAALEELAVEKREVRPQV 135
Score = 140 bits (356), Expect = 9e-39
Identities = 49/77 (63%), Positives = 60/77 (77%), Gaps = 2/77 (2%)
Query: 247 NLYGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINAL 306
N YG ESL+DG+ RAT+++LAGK VVAGYGDVGKG A LR G+RVIVTEIDPI AL
Sbjct: 1 NRYGTGESLLDGILRATNVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVTEIDPIRAL 60
Query: 307 QASMEGYELD--EEVAA 321
+A+M+G+E+ EE A
Sbjct: 61 EAAMDGFEVMKMEEAAK 77
Score = 58.6 bits (143), Expect = 5e-10
Identities = 20/28 (71%), Positives = 21/28 (75%)
Query: 611 VDRYTLPNGNHIILLAEGRLVNLGCAMG 638
VD YTLP+G I LLAEGRLVNL A G
Sbjct: 135 VDEYTLPDGKRIYLLAEGRLVNLAAATG 162
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 130 bits (328), Expect = 2e-33
Identities = 53/206 (25%), Positives = 76/206 (36%), Gaps = 22/206 (10%)
Query: 180 PLNMILDDGGDLTNLVHEKYPQFLSEIRGISEETTTGVHNLYKMFKENKLGVPAINVNDS 239
L+++L LTN Q R + T H + G+ AI V
Sbjct: 64 SLDVVLKVKEPLTN-AEYALIQ-KLGDRLLFTYTIGADHRDLTEAL-ARAGLTAIAVEGV 120
Query: 240 VTKSKFDNLYGCRESLVDGLKRATDI----------MLAGKVAVVAGYGDVGKGCAQSLR 289
N G E V + R ++ +AGK VV G G VGK AQ LR
Sbjct: 121 ELPLLTSNSIGAGELSVQFIARFLEVQQPGRLGGAPDVAGKTVVVVGAGVVGKEAAQMLR 180
Query: 290 LFGSRVIVTEIDPINALQASMEGY----ELDEEVAALHLEHLGVKLTKLTE---DQAKYL 342
G++V++T+I+ Q G EL+E +A + L + +
Sbjct: 181 GLGAQVLITDINVEALEQLEELGGKNVEELEEALAEADVIVTTTLLPGKRAGILVPEELV 240
Query: 343 DIMLAGKVAVVAGYGDVGKGCAQSLR 368
+ M G V V G V GC Q+L
Sbjct: 241 EQMKPGSVIVNVAVGAV--GCVQALH 264
Score = 114 bits (287), Expect = 6e-28
Identities = 36/119 (30%), Positives = 52/119 (43%), Gaps = 6/119 (5%)
Query: 345 MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEG-YEVTTMEEAAKE 403
+AGK VV G G VGK AQ LR G++V++T+I+ Q G V +EEA E
Sbjct: 157 DVAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDINVEALEQLEELGGKNVEELEEALAE 216
Query: 404 GGIFVTTTGCKDIIRG-----EHFLQMRDDAIVCNIGHFDCEIQVSWLDKNAVEKVNVK 457
+ VTTT G E QM+ +++ N+ + + E V
Sbjct: 217 ADVIVTTTLLPGKRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQLLEEGHGVV 275
Score = 51.1 bits (122), Expect = 1e-06
Identities = 19/93 (20%), Positives = 32/93 (34%), Gaps = 7/93 (7%)
Query: 542 IAGCLHMTVQTA------VLIETLLELGAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWK 595
IAG + + ++ TL+E G EV+ + A + A + V K
Sbjct: 1 IAGPKEIKNEEFRVGLSPSVVATLVEAGHEVRVETGAGIGAGFADQAYVQAGAIVVTLAK 60
Query: 596 GETDEEYVWCIEQTLV-DRYTLPNGNHIILLAE 627
+ V +++ L Y L LL
Sbjct: 61 ALWSLDVVLKVKEPLTNAEYALIQKLGDRLLFT 93
Score = 48.4 bits (115), Expect = 6e-06
Identities = 11/49 (22%), Positives = 20/49 (40%)
Query: 610 LVDRYTLPNGNHIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIEL 658
+ L G+ ++ + + GCAMG P N + A ++L
Sbjct: 262 ALHTQLLEEGHGVVHYGDVNMPGPGCAMGVPWDATLRLAANTLPALVKL 310
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomains but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric. Formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of formate ion to carbon
dioxide with the concomitant reduction of NAD+ to NADH.
FDHs of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production and in the stress responses of plants.
Length = 313
Score = 48.7 bits (117), Expect = 4e-06
Identities = 27/96 (28%), Positives = 41/96 (42%), Gaps = 8/96 (8%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGG 405
LAGK ++ G GD+G+ A+ + FG RVI A E Y ++E E
Sbjct: 132 LAGKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVDEVYTPDELDELLPEAD 191
Query: 406 IFVTT------TGCKDIIRGEHFLQMRDDAIVCNIG 435
V T + + E F M+ A++ N+G
Sbjct: 192 YVVNALPLTPET--RGLFNAERFAAMKPGAVLINVG 225
Score = 39.8 bits (94), Expect = 0.003
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVI 296
LAGK ++ G GD+G+ A+ + FG RVI
Sbjct: 132 LAGKTVLIVGLGDIGREIARRAKAFGMRVI 161
>gnl|CDD|240648 cd12171, 2-Hacid_dh_10, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 310
Score = 47.5 bits (114), Expect = 1e-05
Identities = 26/95 (27%), Positives = 46/95 (48%), Gaps = 9/95 (9%)
Query: 345 MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP-INALQASMEGYEVTTMEEAAKE 403
L GK + G+G +G+ A+ L+ FG+ V+V DP ++ + +G + ++EE K
Sbjct: 144 ELRGKTVGIVGFGAIGRRVAKRLKAFGAEVLVY--DPYVDPEKIEADGVKKVSLEELLKR 201
Query: 404 GGIFVT-----TTGCKDIIRGEHFLQMRDDAIVCN 433
+ V+ T + +I E F M+ A N
Sbjct: 202 SDV-VSLHARLTPETRGMIGAEEFALMKPTAYFIN 235
Score = 35.2 bits (82), Expect = 0.10
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 266 MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP-INALQASMEGYELDE 317
L GK + G+G +G+ A+ L+ FG+ V+V DP ++ + +G +
Sbjct: 144 ELRGKTVGIVGFGAIGRRVAKRLKAFGAEVLVY--DPYVDPEKIEADGVKKVS 194
>gnl|CDD|240642 cd12165, 2-Hacid_dh_6, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 314
Score = 46.5 bits (111), Expect = 3e-05
Identities = 26/98 (26%), Positives = 44/98 (44%), Gaps = 11/98 (11%)
Query: 345 MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEG 404
L GK + GYG +G+ A+ L+ FG RVI P + + ++ ++EA ++
Sbjct: 134 ELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSP-KEDEGADFVGTLSDLDEALEQA 192
Query: 405 GIFV-------TTTGCKDIIRGEHFLQMRDDAIVCNIG 435
+ V T G +I M+ AI+ N+G
Sbjct: 193 DVVVVALPLTKQTRG---LIGAAELAAMKPGAILVNVG 227
Score = 32.6 bits (75), Expect = 0.60
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 266 MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIV 297
L GK + GYG +G+ A+ L+ FG RVI
Sbjct: 134 ELRGKTVGILGYGHIGREIARLLKAFGMRVIG 165
>gnl|CDD|240652 cd12175, 2-Hacid_dh_11, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 311
Score = 46.4 bits (111), Expect = 3e-05
Identities = 23/95 (24%), Positives = 38/95 (40%), Gaps = 4/95 (4%)
Query: 345 MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEG 404
L+GK + G G++G+ A+ LR FG VI + + G ++E E
Sbjct: 139 ELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEAEEKDLGVRYVELDELLAES 198
Query: 405 GIFVT----TTGCKDIIRGEHFLQMRDDAIVCNIG 435
+ T + +I E M+ AI+ N
Sbjct: 199 DVVSLHVPLTPETRHLIGAEELAAMKPGAILINTA 233
Score = 38.3 bits (90), Expect = 0.011
Identities = 26/91 (28%), Positives = 37/91 (40%), Gaps = 7/91 (7%)
Query: 252 RESLVDGLKRATDI----MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQ 307
L G + L+GK + G G++G+ A+ LR FG VI + +
Sbjct: 121 DRELRAGRWGRPEGRPSRELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEAE 180
Query: 308 ASMEGY---ELDEEVAALHLEHLGVKLTKLT 335
G ELDE +A + L V LT T
Sbjct: 181 EKDLGVRYVELDELLAESDVVSLHVPLTPET 211
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 44.6 bits (106), Expect = 1e-04
Identities = 26/106 (24%), Positives = 42/106 (39%), Gaps = 10/106 (9%)
Query: 337 DQAKYLDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTT 396
D+ + LAGK + G G +G+ A+ L+ FG +VI + V +
Sbjct: 131 DRKAFRGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGVDGVVGVDS 190
Query: 397 MEEAAKEGGIFV-------TTTGCKDIIRGEHFLQMRDDAIVCNIG 435
++E E I T G +I E +M+ AI+ N
Sbjct: 191 LDELLAEADILTLHLPLTPETRG---LINAEELAKMKPGAILINAA 233
Score = 32.3 bits (74), Expect = 0.93
Identities = 15/58 (25%), Positives = 23/58 (39%)
Query: 260 KRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDE 317
K LAGK + G G +G+ A+ L+ FG +VI + +D
Sbjct: 133 KAFRGTELAGKTVGIIGLGRIGRAVAKRLKAFGMKVIGYDPYSPRERAGVDGVVGVDS 190
>gnl|CDD|217244 pfam02826, 2-Hacid_dh_C, D-isomer specific 2-hydroxyacid
dehydrogenase, NAD binding domain. This domain is
inserted into the catalytic domain, the large
dehydrogenase and D-lactate dehydrogenase families in
SCOP. N-terminal portion of which is represented by
family pfam00389.
Length = 175
Score = 42.5 bits (101), Expect = 2e-04
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 12/97 (12%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGG 405
L+GK + G G +G+ A+ L+ FG +VI D +A G +++E E
Sbjct: 33 LSGKTVGIIGLGRIGRAVARRLKAFGMKVIAY--DRYPKAEAEALGARYVSLDELLAESD 90
Query: 406 IFV-------TTTGCKDIIRGEHFLQMRDDAIVCNIG 435
+ T +I E M+ AI+ N
Sbjct: 91 VVSLHLPLTPETRH---LINAERLALMKPGAILINTA 124
Score = 28.6 bits (65), Expect = 8.8
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIV 297
L+GK + G G +G+ A+ L+ FG +VI
Sbjct: 33 LSGKTVGIIGLGRIGRAVARRLKAFGMKVIA 63
>gnl|CDD|240622 cd05198, formate_dh_like, Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxy acid
dehydrogenase family. Formate dehydrogenase, D-specific
2-hydroxy acid dehydrogenase, Phosphoglycerate
Dehydrogenase, Lactate dehydrogenase, Thermostable
Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate
reductase, among others, share a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. 2-hydroxyacid
dehydrogenases are enzymes that catalyze the conversion
of a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
The NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal NAD
binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Formate dehydrogenase
(FDH) catalyzes the NAD+-dependent oxidation of formate
ion to carbon dioxide with the concomitant reduction of
NAD+ to NADH. FDHs of this family contain no metal ions
or prosthetic groups. Catalysis occurs though direct
transfer of hydride ion to NAD+ without the stages of
acid-base catalysis typically found in related
dehydrogenases. FDHs are found in all methylotrophic
microorganisms in energy production and in the stress
responses of plants. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase,
among others. While many members of this family are
dimeric, alanine DH is hexameric and phosphoglycerate DH
is tetrameric.
Length = 302
Score = 40.7 bits (96), Expect = 0.002
Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 11/97 (11%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGG 405
L GK + G G +G+ A+ L+ FG +V+ + G+ V +++E +
Sbjct: 138 LEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRTR-KPEPEEDLGFRVVSLDELLAQSD 196
Query: 406 IFV-------TTTGCKDIIRGEHFLQMRDDAIVCNIG 435
+ V T +I E M+ A++ N
Sbjct: 197 VVVLHLPLTPETRH---LINEEELALMKPGAVLVNTA 230
Score = 29.5 bits (67), Expect = 6.6
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVT 298
L GK + G G +G+ A+ L+ FG +V+
Sbjct: 138 LEGKTVGIVGLGRIGQRVAKRLQAFGMKVLYY 169
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 40.9 bits (97), Expect = 0.002
Identities = 28/94 (29%), Positives = 48/94 (51%), Gaps = 9/94 (9%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP-INALQASMEGYEVTTMEEAAKEG 404
L GK + G G +G+ A+ R FG +V+ DP I+A +A+ G E+ +++E E
Sbjct: 136 LRGKTLGIVGLGRIGREVARRARAFGMKVLAY--DPYISAERAAAGGVELVSLDELLAEA 193
Query: 405 GIFVT-----TTGCKDIIRGEHFLQMRDDAIVCN 433
F++ T + +I E +M+ AI+ N
Sbjct: 194 D-FISLHTPLTPETRGLINAEELAKMKPGAILIN 226
Score = 29.7 bits (68), Expect = 5.9
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP-INALQASMEGYELDE 317
L GK + G G +G+ A+ R FG +V+ DP I+A +A+ G EL
Sbjct: 136 LRGKTLGIVGLGRIGREVARRARAFGMKVLAY--DPYISAERAAAGGVELVS 185
>gnl|CDD|240628 cd05303, PGDH_2, Phosphoglycerate dehydrogenase (PGDH) NAD-binding
and catalytic domains. Phosphoglycerate dehydrogenase
(PGDH) catalyzes the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDH comes in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 301
Score = 39.8 bits (94), Expect = 0.003
Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 7/116 (6%)
Query: 322 LHLEHLGVKLTKLTEDQAKYLDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP 381
+H + +KL K ++ KY I L GK + G+G +G+ A+ R G VI + P
Sbjct: 115 IHRANREMKLGKW--NKKKYKGIELRGKTLGIIGFGRIGREVAKIARALGMNVIAYDPYP 172
Query: 382 INALQASMEGYEVTTMEEAAKEG---GIFVTTTGC-KDIIRGEHFLQMRDDAIVCN 433
+ QA G + ++EE K + V T K +I + M+D AI+ N
Sbjct: 173 KDE-QAVELGVKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIIN 227
>gnl|CDD|240654 cd12177, 2-Hacid_dh_12, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 321
Score = 38.1 bits (89), Expect = 0.011
Identities = 25/104 (24%), Positives = 49/104 (47%), Gaps = 8/104 (7%)
Query: 336 EDQAKYLDIMLAGKVAVVAGYGDVGKGCAQSLRL-FGSRVIVTEIDP-INALQASMEGYE 393
++A ++ L+GK + GYG++G A+ L+ F ++V+ DP ++ +G +
Sbjct: 135 TERANFVGHELSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAY--DPYVSEEVIKKKGAK 192
Query: 394 VTTMEEAAKEGGIFV----TTTGCKDIIRGEHFLQMRDDAIVCN 433
++EE E I T +I + F +M+ I+ N
Sbjct: 193 PVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVN 236
>gnl|CDD|240656 cd12179, 2-Hacid_dh_14, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 306
Score = 38.0 bits (89), Expect = 0.011
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 9/75 (12%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPI----NALQASMEGYELDEEVAAL 322
L GK + GYG++GK A+ L FG +VI + A Q S+E + ++ +L
Sbjct: 136 LMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNFGDAYAEQVSLETLFKEADILSL 195
Query: 323 HLEHLGVKLTKLTED 337
H + LT T
Sbjct: 196 H-----IPLTPETRG 205
Score = 33.8 bits (78), Expect = 0.31
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPI----NALQASMEGYEVTTMEEA 400
L GK + GYG++GK A+ L FG +VI + A Q S+E T +EA
Sbjct: 136 LMGKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNFGDAYAEQVSLE----TLFKEA 190
>gnl|CDD|240649 cd12172, PGDH_like_2, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 306
Score = 37.9 bits (89), Expect = 0.014
Identities = 27/93 (29%), Positives = 42/93 (45%), Gaps = 7/93 (7%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGG 405
L GK + G G +GK A+ L FG +V+ + P + A G E ++EE KE
Sbjct: 140 LYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYP-DEEFAKEHGVEFVSLEELLKESD 198
Query: 406 IFVT-----TTGCKDIIRGEHFLQMRDDAIVCN 433
F++ T + +I M+ AI+ N
Sbjct: 199 -FISLHLPLTPETRHLINAAELALMKPGAILIN 230
Score = 29.4 bits (67), Expect = 6.9
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEI--DPINALQASMEGYELDE 317
L GK + G G +GK A+ L FG +V+ + D A + +E L+E
Sbjct: 140 LYGKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYPDEEFAKEHGVEFVSLEE 192
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 35.6 bits (83), Expect = 0.015
Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 9/70 (12%)
Query: 352 VVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEV--------TTMEEA-AK 402
++ GYG VG+ A+ LR G V+V + DP + EG V +EEA +
Sbjct: 2 IIIGYGRVGRSLAEELREGGPDVVVIDKDPERVEELREEGVPVVVGDATDEEVLEEAGIE 61
Query: 403 EGGIFVTTTG 412
E V TG
Sbjct: 62 EADAVVAATG 71
Score = 35.2 bits (82), Expect = 0.023
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 10/64 (15%)
Query: 273 VVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYE------LDEEVAALHLEH 326
++ GYG VG+ A+ LR G V+V + DP + EG DEEV LE
Sbjct: 2 IIIGYGRVGRSLAEELREGGPDVVVIDKDPERVEELREEGVPVVVGDATDEEV----LEE 57
Query: 327 LGVK 330
G++
Sbjct: 58 AGIE 61
>gnl|CDD|240651 cd12174, PGDH_like_3, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 305
Score = 37.2 bits (87), Expect = 0.020
Identities = 29/111 (26%), Positives = 48/111 (43%), Gaps = 9/111 (8%)
Query: 331 LTKLTEDQAKYLD-IMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIV--TEIDPINALQA 387
++K E K L GK V G G++G+ A + G +VI + A +
Sbjct: 117 ISKGVEKGKKQFVGTELRGKTLGVIGLGNIGRLVANAALALGMKVIGYDPYLSVEAAWKL 176
Query: 388 SMEGYEVTTMEEAAKEGGIFVT-----TTGCKDIIRGEHFLQMRDDAIVCN 433
S+E VT++EE ++T T + +I E +M+ AI+ N
Sbjct: 177 SVEVQRVTSLEELLATAD-YITLHVPLTDETRGLINAELLAKMKPGAILLN 226
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 35.9 bits (82), Expect = 0.056
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 345 MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQ-ASMEGYEVTTMEEAAKE 403
+L GK V GYG G AQ+LR G V+V + P + + A +G+EV ++ EA +
Sbjct: 13 LLQGKTVAVIGYGSQGHAQAQNLRDSGVEVVVG-VRPGKSFEVAKADGFEVMSVSEAVRT 71
Query: 404 GGI 406
+
Sbjct: 72 AQV 74
Score = 30.1 bits (67), Expect = 4.6
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 266 MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQ-ASMEGYEL 315
+L GK V GYG G AQ+LR G V+V + P + + A +G+E+
Sbjct: 13 LLQGKTVAVIGYGSQGHAQAQNLRDSGVEVVVG-VRPGKSFEVAKADGFEV 62
>gnl|CDD|236209 PRK08265, PRK08265, short chain dehydrogenase; Provisional.
Length = 261
Score = 35.8 bits (83), Expect = 0.058
Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 12/74 (16%)
Query: 267 LAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEEVAALHLE 325
LAGKVA+V G +G A++L G+RV + +ID N VAA E
Sbjct: 4 LAGKVAIVTGGATLIGAAVARALVAAGARVAIVDIDADNG-----------AAVAASLGE 52
Query: 326 HLGVKLTKLTEDQA 339
T +T+D A
Sbjct: 53 RARFIATDITDDAA 66
Score = 34.2 bits (79), Expect = 0.17
Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 346 LAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEIDPIN 383
LAGKVA+V G +G A++L G+RV + +ID N
Sbjct: 4 LAGKVAIVTGGATLIGAAVARALVAAGARVAIVDIDADN 42
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of leucine
dehydrogenase, phenylalanine dehydrogenase, and valine
dehydrogenase. Amino acid dehydrogenase (DH) is a
widely distributed family of enzymes that catalyzes the
oxidative deamination of an amino acid to its keto acid
and ammonia with concomitant reduction of NADP+. For
example, leucine DH catalyzes the reversible oxidative
deamination of L-leucine and several other straight or
branched chain amino acids to the corresponding
2-oxoacid derivative. Amino acid DH -like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 200
Score = 35.3 bits (82), Expect = 0.062
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTME 398
L GK V G G VG A+ L G+++IV +I+ A+ + E + T +
Sbjct: 26 LEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINE-EAVARAAELFGATVVA 77
Score = 32.6 bits (75), Expect = 0.51
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQA 308
L GK V G G VG A+ L G+++IV +I+ +A
Sbjct: 26 LEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEAVARA 67
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 35.6 bits (83), Expect = 0.098
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 267 LAGKVAVVAG-YGDVGKGCAQSLRLFGSRVIVTEIDPINALQA 308
LAGKVA+V G G +GK A+ L G+ V++ ++D A +A
Sbjct: 420 LAGKVALVTGAAGGIGKATAKRLAAEGACVVLADLDE-EAAEA 461
Score = 35.6 bits (83), Expect = 0.098
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 346 LAGKVAVVAG-YGDVGKGCAQSLRLFGSRVIVTEIDPINALQA 387
LAGKVA+V G G +GK A+ L G+ V++ ++D A +A
Sbjct: 420 LAGKVALVTGAAGGIGKATAKRLAAEGACVVLADLDE-EAAEA 461
>gnl|CDD|116601 pfam07991, IlvN, Acetohydroxy acid isomeroreductase, catalytic
domain. Acetohydroxy acid isomeroreductase catalyzes
the conversion of acetohydroxy acids into dihydroxy
valerates. This reaction is the second in the synthetic
pathway of the essential branched side chain amino acids
valine and isoleucine.
Length = 165
Score = 34.1 bits (79), Expect = 0.10
Identities = 23/59 (38%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIV-TEIDPINALQASMEGYEVTTMEEAAKE 403
L GK V GYG G A +LR G VIV + +A +G+EV T+ EA K+
Sbjct: 2 LKGKKIAVIGYGSQGHAHALNLRDSGVNVIVGLRPGSKSWEKAKKDGFEVYTVAEAVKK 60
>gnl|CDD|187648 cd08944, SDR_c12, classical (c) SDR, subgroup 12. These are
classical SDRs, with the canonical active site tetrad
and glycine-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 246
Score = 34.8 bits (80), Expect = 0.10
Identities = 18/36 (50%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 267 LAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEID 301
L GKVA+V G G +G CA L G+RV+V +ID
Sbjct: 1 LEGKVAIVTGAGAGIGAACAARLAREGARVVVADID 36
Score = 34.8 bits (80), Expect = 0.10
Identities = 18/36 (50%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 346 LAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEID 380
L GKVA+V G G +G CA L G+RV+V +ID
Sbjct: 1 LEGKVAIVTGAGAGIGAACAARLAREGARVVVADID 36
>gnl|CDD|180669 PRK06720, PRK06720, hypothetical protein; Provisional.
Length = 169
Score = 34.2 bits (78), Expect = 0.10
Identities = 24/57 (42%), Positives = 37/57 (64%), Gaps = 4/57 (7%)
Query: 342 LDIMLAGKVAVVAGYG-DVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTM 397
+ + LAGKVA+V G G +G+ A L G++VIVT+ID + QA++E E+T +
Sbjct: 10 MKMKLAGKVAIVTGGGIGIGRNTALLLAKQGAKVIVTDIDQESG-QATVE--EITNL 63
Score = 33.8 bits (77), Expect = 0.16
Identities = 22/46 (47%), Positives = 31/46 (67%), Gaps = 2/46 (4%)
Query: 267 LAGKVAVVAGYG-DVGKGCAQSLRLFGSRVIVTEIDPINALQASME 311
LAGKVA+V G G +G+ A L G++VIVT+ID + QA++E
Sbjct: 14 LAGKVAIVTGGGIGIGRNTALLLAKQGAKVIVTDIDQESG-QATVE 58
>gnl|CDD|240662 cd12186, LDH, D-Lactate dehydrogenase and D-2-Hydroxyisocaproic
acid dehydrogenase (D-HicDH), NAD-binding and catalytic
domains. D-Lactate dehydrogenase (LDH) catalyzes the
interconversion of pyruvate and lactate, and is a member
of the 2-hydroxyacid dehydrogenases family. LDH is
homologous to D-2-hydroxyisocaproic acid
dehydrogenase(D-HicDH) and shares the 2 domain structure
of formate dehydrogenase. D-HicDH is a NAD-dependent
member of the hydroxycarboxylate dehydrogenase family,
and shares the Rossmann fold typical of many NAD binding
proteins. HicDH from Lactobacillus casei forms a monomer
and catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 35.2 bits (82), Expect = 0.10
Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 9/90 (10%)
Query: 349 KVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGGIFV 408
V ++ G G +G A+ + FG++VI + P L+ ++E+ K+ I +
Sbjct: 147 TVGII-GTGRIGSAAAKIFKGFGAKVIAYDPYPNPELEK--FLLYYDSLEDLLKQADI-I 202
Query: 409 T-----TTGCKDIIRGEHFLQMRDDAIVCN 433
+ T +I E F +M+D AI+ N
Sbjct: 203 SLHVPLTKENHHLINAEAFAKMKDGAILVN 232
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 34.9 bits (81), Expect = 0.13
Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 345 MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIV-TEIDPINALQASMEGYEVTTMEEAAKE 403
+L GK + GYG G A +LR G VI+ + +A +G++V T+EEAAK
Sbjct: 15 LLKGKKVAIIGYGSQGHAQALNLRDSGLNVIIGLRKGSSSWKKAKEDGFKVYTVEEAAKR 74
Query: 404 G 404
Sbjct: 75 A 75
>gnl|CDD|180371 PRK06057, PRK06057, short chain dehydrogenase; Provisional.
Length = 255
Score = 34.7 bits (80), Expect = 0.14
Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 15/67 (22%)
Query: 346 LAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKE- 403
LAG+VAV+ G G +G A+ L G+ V+V +IDP + AA E
Sbjct: 5 LAGRVAVITGGGSGIGLATARRLAAEGATVVVGDIDP-------------EAGKAAADEV 51
Query: 404 GGIFVTT 410
GG+FV T
Sbjct: 52 GGLFVPT 58
Score = 31.2 bits (71), Expect = 1.5
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 267 LAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEIDPINALQASME 311
LAG+VAV+ G G +G A+ L G+ V+V +IDP A+ E
Sbjct: 5 LAGRVAVITGGGSGIGLATARRLAAEGATVVVGDIDPEAGKAAADE 50
>gnl|CDD|188426 TIGR03911, pyrrolys_PylD, pyrrolysine biosynthesis protein PylD.
This protein is PylD, part of a three-gene cassette that
is sufficient to direct the biosynthesis of pyrrolysine,
the twenty-second amino acid, incorporated in some
species at a UAG canonical stop codon [Amino acid
biosynthesis, Other].
Length = 266
Score = 34.4 bits (79), Expect = 0.18
Identities = 47/187 (25%), Positives = 69/187 (36%), Gaps = 32/187 (17%)
Query: 261 RATDIMLAGKVAVV---AGYGDVGKGCAQSLR----LFGSRVIVTEIDPINAL-QASMEG 312
+ DI GKVAVV G G +G G ++S+ G R VT+ + +A G
Sbjct: 41 TSADIPDPGKVAVVPITCGNGIIG-GFSESVAAITEFLGFRAFVTDSPDVKGYAEAVERG 99
Query: 313 YEL-----DEEVAALHLEHLGVKLTKLTEDQ-------AKYLDIMLAG---KVAVVAGYG 357
E+ D A +L K K+ ++ A LD + G K +V G G
Sbjct: 100 AEIIFMADDNRFIAHNL-----KTGKIADNSEATGRGYAAALDCLTGGLKSKDVLVIGLG 154
Query: 358 DVGKGCAQSLRLFGSRVIVTEIDP--INALQASMEGYEVTTME-EAAKEGGIFVTTTGCK 414
VG+ A L G V V + + L + + EA + T
Sbjct: 155 PVGRAAAFHLVDKGFHVYVYDKNLEVSEKLAQDLCSIGIERELDEAMHKFSAIFEATPEA 214
Query: 415 DIIRGEH 421
IR +H
Sbjct: 215 GTIREDH 221
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 34.0 bits (79), Expect = 0.19
Identities = 16/50 (32%), Positives = 25/50 (50%)
Query: 249 YGCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVT 298
YG + + LK+ L GK V G+G+VG A+ L G++V+
Sbjct: 12 YGVVYFVEEALKKLGGDSLEGKTVAVQGFGNVGSYAAEKLLELGAKVVAV 61
Score = 32.9 bits (76), Expect = 0.44
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 339 AKYLDI-MLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVT 377
K L L GK V G+G+VG A+ L G++V+
Sbjct: 22 LKKLGGDSLEGKTVAVQGFGNVGSYAAEKLLELGAKVVAV 61
>gnl|CDD|240663 cd12187, LDH_like_1, D-Lactate and related Dehydrogenase like
proteins, NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase(D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 34.2 bits (79), Expect = 0.20
Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 7/93 (7%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGG 405
LAGK V G G +G+ A+ R FG +V+ ++ P L A G+ ++EE +E
Sbjct: 137 LAGKTLGVVGTGRIGRRVARIARGFGMKVLAYDVVPDEEL-AERLGFRYVSLEELLQESD 195
Query: 406 IFVT-----TTGCKDIIRGEHFLQMRDDAIVCN 433
I ++ T +I E+F M+ A++ N
Sbjct: 196 I-ISLHVPYTPQTHHLINRENFALMKPGAVLIN 227
>gnl|CDD|133445 cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 1. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
assimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 227
Score = 33.7 bits (78), Expect = 0.20
Identities = 27/95 (28%), Positives = 44/95 (46%), Gaps = 6/95 (6%)
Query: 327 LGVKLTKLTEDQAKYLDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVI-VTEIDPINAL 385
GV T + K L I LAG + G+G+VG A+ L G++V+ V++ D +
Sbjct: 12 RGVAYA--TREALKKLGIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVAVSDSD--GTI 67
Query: 386 QASMEGYEVTTMEEAAKEGGIFVTTTGCKDIIRGE 420
+ +G +V + KE G + G + I E
Sbjct: 68 -YNPDGLDVPALLAYKKEHGSVLGFPGAERITNEE 101
>gnl|CDD|240659 cd12183, LDH_like_2, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2-domain structure of formate dehydrogenase.
D-2-hydroxyisocaproate dehydrogenase-like (HicDH)
proteins are NAD-dependent members of the
hydroxycarboxylate dehydrogenase family, and share the
Rossmann fold typical of many NAD binding proteins.
HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 328
Score = 34.0 bits (79), Expect = 0.22
Identities = 26/93 (27%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGG 405
L GK V G G +G+ A+ L+ FG RV+ + P L G E ++E E
Sbjct: 142 LHGKTVGVIGTGKIGQAFARILKGFGCRVLAYDPYPNPELAK--LGVEYVDLDELLAESD 199
Query: 406 IFVT-----TTGCKDIIRGEHFLQMRDDAIVCN 433
I ++ T +I E +M+D ++ N
Sbjct: 200 I-ISLHCPLTPETHHLINAETIAKMKDGVMLIN 231
>gnl|CDD|240644 cd12167, 2-Hacid_dh_8, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 330
Score = 33.7 bits (78), Expect = 0.32
Identities = 27/99 (27%), Positives = 42/99 (42%), Gaps = 13/99 (13%)
Query: 343 DIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP-INALQASMEGYEVTTMEEAA 401
L G+ + G+G +G+ + LR FG RV+V DP + A +A+ G E+ +++E
Sbjct: 145 GRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVY--DPYLPAAEAAALGVELVSLDELL 202
Query: 402 KEGGIFVT-------TTGCKDIIRGEHFLQMRDDAIVCN 433
+ T G I MRD A N
Sbjct: 203 ARSDVVSLHAPLTPETRGM---IDARLLALMRDGATFIN 238
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 33.4 bits (77), Expect = 0.34
Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 12/96 (12%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGG 405
+ GK + G G +GK A+ + FG++V+ N E YE ++EE K
Sbjct: 143 IKGKKWGIIGLGTIGKRVAKIAQAFGAKVVYYSTSGKN----KNEEYERVSLEELLKTSD 198
Query: 406 I------FVTTTGCKDIIRGEHFLQMRDDAIVCNIG 435
I T K++I + ++D AI+ N+G
Sbjct: 199 IISIHAPLNEKT--KNLIAYKELKLLKDGAILINVG 232
>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 33.7 bits (78), Expect = 0.34
Identities = 27/109 (24%), Positives = 46/109 (42%), Gaps = 2/109 (1%)
Query: 303 INALQASMEGYELDEEVAALHLEHLGVKLTKLTEDQAKYLDIMLAGKVAVVAGYGDVGKG 362
+NA++ S + L + AL + H+G K L+ +LA +A +G+
Sbjct: 496 LNAIEKSKKQP-LARFLYALGIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEV 554
Query: 363 CAQSL-RLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGGIFVTT 410
A+S+ F + ID + A E E ++E + G FV T
Sbjct: 555 VARSIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLAGKTFVLT 603
>gnl|CDD|234662 PRK00141, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 473
Score = 33.6 bits (77), Expect = 0.37
Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 5/82 (6%)
Query: 335 TEDQAKYLDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINA--LQASMEGY 392
L L+G+V +VAG G G+G A L G V+V + + L
Sbjct: 3 ILVPLSALPQELSGRV-LVAGAGVSGRGIAAMLSELGCDVVVADDNETARHKLIEVTGVA 61
Query: 393 EVTTME--EAAKEGGIFVTTTG 412
+++T E + + VT+ G
Sbjct: 62 DISTAEASDQLDSFSLVVTSPG 83
Score = 29.4 bits (66), Expect = 7.3
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 262 ATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEEVAA 321
A L+G+V +VAG G G+G A L G V+V + + + VA
Sbjct: 9 ALPQELSGRV-LVAGAGVSGRGIAAMLSELGCDVVVADDNE-----TARHKLIEVTGVAD 62
Query: 322 LHLEH 326
+
Sbjct: 63 ISTAE 67
>gnl|CDD|240632 cd12155, PGDH_1, Phosphoglycerate Dehydrogenase, 2-hydroxyacid
dehydrogenase family. Phosphoglycerate Dehydrogenase
(PGDH) catalyzes the NAD-dependent conversion of
3-phosphoglycerate into 3-phosphohydroxypyruvate, which
is the first step in serine biosynthesis.
Over-expression of PGDH has been implicated as
supporting proliferation of certain breast cancers,
while PGDH deficiency is linked to defects in mammalian
central nervous system development. PGDH is a member of
the 2-hydroxyacid dehydrogenase family, enzymes that
catalyze the conversion of a wide variety of D-2-hydroxy
acids to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-Adenosylhomocysteine Hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members of
this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 314
Score = 33.3 bits (77), Expect = 0.44
Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 13/98 (13%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEG----YEVTTMEEAA 401
L GK + G G +G+ A+ L+ FG +VI +N +E Y + ++E
Sbjct: 133 LYGKTILFLGTGSIGQEIAKRLKAFGMKVI-----GVNTSGRDVEYFDKCYPLEELDEVL 187
Query: 402 KEGGIFV----TTTGCKDIIRGEHFLQMRDDAIVCNIG 435
KE I V T + F QM+ A+ N+G
Sbjct: 188 KEADIVVNVLPLTEETHHLFDEAFFEQMKKGALFINVG 225
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 32.7 bits (75), Expect = 0.56
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 268 AGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP 302
G +V G G VG AQ + G+RVIVT+
Sbjct: 134 PGDTVLVLGAGGVGLLAAQLAKAAGARVIVTDRSD 168
Score = 32.7 bits (75), Expect = 0.56
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 347 AGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP 381
G +V G G VG AQ + G+RVIVT+
Sbjct: 134 PGDTVLVLGAGGVGLLAAQLAKAAGARVIVTDRSD 168
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 33.0 bits (76), Expect = 0.58
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 16/62 (25%)
Query: 321 ALHLEHLGVKLTKLTEDQAKYLDIMLAGKVAVVAGYGDVGKGCAQSLRLFG-SRVIVTEI 379
ALH V+L +T G VV G G +G Q L++ G RVI +I
Sbjct: 148 ALH----AVRLAGIT-----------LGDTVVVIGAGTIGLLAIQWLKILGAKRVIAVDI 192
Query: 380 DP 381
D
Sbjct: 193 DD 194
Score = 32.2 bits (74), Expect = 0.87
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 268 AGKVAVVAGYGDVGKGCAQSLRLFG-SRVIVTEIDP 302
G VV G G +G Q L++ G RVI +ID
Sbjct: 159 LGDTVVVIGAGTIGLLAIQWLKILGAKRVIAVDIDD 194
>gnl|CDD|236399 PRK09186, PRK09186, flagellin modification protein A; Provisional.
Length = 256
Score = 32.7 bits (75), Expect = 0.63
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 266 MLAGKVAVVAGY-GDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEEVAALHL 324
ML GK ++ G G +G +++ G VI +ID AL +E + + L L
Sbjct: 1 MLKGKTILITGAGGLIGSALVKAILEAGGIVIAADID-KEALNELLESLGKEFKSKKLSL 59
Query: 325 EHLGV 329
L +
Sbjct: 60 VELDI 64
Score = 31.5 bits (72), Expect = 1.3
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 345 MLAGKVAVVAGY-GDVGKGCAQSLRLFGSRVIVTEID 380
ML GK ++ G G +G +++ G VI +ID
Sbjct: 1 MLKGKTILITGAGGLIGSALVKAILEAGGIVIAADID 37
>gnl|CDD|234025 TIGR02819, fdhA_non_GSH, formaldehyde dehydrogenase,
glutathione-independent. Members of this family
represent a distinct clade within the larger family of
zinc-dependent dehydrogenases of medium chain alcohols,
a family that also includes the so-called
glutathione-dependent formaldehyde dehydrogenase.
Members of this protein family have a tightly bound NAD
that can act as a true cofactor, rather than a
cosubstrate in dehydrogenase reactions, in dismutase
reactions for some aldehydes. The name given to this
family, however, is formaldehyde dehydrogenase,
glutathione-independent [Central intermediary
metabolism, One-carbon metabolism].
Length = 393
Score = 32.9 bits (75), Expect = 0.63
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 348 GKVAVVAGYGDVGKGCAQSLRLFG-SRVIVTEIDPINALQASMEGYEVTTMEEAA 401
G +AG G VG A S +L G + VIV +++P QA G E + + A
Sbjct: 186 GSTVYIAGAGPVGLAAAASAQLLGAAVVIVGDLNPARLAQARSFGCETVDLSKDA 240
Score = 32.1 bits (73), Expect = 1.1
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 269 GKVAVVAGYGDVGKGCAQSLRLFG-SRVIVTEIDPINALQASMEGYE 314
G +AG G VG A S +L G + VIV +++P QA G E
Sbjct: 186 GSTVYIAGAGPVGLAAAASAQLLGAAVVIVGDLNPARLAQARSFGCE 232
>gnl|CDD|224593 COG1679, COG1679, Predicted aconitase [General function
prediction only].
Length = 403
Score = 32.7 bits (75), Expect = 0.66
Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 4/51 (7%)
Query: 21 MPGLMALRRKYGAQKIL--KGARIAGCLHMTVQTAVL--IETLLELGAEVQ 67
M L+AL YGA++++ K A I+G + T+ A L +E L E+GA V
Sbjct: 26 MEILVALGDAYGAERLVPIKSAHISGVSYKTIGDAGLEFLEDLAEMGARVS 76
Score = 32.7 bits (75), Expect = 0.66
Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 4/51 (7%)
Query: 521 MPGLMALRRKYGAQKIL--KGARIAGCLHMTVQTAVL--IETLLELGAEVQ 567
M L+AL YGA++++ K A I+G + T+ A L +E L E+GA V
Sbjct: 26 MEILVALGDAYGAERLVPIKSAHISGVSYKTIGDAGLEFLEDLAEMGARVS 76
>gnl|CDD|240620 cd01619, LDH_like, D-Lactate and related Dehydrogenases,
NAD-binding and catalytic domains. D-Lactate
dehydrogenase (LDH) catalyzes the interconversion of
pyruvate and lactate, and is a member of the
2-hydroxyacid dehydrogenase family. LDH is homologous to
D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH) and
shares the 2 domain structure of formate dehydrogenase.
D-HicDH is a NAD-dependent member of the
hydroxycarboxylate dehydrogenase family, and shares the
Rossmann fold typical of many NAD binding proteins.
D-HicDH from Lactobacillus casei forms a monomer and
catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. Similar to the structurally
distinct L-HicDH, D-HicDH exhibits low side-chain R
specificity, accepting a wide range of 2-oxocarboxylic
acid side chains. (R)-2-hydroxyglutarate dehydrogenase
(HGDH) catalyzes the NAD-dependent reduction of
2-oxoglutarate to (R)-2-hydroxyglutarate.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 323
Score = 32.3 bits (74), Expect = 0.77
Identities = 22/113 (19%), Positives = 39/113 (34%), Gaps = 10/113 (8%)
Query: 329 VKLTKLTEDQAKYLDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQAS 388
+ A + L + V G G +G+ AQ + FG +VI + L+
Sbjct: 124 ERDKNQDLQDAGVIGRELEDQTVGVVGTGKIGRAVAQRAKGFGMKVIAYDPFRNPELED- 182
Query: 389 MEGYEVTTMEEAAKEGGIFVTTTGCKDIIRGEHFL------QMRDDAIVCNIG 435
+G + ++EE K I + H + M+ I+ N
Sbjct: 183 -KGVKYVSLEELFKNSDII--SLHVPLTPENHHMINEEAFKLMKKGVIIINTA 232
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 32.3 bits (74), Expect = 0.82
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVT 298
L GK + GYG +G A+ LR FG +++ T
Sbjct: 157 LFGKTVFILGYGAIGIELAKRLRPFGVKLLAT 188
Score = 32.3 bits (74), Expect = 0.82
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVT 377
L GK + GYG +G A+ LR FG +++ T
Sbjct: 157 LFGKTVFILGYGAIGIELAKRLRPFGVKLLAT 188
>gnl|CDD|176222 cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family. This
group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group includes
various activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
ADH-like proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and generally have 2 tightly bound zinc atoms per
subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 32.2 bits (74), Expect = 0.90
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 268 AGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP 302
AG +V G G +G G Q + G+RVIV +ID
Sbjct: 159 AGDTVLVVGAGPIGLGVIQVAKARGARVIVVDIDD 193
Score = 32.2 bits (74), Expect = 0.90
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 347 AGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP 381
AG +V G G +G G Q + G+RVIV +ID
Sbjct: 159 AGDTVLVVGAGPIGLGVIQVAKARGARVIVVDIDD 193
>gnl|CDD|129557 TIGR00465, ilvC, ketol-acid reductoisomerase. This is the second
enzyme in the parallel isoleucine-valine biosynthetic
pathway [Amino acid biosynthesis, Pyruvate family].
Length = 314
Score = 32.0 bits (73), Expect = 0.91
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIV-TEIDPINALQASMEGYEVTTMEEAAKEG 404
L GK + GYG G A +LR G VIV + +A+ +G++V T+EEA +
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGASWKKATEDGFKVGTVEEAIPQA 60
Query: 405 GI 406
+
Sbjct: 61 DL 62
>gnl|CDD|176188 cd05285, sorbitol_DH, Sorbitol dehydrogenase. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Sorbitol dehydrogenase is tetrameric and has a single
catalytic zinc per subunit. Aldose reductase catalyzes
the NADP(H)-dependent conversion of glucose to sorbital,
and SDH uses NAD(H) in the conversion of sorbitol to
fructose. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 343
Score = 32.1 bits (74), Expect = 0.96
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 269 GKVAVVAGYGDVGKGCAQSLRLFG-SRVIVTEIDP 302
G +V G G +G A + FG ++V+VT+IDP
Sbjct: 163 GDTVLVFGAGPIGLLTAAVAKAFGATKVVVTDIDP 197
Score = 32.1 bits (74), Expect = 0.96
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 348 GKVAVVAGYGDVGKGCAQSLRLFG-SRVIVTEIDP 381
G +V G G +G A + FG ++V+VT+IDP
Sbjct: 163 GDTVLVFGAGPIGLLTAAVAKAFGATKVVVTDIDP 197
>gnl|CDD|234539 TIGR04317, W_rSAM_matur, tungsten cofactor oxidoreducase radical
SAM maturase. Members of this family are radical SAM
enzymes involved in the maturation of tungsten
(W)-containing cofactors in the enzymes aldehyde
ferredoxin oxidoreductase, formaldehyde ferredoxin
oxidoreductase, and others, and tend to be encoded by an
adjacent gene.
Length = 349
Score = 31.9 bits (73), Expect = 1.0
Identities = 28/133 (21%), Positives = 48/133 (36%), Gaps = 15/133 (11%)
Query: 127 DLTNLVHEKYPQF--LSEI--RGISEETTTGVH-NLYKM---FKENKLGVPAINVNDS-V 177
DL + E+ + L EI GI E T VH + M KE V ++ N +
Sbjct: 36 DLFEKILEEAVELPELKEIVLGGIGEPT---VHPDFIDMLTEAKERGFAV-GLSTNGYLL 91
Query: 178 TKPLNMILDDGGDLTNLVHEKYPQFLSEIRG--ISEETTTGVHNLYKMFKENKLGVPAIN 235
+ ++ G D + + P I G + + LY++ + P +
Sbjct: 92 EEMAEELVGLGVDKIYVSIDALPDKPYRIIGHGDLAKVLENLKKLYEIKIKKGSDKPHVG 151
Query: 236 VNDSVTKSKFDNL 248
+ TK + L
Sbjct: 152 IEFVATKENYKEL 164
>gnl|CDD|132245 TIGR03201, dearomat_had, 6-hydroxycyclohex-1-ene-1-carbonyl-CoA
dehydrogenase. Members of this protein family are
6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase, an
enzyme in the anaerobic metabolism of aromatic enzymes
by way of benzoyl-CoA, as seen in Thauera aromatica,
Geobacter metallireducens, and Azoarcus sp. The
experimentally characterized form from T. aromatica uses
only NAD+, not NADP+. Note that Rhodopseudomonas
palustris uses a different pathway to perform a similar
degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.
Length = 349
Score = 31.8 bits (72), Expect = 1.1
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 320 AALHLEHLGVKLTKLTED-QAKYLDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTE 378
A L LEH+ V +T QA + G + +V G G VG Q+ + G+ V+ +
Sbjct: 138 AGLPLEHVSVVADAVTTPYQAAVQAGLKKGDLVIVIGAGGVGGYMVQTAKAMGAAVVAID 197
Query: 379 IDP 381
IDP
Sbjct: 198 IDP 200
Score = 31.0 bits (70), Expect = 1.9
Identities = 27/111 (24%), Positives = 44/111 (39%), Gaps = 25/111 (22%)
Query: 269 GKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP--------------INALQASMEGYE 314
G + +V G G VG Q+ + G+ V+ +IDP +N S E
Sbjct: 167 GDLVIVIGAGGVGGYMVQTAKAMGAAVVAIDIDPEKLEMMKGFGADLTLNPKDKS--ARE 224
Query: 315 LDEEVAALHLEHLGVKLT--KLTE------DQAKYLDIMLAGKVAVVAGYG 357
+ + + A + G++ T K+ E Q L ++ G VV GY
Sbjct: 225 VKKLIKA-FAKARGLRSTGWKIFECSGSKPGQESALSLLSHGGTLVVVGYT 274
>gnl|CDD|235491 PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional.
Length = 330
Score = 31.6 bits (73), Expect = 1.2
Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 15/66 (22%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINAL--------QASMEGYEVTTM 397
+ GK + GYG G A +LR G V+V L +A +G+EV T+
Sbjct: 15 IKGKKVAIIGYGSQGHAHALNLRDSGVDVVV-------GLREGSKSWKKAEADGFEVLTV 67
Query: 398 EEAAKE 403
EAAK
Sbjct: 68 AEAAKW 73
>gnl|CDD|233635 TIGR01915, npdG, NADPH-dependent F420 reductase. This model
represents a subset of a parent family described by
pfam03807. Unlike the parent family, members of this
family are found only in species with evidence of
coenzyme F420. All members of this family are believed
to act as NADPH-dependent F420 reductase [Energy
metabolism, Electron transport].
Length = 219
Score = 31.3 bits (71), Expect = 1.2
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 349 KVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGGIFV 408
K+AV+ G GD GKG A L G+++I+ D A +A+ E GG +
Sbjct: 2 KIAVLGGTGDQGKGLALRLAKAGNKIIIGSRDLEKAEEAA------AKALEELGHGGSDI 55
Query: 409 TTTG 412
TG
Sbjct: 56 KVTG 59
Score = 30.9 bits (70), Expect = 1.7
Identities = 29/91 (31%), Positives = 40/91 (43%), Gaps = 23/91 (25%)
Query: 270 KVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEEVAALHLEHLG- 328
K+AV+ G GD GKG A L G+++I+ D A EE AA LE LG
Sbjct: 2 KIAVLGGTGDQGKGLALRLAKAGNKIIIGSRDLEKA-----------EEAAAKALEELGH 50
Query: 329 ----VKLTKLT-EDQAKYLDIMLAGKVAVVA 354
+K+T + AK V ++A
Sbjct: 51 GGSDIKVTGADNAEAAK------RADVVILA 75
>gnl|CDD|235693 PRK06077, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 252
Score = 31.6 bits (72), Expect = 1.3
Identities = 25/79 (31%), Positives = 34/79 (43%), Gaps = 12/79 (15%)
Query: 346 LAGKVAVVAGYG-DVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEG 404
L KV VV G G +G+ A L GS V+V NA + + E E M +
Sbjct: 4 LKDKVVVVTGSGRGIGRAIAVRLAKEGSLVVV------NAKKRAEEMNETLKMVKENGGE 57
Query: 405 GIFV-----TTTGCKDIIR 418
GI V T GC+ + +
Sbjct: 58 GIGVLADVSTREGCETLAK 76
>gnl|CDD|240653 cd12176, PGDH_3, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 31.4 bits (72), Expect = 1.5
Identities = 30/95 (31%), Positives = 40/95 (42%), Gaps = 17/95 (17%)
Query: 348 GKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPI----NALQASMEGYEVTTMEEAAKE 403
GK + GYG +G + G RVI +I NA Q S ++EE E
Sbjct: 140 GKTLGIIGYGHIGSQLSVLAEALGMRVIFYDIAEKLPLGNARQVS-------SLEELLAE 192
Query: 404 GGIFVT-----TTGCKDIIRGEHFLQMRDDAIVCN 433
FVT T K++I E QM+ AI+ N
Sbjct: 193 AD-FVTLHVPATPSTKNMIGAEEIAQMKKGAILIN 226
>gnl|CDD|235736 PRK06196, PRK06196, oxidoreductase; Provisional.
Length = 315
Score = 31.6 bits (72), Expect = 1.5
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 9/73 (12%)
Query: 262 ATDIM----LAGKVAVVAG-YGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELD 316
A +++ L+GK A+V G Y +G ++L G+ VIV P A +A +D
Sbjct: 15 AEEVLAGHDLSGKTAIVTGGYSGLGLETTRALAQAGAHVIVPARRPDVAREALA---GID 71
Query: 317 E-EVAALHLEHLG 328
EV L L L
Sbjct: 72 GVEVVMLDLADLE 84
Score = 29.7 bits (67), Expect = 5.0
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 346 LAGKVAVVAG-YGDVGKGCAQSLRLFGSRVIVTEIDPINALQA--SMEGYEVTTME 398
L+GK A+V G Y +G ++L G+ VIV P A +A ++G EV ++
Sbjct: 24 LSGKTAIVTGGYSGLGLETTRALAQAGAHVIVPARRPDVAREALAGIDGVEVVMLD 79
>gnl|CDD|133446 cd01078, NAD_bind_H4MPT_DH, NADP binding domain of methylene
tetrahydromethanopterin dehydrogenase. Methylene
Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP
binding domain. NADP-dependent H4MPT DH catalyzes the
dehydrogenation of methylene- H4MPT and
methylene-tetrahydrofolate (H4F) with NADP+ as cofactor.
H4F and H4MPT are both cofactors that carry the
one-carbon units between the formyl and methyl oxidation
level. H4F and H4MPT are structurally analogous to each
other with respect to the pterin moiety, but each has
distinct side chain. H4MPT is present only in anaerobic
methanogenic archaea and aerobic methylotrophic
proteobacteria. H4MPT seems to have evolved
independently from H4F and functions as a distinct
carrier in C1 metabolism. Amino acid DH-like
NAD(P)-binding domains are members of the Rossmann fold
superfamily and include glutamate, leucine, and
phenylalanine DHs, methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 194
Score = 30.8 bits (70), Expect = 1.6
Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 13/80 (16%)
Query: 346 LAGK-VAVVAGYGDVGKGCAQSLRLFGSRVIVTE---------IDPINALQ-ASMEGYEV 394
L GK V+ G G VG+ A L G+RV++ D + A + E
Sbjct: 26 LKGKTAVVLGGTGPVGQRAAVLLAREGARVVLVGRDLERAQKAADSLRARFGEGVGAVET 85
Query: 395 TTMEE--AAKEGGIFVTTTG 412
+ AA +G V G
Sbjct: 86 SDDAARAAAIKGADVVFAAG 105
Score = 30.8 bits (70), Expect = 1.7
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 267 LAGK-VAVVAGYGDVGKGCAQSLRLFGSRVIVT 298
L GK V+ G G VG+ A L G+RV++
Sbjct: 26 LKGKTAVVLGGTGPVGQRAAVLLAREGARVVLV 58
>gnl|CDD|235787 PRK06370, PRK06370, mercuric reductase; Validated.
Length = 463
Score = 31.3 bits (72), Expect = 1.8
Identities = 28/112 (25%), Positives = 42/112 (37%), Gaps = 26/112 (23%)
Query: 337 DQAKYL---DIM----LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP--IN---- 383
D+ YL I L + ++ G G +G AQ R FGS V V E P +
Sbjct: 154 DEVGYLTNETIFSLDELPEHLVIIGG-GYIGLEFAQMFRRFGSEVTVIERGPRLLPREDE 212
Query: 384 ----ALQASM--EGYEV---TTMEEAAKEGG---IFVTTTGCKDIIRGEHFL 423
A++ + EG +V ++G + + G I G H L
Sbjct: 213 DVAAAVREILEREGIDVRLNAECIRVERDGDGIAVGLDCNGGAPEITGSHIL 264
Score = 29.8 bits (68), Expect = 6.4
Identities = 24/62 (38%), Positives = 29/62 (46%), Gaps = 10/62 (16%)
Query: 273 VVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEEVAAL---HLEHLGV 329
V+ G G +G AQ R FGS V V E P L E DE+VAA LE G+
Sbjct: 175 VIIGGGYIGLEFAQMFRRFGSEVTVIERGP--RL-LPRE----DEDVAAAVREILEREGI 227
Query: 330 KL 331
+
Sbjct: 228 DV 229
>gnl|CDD|184944 PRK14982, PRK14982, acyl-ACP reductase; Provisional.
Length = 340
Score = 31.1 bits (71), Expect = 1.9
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 13/82 (15%)
Query: 336 EDQAKYLDIMLA-GKVAVVAGYGDVGKG-CAQSLRLFGSRVIVTEI-------DPINALQ 386
E A L I L+ VAVV GD+G C R ++ V E+ + + LQ
Sbjct: 143 EQNAPRLGIDLSKATVAVVGATGDIGSAVC----RWLDAKTGVAELLLVARQQERLQELQ 198
Query: 387 ASMEGYEVTTMEEAAKEGGIFV 408
A + G ++ ++EEA E I V
Sbjct: 199 AELGGGKILSLEEALPEADIVV 220
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 31.3 bits (72), Expect = 1.9
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTE 299
LAGK + GYG++G+ A+ R FG +V+ E
Sbjct: 145 LAGKTLGIIGYGNIGQAVARIARAFGMKVLFAE 177
Score = 31.3 bits (72), Expect = 1.9
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTE 378
LAGK + GYG++G+ A+ R FG +V+ E
Sbjct: 145 LAGKTLGIIGYGNIGQAVARIARAFGMKVLFAE 177
>gnl|CDD|236326 PRK08655, PRK08655, prephenate dehydrogenase; Provisional.
Length = 437
Score = 31.1 bits (71), Expect = 2.0
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 349 KVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASME-GYEVTT-MEEAAKEGGI 406
K++++ G G +GK A+ L+ G VIVT DP + + E G E +AAK+ I
Sbjct: 2 KISIIGGTGGLGKWFARFLKEKGFEVIVTGRDPKKGKEVAKELGVEYANDNIDAAKDADI 61
Query: 407 FV 408
+
Sbjct: 62 VI 63
Score = 30.0 bits (68), Expect = 4.6
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 270 KVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEEVAALHLEHLGV 329
K++++ G G +GK A+ L+ G VIVT DP +EVA + LGV
Sbjct: 2 KISIIGGTGGLGKWFARFLKEKGFEVIVTGRDPKKG-----------KEVA----KELGV 46
Query: 330 KLTKLTEDQAKYLDI 344
+ D AK DI
Sbjct: 47 EYANDNIDAAKDADI 61
>gnl|CDD|176224 cd08263, Zn_ADH10, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 367
Score = 31.2 bits (71), Expect = 2.0
Identities = 34/130 (26%), Positives = 48/130 (36%), Gaps = 19/130 (14%)
Query: 259 LKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEE 318
LK A D + G+ V G G VG Q + FG+ I+ A+ E +E
Sbjct: 179 LKHAAD-VRPGETVAVIGVGGVGSSAIQLAKAFGASPII-------AVDVRDEKLAKAKE 230
Query: 319 VAALHLEHLGVKLTKLTEDQAKYLDIMLAGKVAVVAGYGDVGK----GCAQSLRLFGSRV 374
+ A H V K + A +I V VV +GK A + G R
Sbjct: 231 LGATHT----VNAAK-EDAVAAIREITGGRGVDVV--VEALGKPETFKLALDVVRDGGRA 283
Query: 375 IVTEIDPINA 384
+V + P A
Sbjct: 284 VVVGLAPGGA 293
>gnl|CDD|180363 PRK06038, PRK06038, N-ethylammeline chlorohydrolase; Provisional.
Length = 430
Score = 31.3 bits (71), Expect = 2.1
Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 486 LVNT-IHEAPTLLVHLSTDIKLAEWGRKTIIMAENEMPGLMALRRKYGAQKILKGARIAG 544
LVNT H A TL + D+ LAEW I AE ++ A+ + G+ +A
Sbjct: 57 LVNTHTHAAMTLFRGYADDLPLAEWLNDHIWPAEAKL----------TAEDVYAGSLLA- 105
Query: 545 CLHM 548
CL M
Sbjct: 106 CLEM 109
>gnl|CDD|235975 PRK07231, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 251
Score = 30.6 bits (70), Expect = 2.2
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 266 MLAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEIDP 302
L GKVA+V G +G+G A+ G+RV+VT+ +
Sbjct: 2 RLEGKVAIVTGASSGIGEGIARRFAAEGARVVVTDRNE 39
Score = 30.6 bits (70), Expect = 2.2
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 345 MLAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEIDP 381
L GKVA+V G +G+G A+ G+RV+VT+ +
Sbjct: 2 RLEGKVAIVTGASSGIGEGIARRFAAEGARVVVTDRNE 39
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 30.7 bits (70), Expect = 2.3
Identities = 25/82 (30%), Positives = 38/82 (46%), Gaps = 19/82 (23%)
Query: 346 LAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEIDP--INALQASMEG----YEVTT-- 396
LAGKV VV G +G A+ L G+++ + +++ + AL A + G V
Sbjct: 7 LAGKVVVVTGAARGIGAELARRLHARGAKLALVDLEEAELAALAAELGGDDRVLTVVADV 66
Query: 397 -----MEEAAKE-----GGIFV 408
M+ AA+E GGI V
Sbjct: 67 TDLAAMQAAAEEAVERFGGIDV 88
Score = 29.6 bits (67), Expect = 5.7
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 267 LAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEIDP--INALQASMEGYELDEEVAA 321
LAGKV VV G +G A+ L G+++ + +++ + AL A + G + V A
Sbjct: 7 LAGKVVVVTGAARGIGAELARRLHARGAKLALVDLEEAELAALAAELGGDDRVLTVVA 64
>gnl|CDD|219630 pfam07901, DUF1672, Protein of unknown function (DUF1672). This
family is composed of hypothetical bacterial proteins of
unknown function.
Length = 277
Score = 31.0 bits (70), Expect = 2.3
Identities = 24/81 (29%), Positives = 34/81 (41%), Gaps = 16/81 (19%)
Query: 95 KGETDEEYVWCIEQTLVFPDGKPLNMIL----------DDGGDLTNLVHEKYPQFLSEIR 144
G+ E YV C + +VF P + + D G D++ LV F E R
Sbjct: 62 SGDGVEVYVHCDDHDIVFNASIPFDKSIIHSDSSLRSEDKGDDMSTLVGTVLSGF--EYR 119
Query: 145 GISEETTTGVHNLYKMFKENK 165
E+ NLYK FK+N+
Sbjct: 120 AQKEK----YDNLYKFFKDNE 136
>gnl|CDD|240643 cd12166, 2-Hacid_dh_7, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 300
Score = 31.0 bits (71), Expect = 2.3
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVI 296
LA + ++ GYG +G+ + L F RV
Sbjct: 130 LADRRVLIVGYGSIGRAIERRLAPFEVRVT 159
Score = 31.0 bits (71), Expect = 2.3
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVI 375
LA + ++ GYG +G+ + L F RV
Sbjct: 130 LADRRVLIVGYGSIGRAIERRLAPFEVRVT 159
>gnl|CDD|224147 COG1226, Kch, Kef-type K+ transport systems, predicted NAD-binding
component [Inorganic ion transport and metabolism].
Length = 212
Score = 30.5 bits (68), Expect = 2.3
Identities = 12/43 (27%), Positives = 20/43 (46%)
Query: 352 VVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEV 394
++ G+G VG+ A++L G V+V + D G V
Sbjct: 25 IIVGFGRVGQIVARALLASGIPVVVIDSDEDRVELLRELGLLV 67
Score = 29.7 bits (66), Expect = 4.3
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 2/62 (3%)
Query: 252 RESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASME 311
E + L A + + ++ G+G VG+ A++L G V+V + D
Sbjct: 6 LELIFALLIFAIVRLK--RHVIIVGFGRVGQIVARALLASGIPVVVIDSDEDRVELLREL 63
Query: 312 GY 313
G
Sbjct: 64 GL 65
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 31.1 bits (71), Expect = 2.4
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 339 AKYLDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIV 376
K L L G V G+G+VG+ A+ L G++V+
Sbjct: 198 LKALGDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVA 235
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 30.7 bits (70), Expect = 2.8
Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 9/96 (9%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGG 405
L GK + G G +G+ A+ L+ FG +V+ + P + + G ++E E
Sbjct: 144 LRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNPEAEKEL-GARYVDLDELLAESD 202
Query: 406 IFVTTTGC------KDIIRGEHFLQMRDDAIVCNIG 435
I C + +I E +M+ AI+ N
Sbjct: 203 IISLH--CPLTPETRHLINAEELAKMKPGAILVNTA 236
>gnl|CDD|179571 PRK03369, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 488
Score = 30.9 bits (70), Expect = 2.8
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 342 LDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASME-GYEVTTMEEA 400
LD +L G +VAG G G+ +L FG+R V + DP +AL+ E G + +A
Sbjct: 6 LDPLLPGAPVLVAGAGVTGRAVLAALTRFGARPTVCDDDP-DALRPHAERGVATVSTSDA 64
Query: 401 AK---EGGIFVTTTG 412
+ + + VT+ G
Sbjct: 65 VQQIADYALVVTSPG 79
>gnl|CDD|240634 cd12157, PTDH, Thermostable Phosphite Dehydrogenase. Phosphite
dehydrogenase (PTDH), a member of the D-specific
2-hydroxyacid dehydrogenase family, catalyzes the
NAD-dependent formation of phosphate from phosphite
(hydrogen phosphonate). PTDH has been suggested as a
potential enzyme for cofactor regeneration systems. The
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD-binding
domain.
Length = 318
Score = 30.3 bits (69), Expect = 3.1
Identities = 19/94 (20%), Positives = 38/94 (40%), Gaps = 4/94 (4%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEGG 405
L GK + G G +G+ A+ L FG+ ++ + P++ + ++E +
Sbjct: 142 LDGKTVGILGMGALGRAIARRLSGFGATLLYYDPHPLDQAEEQALNLRRVELDELLESSD 201
Query: 406 IFVT----TTGCKDIIRGEHFLQMRDDAIVCNIG 435
V T +I E +M+ A++ N
Sbjct: 202 FLVLALPLTPDTLHLINAEALAKMKPGALLVNPC 235
>gnl|CDD|179580 PRK03449, PRK03449, putative inner membrane protein translocase
component YidC; Provisional.
Length = 304
Score = 30.4 bits (69), Expect = 3.5
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 12/47 (25%)
Query: 22 PGLMALRRKYG---------AQKILK--GAR-IAGCLHMTVQTAVLI 56
P + AL++KYG QK+ K G I GCL M Q V +
Sbjct: 66 PQIKALQKKYGNDRQKMALEMQKLQKEHGFNPILGCLPMLAQIPVFL 112
Score = 30.4 bits (69), Expect = 3.5
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 12/47 (25%)
Query: 522 PGLMALRRKYG---------AQKILK--GAR-IAGCLHMTVQTAVLI 556
P + AL++KYG QK+ K G I GCL M Q V +
Sbjct: 66 PQIKALQKKYGNDRQKMALEMQKLQKEHGFNPILGCLPMLAQIPVFL 112
>gnl|CDD|237100 PRK12429, PRK12429, 3-hydroxybutyrate dehydrogenase; Provisional.
Length = 258
Score = 29.9 bits (68), Expect = 3.9
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 11/71 (15%)
Query: 345 MLAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEID----PINALQASMEGYEVT---- 395
ML GKVA+V G +G A +L G++V++ +++ A G +
Sbjct: 1 MLKGKVALVTGAASGIGLEIALALAKEGAKVVIADLNDEAAAAAAEALQKAGGKAIGVAM 60
Query: 396 --TMEEAAKEG 404
T EEA G
Sbjct: 61 DVTDEEAINAG 71
Score = 28.7 bits (65), Expect = 9.2
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 266 MLAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEIDPINALQA 308
ML GKVA+V G +G A +L G++V++ +++ A A
Sbjct: 1 MLKGKVALVTGAASGIGLEIALALAKEGAKVVIADLNDEAAAAA 44
>gnl|CDD|178135 PLN02520, PLN02520, bifunctional 3-dehydroquinate
dehydratase/shikimate dehydrogenase.
Length = 529
Score = 30.5 bits (69), Expect = 4.1
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 250 GCRESLVDGLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIV 297
G R S G A+ LAGK+ VV G G GK A + G+RV++
Sbjct: 363 GLRAS---GSSPASGSPLAGKLFVVIGAGGAGKALAYGAKEKGARVVI 407
Score = 29.3 bits (66), Expect = 9.1
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIV 376
LAGK+ VV G G GK A + G+RV++
Sbjct: 377 LAGKLFVVIGAGGAGKALAYGAKEKGARVVI 407
>gnl|CDD|132409 TIGR03366, HpnZ_proposed, putative phosphonate catabolism
associated alcohol dehydrogenase. This clade of
zinc-binding alcohol dehydrogenases (members of
pfam00107) are repeatedly associated with genes proposed
to be involved with the catabolism of phosphonate
compounds.
Length = 280
Score = 29.8 bits (67), Expect = 4.2
Identities = 15/72 (20%), Positives = 24/72 (33%), Gaps = 1/72 (1%)
Query: 346 LAGKVAVVAGYGDVG-KGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKEG 404
L G+ +V G G +G A + +RV+ + P A G E E
Sbjct: 119 LKGRRVLVVGAGMLGLTAAAAAAAAGAARVVAADPSPDRRELALSFGATALAEPEVLAER 178
Query: 405 GIFVTTTGCKDI 416
+ D+
Sbjct: 179 QGGLQNGRGVDV 190
>gnl|CDD|211705 TIGR01963, PHB_DH, 3-hydroxybutyrate dehydrogenase. This model
represents a subfamily of the short chain
dehydrogenases. Characterized members so far as
3-hydroxybutyrate dehydrogenases and are found in
species that accumulate ester polmers called
polyhydroxyalkanoic acids (PHAs) under certain
conditions. Several members of the family are from
species not known to accumulate PHAs, including
Oceanobacillus iheyensis and Bacillus subtilis. However,
polymer formation is not required for there be a role
for 3-hydroxybutyrate dehydrogenase; it may be members
of this family have the same function in those species.
Length = 255
Score = 29.6 bits (67), Expect = 4.4
Identities = 25/95 (26%), Positives = 39/95 (41%), Gaps = 18/95 (18%)
Query: 269 GKVAVVAGY-GDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEEVAALH---L 324
GK A+V G +G A++L G+ V+V + EG E +VA +
Sbjct: 1 GKTALVTGAASGIGLAIARALAAAGANVVVNDFGE--------EGAEAAAKVAGDAGGSV 52
Query: 325 EHLGVKLTKLTEDQAKYLDIMLAGKVAVVAGYGDV 359
+L +TK E + M+A A G D+
Sbjct: 53 IYLPADVTKEDE-----IADMIA-AAAAEFGGLDI 81
>gnl|CDD|235776 PRK06300, PRK06300, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 299
Score = 29.8 bits (67), Expect = 4.5
Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 342 LDIMLAGKVAVVAGYGD---VGKGCAQSLRLFGSRVIVTEIDPI 382
L I L GK+A +AG GD G G A++L G+ ++V PI
Sbjct: 2 LKIDLTGKIAFIAGIGDDQGYGWGIAKALAEAGATILVGTWVPI 45
>gnl|CDD|223567 COG0493, GltD, NADPH-dependent glutamate synthase beta chain and
related oxidoreductases [Amino acid transport and
metabolism / General function prediction only].
Length = 457
Score = 30.0 bits (68), Expect = 4.9
Identities = 24/106 (22%), Positives = 36/106 (33%), Gaps = 14/106 (13%)
Query: 310 MEGYELDEEVAALHLEHLGVKLTKLT----EDQAKYLDIMLAGKVAVVAGYGDVGKGCAQ 365
+ G + AL LT+L D A+ GK VV G GD CA
Sbjct: 226 IPGEDAKGVAFALD------FLTRLNKEVLGDFAEDRTPPAKGKRVVVIGGGDTAMDCAG 279
Query: 366 SLRLFGSRVIVTEIDPINALQASMEGYE---VTTMEEAAKEGGIFV 408
+ G++ VT + + E + A +EG +
Sbjct: 280 TALRLGAKS-VTCFYREDRDDETNEWPTWAAQLEVRSAGEEGVERL 324
>gnl|CDD|225688 COG3146, COG3146, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 387
Score = 30.0 bits (68), Expect = 5.1
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 5/54 (9%)
Query: 52 TAVLIETLLELGAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWC 105
L+ L EL + SS ++ + A+ G + D+++ WC
Sbjct: 133 RQALLAGLDELCEQSGLSSAHVTFVDEDEQPALEKAG-----FLHRLDQQFHWC 181
Score = 30.0 bits (68), Expect = 5.1
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 5/54 (9%)
Query: 552 TAVLIETLLELGAEVQWSSCNIFSTQDHAAAAIAARGVAVYAWKGETDEEYVWC 605
L+ L EL + SS ++ + A+ G + D+++ WC
Sbjct: 133 RQALLAGLDELCEQSGLSSAHVTFVDEDEQPALEKAG-----FLHRLDQQFHWC 181
>gnl|CDD|130583 TIGR01520, FruBisAldo_II_A, fructose-bisphosphate aldolase, class
II, yeast/E. coli subtype. Members of this family are
class II examples of the glycolytic enzyme
fructose-bisphosphate aldolase (FBA). This model
represents one of two deeply split, architecturally
distinct clades of the family that includes class II
fructose-bisphosphate aldolases, tagatose-bisphosphate
aldolases, and related uncharacterized proteins. This
family is well-conserved and includes characterized FBA
from Saccharomyces cerevisiae, Escherichia coli, and
Corynebacterium glutamicum. Proteins outside the scope
of this model may also be designated as class II
fructose-bisphosphate aldolases, but are well separated
in an alignment-based phylogenetic tree [Energy
metabolism, Glycolysis/gluconeogenesis].
Length = 357
Score = 29.8 bits (67), Expect = 5.3
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 154 VHNLYKMFKENKLGVPAINVNDSVT 178
VH L++ KEN +PAIN S T
Sbjct: 15 VHKLFQYAKENNFAIPAINCTSSST 39
Score = 29.8 bits (67), Expect = 5.3
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 217 VHNLYKMFKENKLGVPAINVNDSVT 241
VH L++ KEN +PAIN S T
Sbjct: 15 VHKLFQYAKENNFAIPAINCTSSST 39
>gnl|CDD|133449 cd05191, NAD_bind_amino_acid_DH, NAD(P) binding domain of amino
acid dehydrogenase-like proteins. Amino acid
dehydrogenase(DH)-like NAD(P)-binding domains are
members of the Rossmann fold superfamily and are found
in glutamate, leucine, and phenylalanine DHs (DHs),
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 86
Score = 27.7 bits (62), Expect = 5.7
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 332 TKLTEDQAKYLDIMLAGKVAVVAGYGDVGKGCAQSL-RLFGSRVIVTEID 380
L + K + L GK VV G G+VGKG A+ L G +V++ + D
Sbjct: 7 VALLKAAGKVTNKSLKGKTVVVLGAGEVGKGIAKLLADEGGKKVVLCDRD 56
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
D-isomer-specific 2-hydroxyacid dehydrogenases related
repressor. The transcriptional corepressor CtBP is a
dehydrogenase with sequence and structural similarity to
the d2-hydroxyacid dehydrogenase family. CtBP was
initially identified as a protein that bound the PXDLS
sequence at the adenovirus E1A C terminus, causing the
loss of CR-1-mediated transactivation. CtBP binds NAD(H)
within a deep cleft, undergoes a conformational change
upon NAD binding, and has NAD-dependent dehydrogenase
activity.
Length = 312
Score = 29.4 bits (67), Expect = 6.0
Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 13/96 (13%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDP-INALQASMEGYEVTTMEEAAKEG 404
L G + G+G +G+ A+ + FG RVI DP + A++ G V +++E
Sbjct: 140 LRGLTLGLVGFGRIGRAVAKRAKAFGFRVIAY--DPYVPDGVAALGGVRVVSLDELLARS 197
Query: 405 GIFV-------TTTGCKDIIRGEHFLQMRDDAIVCN 433
+ T +I E M+ A + N
Sbjct: 198 DVVSLHCPLTPETRH---LIDAEALALMKPGAFLVN 230
>gnl|CDD|133450 cd05211, NAD_bind_Glu_Leu_Phe_Val, NAD(P) binding domain of
glutamate dehydrogenase, leucine dehydrogenase,
phenylalanine dehydrogenase, and valine dehydrogenase.
Amino acid dehydrogenase (DH) is a widely distributed
family of enzymes that catalyzes the oxidative
deamination of an amino acid to its keto acid and
ammonia with concomitant reduction of NAD(P)+. This
subfamily includes glutamate, leucine, phenylalanine,
and valine DHs. Glutamate DH is a multi-domain enzyme
that catalyzes the reaction from glutamate to
2-oxyoglutarate and ammonia in the presence of NAD or
NADP. It is present in all organisms. Enzymes involved
in ammonia assimilation are typically NADP+-dependent,
while those involved in glutamate catabolism are
generally NAD+-dependent. As in other NAD+-dependent
DHs, monomers in this family have 2 domains separated by
a deep cleft. Here the c-terminal domain contains a
modified NAD-binding Rossmann fold with 7 rather than
the usual 6 beta strands and one strand anti-parrallel
to the others. Amino acid DH-like NAD(P)-binding domains
are members of the Rossmann fold superfamily and include
glutamate, leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 217
Score = 29.1 bits (65), Expect = 6.3
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 335 TEDQAKYLDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVI-VTEID 380
+ K+L L G V G G+VG G A+ L G +V+ V++ D
Sbjct: 10 MKAAMKHLGDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPD 56
>gnl|CDD|219686 pfam07992, Pyr_redox_2, Pyridine nucleotide-disulphide
oxidoreductase. This family includes both class I and
class II oxidoreductases and also NADH oxidases and
peroxidases. This domain is actually a small NADH
binding domain within a larger FAD binding domain.
Length = 283
Score = 29.3 bits (66), Expect = 6.5
Identities = 20/100 (20%), Positives = 33/100 (33%), Gaps = 10/100 (10%)
Query: 346 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEI-DPINALQASMEGYEVTTMEEAAKEG 404
L +V VV G G +G A +L G V V E D + A + E G
Sbjct: 141 LPKRVVVVGG-GYIGLELAAALAKLGKEVTVVERRDRLLARADDEISAALLEKLEKLLLG 199
Query: 405 GIFVTTTGCKDIIRGEHFLQMRD--------DAIVCNIGH 436
+ + ++++ D ++ IG
Sbjct: 200 VTVLLVVVVVVKVGDGKVVEVKLGDGEELDADVVLVAIGR 239
>gnl|CDD|180440 PRK06172, PRK06172, short chain dehydrogenase; Provisional.
Length = 253
Score = 29.3 bits (66), Expect = 6.8
Identities = 30/127 (23%), Positives = 48/127 (37%), Gaps = 26/127 (20%)
Query: 345 MLAGKVAVVAG-YGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYEVTTMEEAAKE 403
+GKVA+V G +G+ A + G++V+V + D G E + A
Sbjct: 4 TFSGKVALVTGGAAGIGRATALAFAREGAKVVVADRDAA-------GGEETVALIREAGG 56
Query: 404 GGIFVTTTGCKDIIRGEHFLQMRDDAIVCNIGHFDC-------EIQVSWL------DKNA 450
+FV D+ R + + I G D EI+ L + +A
Sbjct: 57 EALFVAC----DVTRDAEVKALVEQTIAA-YGRLDYAFNNAGIEIEQGRLAEGSEAEFDA 111
Query: 451 VEKVNVK 457
+ VNVK
Sbjct: 112 IMGVNVK 118
>gnl|CDD|176201 cd08239, THR_DH_like, L-threonine dehydrogenase (TDH)-like.
MDR/AHD-like proteins, including a protein annotated as
a threonine dehydrogenase. L-threonine dehydrogenase
(TDH) catalyzes the zinc-dependent formation of
2-amino-3-ketobutyrate from L-threonine via
NAD(H)-dependent oxidation. The zinc-dependent alcohol
dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent
interconversion of alcohols to aldehydes or ketones.
Zinc-dependent ADHs are medium chain
dehydrogenase/reductase type proteins (MDRs) and have a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. In addition to alcohol
dehydrogenases, this group includes quinone reductase,
sorbitol dehydrogenase, formaldehyde dehydrogenase,
butanediol DH, ketose reductase, cinnamyl reductase, and
numerous others. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 339
Score = 29.6 bits (67), Expect = 6.8
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 258 GLKRATDIMLAGKVAVVAGYGDVGKGCAQSLRLFGSR-VIVTEIDP 302
L+R + V VV G G VG G R G+ VI + P
Sbjct: 155 ALRRV-GVSGRDTVLVV-GAGPVGLGALMLARALGAEDVIGVDPSP 198
>gnl|CDD|233266 TIGR01087, murD, UDP-N-acetylmuramoylalanine--D-glutamate ligase.
[Cell envelope, Biosynthesis and degradation of murein
sacculus and peptidoglycan].
Length = 433
Score = 29.6 bits (67), Expect = 6.9
Identities = 17/55 (30%), Positives = 26/55 (47%)
Query: 273 VVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEEVAALHLEHL 327
++ G G G+ A+ L G+ V VT++ P L+ SM L+E HL
Sbjct: 3 LILGLGKTGRAVARFLHKKGAEVTVTDLKPNEELEPSMGQLRLNEGSVLHTGLHL 57
>gnl|CDD|224562 COG1648, CysG, Siroheme synthase (precorrin-2
oxidase/ferrochelatase domain) [Coenzyme metabolism].
Length = 210
Score = 29.2 bits (66), Expect = 6.9
Identities = 22/88 (25%), Positives = 33/88 (37%), Gaps = 19/88 (21%)
Query: 267 LAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEEVAALHLEH 326
L GK +V G G V A+ L G+ V V + P E + E+ AL E
Sbjct: 10 LEGKKVLVVGGGSVALRKARLLLKAGADVTV--VSP-----------EFEPELKALIEEG 56
Query: 327 LGVKLTKLTEDQAKYLDIMLAGKVAVVA 354
K+ + ++ L V+A
Sbjct: 57 ------KIKWIEREFDAEDLDDAFLVIA 78
>gnl|CDD|153130 cd01355, AcnX, Putative Aconitase X catalytic domain. Putative
Aconitase X catalytic domain. It is predicted by
comparative genomic analysis. The proteins are mainly
found in archaea and proteobacteria. They are distantly
related to Aconitase family of proteins by sequence
similarity and seconary structure prediction. The
functions have not yet been experimentally
characterized. Thus, the prediction should be treated
with caution.
Length = 389
Score = 29.3 bits (66), Expect = 7.4
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 24 LMALRRKYGAQKIL--KGARIAGCLHMTVQTAVL--IETLLELGAEVQ 67
L+A+ YGA++++ K A I+G + T+ A L +E L + GA+V
Sbjct: 19 LVAVGELYGAERLIDIKSAHISGVSYKTIGDAGLEFLERLADQGAKVA 66
Score = 29.3 bits (66), Expect = 7.4
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 524 LMALRRKYGAQKIL--KGARIAGCLHMTVQTAVL--IETLLELGAEVQ 567
L+A+ YGA++++ K A I+G + T+ A L +E L + GA+V
Sbjct: 19 LVAVGELYGAERLIDIKSAHISGVSYKTIGDAGLEFLERLADQGAKVA 66
>gnl|CDD|223842 COG0771, MurD, UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell
envelope biogenesis, outer membrane].
Length = 448
Score = 29.2 bits (66), Expect = 7.8
Identities = 15/61 (24%), Positives = 21/61 (34%)
Query: 264 DIMLAGKVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGYELDEEVAALH 323
GK +V G G G A+ L G+ V V++ P A+ EV
Sbjct: 2 MEDFQGKKVLVLGLGKSGLAAARFLLKLGAEVTVSDDRPAPEGLAAQPLLLEGIEVELGS 61
Query: 324 L 324
Sbjct: 62 H 62
>gnl|CDD|223991 COG1063, Tdh, Threonine dehydrogenase and related Zn-dependent
dehydrogenases [Amino acid transport and metabolism /
General function prediction only].
Length = 350
Score = 29.3 bits (66), Expect = 7.9
Identities = 22/79 (27%), Positives = 27/79 (34%), Gaps = 27/79 (34%)
Query: 314 ELDEEVAAL----------HLEHLGVKLTKLTEDQAKYLDIMLAGKVAVVAGYGDVGKGC 363
+DEE AAL H E V+ G VV G G +G
Sbjct: 141 GIDEEAAALTEPLATAYHGHAERAAVR----------------PGGTVVVVGAGPIGLLA 184
Query: 364 AQSLRLFG-SRVIVTEIDP 381
+L G S VIV + P
Sbjct: 185 IALAKLLGASVVIVVDRSP 203
Score = 28.9 bits (65), Expect = 9.6
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 269 GKVAVVAGYGDVGKGCAQSLRLFG-SRVIVTEIDP 302
G VV G G +G +L G S VIV + P
Sbjct: 169 GGTVVVVGAGPIGLLAIALAKLLGASVVIVVDRSP 203
>gnl|CDD|173712 cd05622, STKc_ROCK1, Catalytic domain of the Protein
Serine/Threonine Kinase, Rho-associated coiled-coil
containing protein kinase 1. Serine/Threonine Kinases
(STKs), ROCK subfamily, ROCK1 (or ROK-beta) isoform,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The ROCK subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. ROCK contains an
N-terminal extension, a catalytic kinase domain, and a
C-terminal extension, which contains a coiled-coil
region encompassing a Rho-binding domain (RBD) and a
pleckstrin homology (PH) domain. ROCK is auto-inhibited
by the RBD and PH domain interacting with the catalytic
domain, and is activated via interaction with Rho
GTPases. ROCK1 is preferentially expressed in the liver,
lung, spleen, testes, and kidney. It mediates signaling
from Rho to the actin cytoskeleton. It is implicated in
the development of cardiac fibrosis, cardiomyocyte
apoptosis, and hyperglycemia. Mice deficient with ROCK1
display eyelids open at birth (EOB) and omphalocele
phenotypes due to the disorganization of actin filaments
in the eyelids and the umbilical ring.
Length = 371
Score = 29.2 bits (65), Expect = 8.2
Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 24/95 (25%)
Query: 104 WCIEQTLVFPDGKPLNMILD--DGGDLTNL-----VHEKYPQFLSEIRGISEETTTGVHN 156
W ++ F D + L M+++ GGDL NL V EK+ +F + ++ + +H+
Sbjct: 104 WVVQLFYAFQDDRYLYMVMEYMPGGDLVNLMSNYDVPEKWARFYTAEVVLALD---AIHS 160
Query: 157 LYKMFKENKLGVPAINVNDSVTKPLNMILDDGGDL 191
+ + ++ KP NM+LD G L
Sbjct: 161 MGFIHRD--------------VKPDNMLLDKSGHL 181
>gnl|CDD|180723 PRK06841, PRK06841, short chain dehydrogenase; Provisional.
Length = 255
Score = 28.9 bits (65), Expect = 8.3
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 342 LDIMLAGKVAVVAGYGD-VGKGCAQSLRLFGSRVIVTEIDP 381
L L+GKVAVV G +G A+ G+RV + +
Sbjct: 9 LAFDLSGKVAVVTGGASGIGHAIAELFAAKGARVALLDRSE 49
>gnl|CDD|176223 cd08262, Zn_ADH8, Alcohol dehydrogenases of the MDR family. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 29.2 bits (66), Expect = 9.0
Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 266 MLAGKVAVVAGYGDVGKGCAQSLRLFG-SRVIVTEIDP 302
+ G+VA+V G G +G +L+ G ++ ++ P
Sbjct: 159 LTPGEVALVIGCGPIGLAVIAALKARGVGPIVASDFSP 196
Score = 29.2 bits (66), Expect = 9.0
Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 345 MLAGKVAVVAGYGDVGKGCAQSLRLFG-SRVIVTEIDP 381
+ G+VA+V G G +G +L+ G ++ ++ P
Sbjct: 159 LTPGEVALVIGCGPIGLAVIAALKARGVGPIVASDFSP 196
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 29.1 bits (66), Expect = 9.0
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 270 KVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQA 308
V V+ G G +G Q + G+ VI +I A
Sbjct: 168 TVLVI-GLGGLGLNAVQIAKAMGAAVIAVDIKEEKLELA 205
Score = 29.1 bits (66), Expect = 9.0
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 349 KVAVVAGYGDVGKGCAQSLRLFGSRVIVTEIDPINALQA 387
V V+ G G +G Q + G+ VI +I A
Sbjct: 168 TVLVI-GLGGLGLNAVQIAKAMGAAVIAVDIKEEKLELA 205
>gnl|CDD|182650 PRK10691, PRK10691, hypothetical protein; Provisional.
Length = 219
Score = 28.5 bits (64), Expect = 9.3
Identities = 16/47 (34%), Positives = 19/47 (40%), Gaps = 12/47 (25%)
Query: 44 GCLHMTVQTAVLIETLLELGAEVQWSSCNIFSTQDHAAAAIAARGVA 90
G +H V+ AVLI L E +H AIA GVA
Sbjct: 65 GSVHHEVELAVLIGATLRQATE------------EHVRKAIAGYGVA 99
Score = 28.5 bits (64), Expect = 9.3
Identities = 16/47 (34%), Positives = 19/47 (40%), Gaps = 12/47 (25%)
Query: 544 GCLHMTVQTAVLIETLLELGAEVQWSSCNIFSTQDHAAAAIAARGVA 590
G +H V+ AVLI L E +H AIA GVA
Sbjct: 65 GSVHHEVELAVLIGATLRQATE------------EHVRKAIAGYGVA 99
>gnl|CDD|187647 cd08943, R1PA_ADH_SDR_c, rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase, classical (c) SDRs. This family has
bifunctional proteins with an N-terminal aldolase and a
C-terminal classical SDR domain. One member is
identified as a rhamnulose-1-phosphate aldolase/alcohol
dehydrogenase. The SDR domain has a canonical SDR
glycine-rich NAD(P) binding motif and a match to the
characteristic active site triad. However, it lacks an
upstream active site Asn typical of SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 28.9 bits (65), Expect = 9.6
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 269 GKVAVVAG-YGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGY 313
GKVA+V G +G A+ L G+ V+V +IDP A + +
Sbjct: 1 GKVALVTGGASGIGLAIAKRLAAEGAAVVVADIDPEIAEKVAEAAQ 46
Score = 28.9 bits (65), Expect = 9.6
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 348 GKVAVVAG-YGDVGKGCAQSLRLFGSRVIVTEIDPINALQASMEGY 392
GKVA+V G +G A+ L G+ V+V +IDP A + +
Sbjct: 1 GKVALVTGGASGIGLAIAKRLAAEGAAVVVADIDPEIAEKVAEAAQ 46
>gnl|CDD|216344 pfam01175, Urocanase, Urocanase.
Length = 545
Score = 29.1 bits (66), Expect = 9.7
Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 16/78 (20%)
Query: 340 KYLDIMLAGKVAVVAGYGDVGKGCAQSL--RLFGSRVIVTEIDPINALQASME-GY--EV 394
K+ LAGK+ + AG G G G AQ L + G+ + E+D + + +E GY EV
Sbjct: 148 KHFGGDLAGKLILTAGLG--GMGGAQPLAATMAGAVCLAVEVDE-SRIDKRLETGYLDEV 204
Query: 395 TT--------MEEAAKEG 404
+EA G
Sbjct: 205 ADDLDEALARAKEARAAG 222
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
0.318 0.135 0.397
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,392,014
Number of extensions: 3618797
Number of successful extensions: 4185
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4116
Number of HSP's successfully gapped: 270
Length of query: 718
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 614
Effective length of database: 6,324,786
Effective search space: 3883418604
Effective search space used: 3883418604
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: 63 (27.9 bits)