RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4626
(542 letters)
>gnl|CDD|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 517 bits (1335), Expect = 0.0
Identities = 164/264 (62%), Positives = 200/264 (75%), Gaps = 3/264 (1%)
Query: 33 AAGKLTVPAMNVNDSVTKTKFDNLYMCRESIIDSLKRSTDVMFGGKQVVLCGYGEVGKGC 92
GKL PA+NVNDSVTK+KFDNLY CRES++D +KR+TDVM GK V+CGYG+VGKGC
Sbjct: 163 KKGKLLFPAINVNDSVTKSKFDNLYGCRESLVDGIKRATDVMIAGKVAVVCGYGDVGKGC 222
Query: 93 CQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMD 152
QSL+G G + +TEIDPICALQA MDGF VV + EV DI VT TGNK+V+TREHM
Sbjct: 223 AQSLRGQGARVIVTEIDPICALQAAMDGFEVVTMEEVAPQADIFVTTTGNKDVITREHMR 282
Query: 153 KMKNGCVVCNMGHSNTEIDVNSLRT-PDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNL 211
MK+G +VCN+GH + EIDV SLR P L WE ++ QVDH+ +PDGKRI+LLAEGRLVNL
Sbjct: 283 AMKDGAIVCNIGHFDNEIDVASLRNNPGLKWENIKPQVDHITFPDGKRIILLAEGRLVNL 342
Query: 212 SCSSL-PSFVVSITACTQALALIELFNAPSGRYKSDVYLLPKKMDEYVASLHLPTFDAHL 270
C++ PSFV+S + Q LA IELF P G+YK+ VY+LPKK+DE VA LHL A L
Sbjct: 343 GCATGHPSFVMSNSFTNQVLAQIELFTKP-GKYKNGVYVLPKKLDEKVARLHLEKLGAKL 401
Query: 271 TELSDEQAKYMGLNKAGPFKPSYY 294
T+L+ EQA Y+G+ GPFKP +Y
Sbjct: 402 TKLTKEQADYIGVPVEGPFKPDHY 425
Score = 221 bits (566), Expect = 1e-66
Identities = 70/108 (64%), Positives = 87/108 (80%), Gaps = 3/108 (2%)
Query: 437 TGLPVFAWRGETEEDFWWCIDKCVN---SWQPNMILDDGGDATHWMLKKYPTMFKAIKGI 493
G+PVFAW+GET E++WWCI++ + W PNMILDDGGDAT + KKYP M K I+G+
Sbjct: 88 AGVPVFAWKGETLEEYWWCIEQTLTWPDGWGPNMILDDGGDATLLVHKKYPRMLKKIRGV 147
Query: 494 VEESLTGVHRLYQLSKAGKLTVPAMNVNDSVTKTKFDNLYMCRESIID 541
EE+ TGVHRLYQ++K GKL PA+NVNDSVTK+KFDNLY CRES++D
Sbjct: 148 SEETTTGVHRLYQMAKKGKLLFPAINVNDSVTKSKFDNLYGCRESLVD 195
Score = 210 bits (536), Expect = 3e-62
Identities = 68/114 (59%), Positives = 85/114 (74%), Gaps = 2/114 (1%)
Query: 295 SMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLR 354
+MDGF VV + EV DI VT TGNK+V+TREHM MK+G +VCN+GH + EIDV SLR
Sbjct: 247 AMDGFEVVTMEEVAPQADIFVTTTGNKDVITREHMRAMKDGAIVCNIGHFDNEIDVASLR 306
Query: 355 T-PDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSSL-PSFVVSITACTQ 406
P L WE ++ QVDH+ +PDGKRI+LLAEGRLVNL C++ PSFV+S + Q
Sbjct: 307 NNPGLKWENIKPQVDHITFPDGKRIILLAEGRLVNLGCATGHPSFVMSNSFTNQ 360
Score = 70.6 bits (174), Expect = 5e-13
Identities = 21/33 (63%), Positives = 25/33 (75%)
Query: 1 MPGIMALRKRAGDDKPLKNARIVGCTHINAQTA 33
MPG+MALR+ G +KPLK ARI GC H+ QTA
Sbjct: 22 MPGLMALREEYGAEKPLKGARIAGCLHMTIQTA 54
>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 = 443 bits (1141), Expect = e-153
Identities = 132/280 (47%), Positives = 181/280 (64%), Gaps = 10/280 (3%)
Query: 14 DKPLKNARIVGCT--------HINAQTAAGKLTVPAMNVNDSVTKTKFDNLYMCRESIID 65
+P +I+G + + A GKL PA+ VND+VTK KFDN Y +S ID
Sbjct: 124 KRPDLLKKIIGGSEETTTGVHRLRAMEKEGKLLFPAIAVNDAVTKHKFDNRYGTGQSTID 183
Query: 66 SLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK 125
+KR+T+V+ GK VV+ GYG VGKGC +GLG + +TE+DPICALQA MDGF V+
Sbjct: 184 GIKRATNVLIAGKVVVVAGYGWVGKGCAMRARGLGARVIVTEVDPICALQAAMDGFEVMP 243
Query: 126 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 185
+ E + DI VTATGNK+V+ EH +KMK+G ++CN GH + EIDV +L + ++
Sbjct: 244 MEEAAKIGDIFVTATGNKDVIRGEHFEKMKDGAILCNAGHFDVEIDVAALEELAVEKREI 303
Query: 186 RSQVDHVIWPDGKRIVLLAEGRLVNLSC-SSLPSFVVSITACTQALALIELFNAPSGRYK 244
R QVD PDG+RI+LLAEGRLVNL+C + PSFV+ ++ QALA IEL+ + +
Sbjct: 304 RPQVDEYTLPDGRRIILLAEGRLVNLACATGHPSFVMDMSFANQALAQIELWKNR-DKLE 362
Query: 245 SDVYLLPKKMDEYVASLHLPTFDAHLTELSDEQAKYMGLN 284
VY+LPK++DE VA L L L +L++EQA+Y+G
Sbjct: 363 PGVYVLPKELDEEVARLKLEALGIKLDKLTEEQAEYLGSW 402
Score = 192 bits (491), Expect = 6e-56
Identities = 58/105 (55%), Positives = 74/105 (70%), Gaps = 1/105 (0%)
Query: 437 TGLPVFAWRGETEEDFWWCIDKCVNSWQPNMILDDGGDATHWMLKKYPTMFKAIKGIVEE 496
G+PVFAW+GETEE++WWCI++ + PN+I+DDGGD TH + K P + K I G EE
Sbjct: 80 AGIPVFAWKGETEEEYWWCIEQAL-DHGPNLIIDDGGDLTHLLHTKRPDLLKKIIGGSEE 138
Query: 497 SLTGVHRLYQLSKAGKLTVPAMNVNDSVTKTKFDNLYMCRESIID 541
+ TGVHRL + K GKL PA+ VND+VTK KFDN Y +S ID
Sbjct: 139 TTTGVHRLRAMEKEGKLLFPAIAVNDAVTKHKFDNRYGTGQSTID 183
Score = 191 bits (489), Expect = 1e-55
Identities = 56/112 (50%), Positives = 77/112 (68%), Gaps = 1/112 (0%)
Query: 296 MDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRT 355
MDGF V+ + E + DI VTATGNK+V+ EH +KMK+G ++CN GH + EIDV +L
Sbjct: 236 MDGFEVMPMEEAAKIGDIFVTATGNKDVIRGEHFEKMKDGAILCNAGHFDVEIDVAALEE 295
Query: 356 PDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSC-SSLPSFVVSITACTQ 406
+ ++R QVD PDG+RI+LLAEGRLVNL+C + PSFV+ ++ Q
Sbjct: 296 LAVEKREIRPQVDEYTLPDGRRIILLAEGRLVNLACATGHPSFVMDMSFANQ 347
Score = 62.1 bits (152), Expect = 3e-10
Identities = 21/33 (63%), Positives = 25/33 (75%)
Query: 1 MPGIMALRKRAGDDKPLKNARIVGCTHINAQTA 33
MP +MALR+R +KPLK ARI GC H+ AQTA
Sbjct: 14 MPVLMALRERYAKEKPLKGARIAGCLHMTAQTA 46
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 403 bits (1038), Expect = e-137
Identities = 137/259 (52%), Positives = 182/259 (70%), Gaps = 2/259 (0%)
Query: 33 AAGKLTVPAMNVNDSVTKTKFDNLYMCRESIIDSLKRSTDVMFGGKQVVLCGYGEVGKGC 92
G L PA+NVNDSVTK+KFDN Y ES++D +KR+T+V+ GK VV+ GYG+VGKGC
Sbjct: 168 KDGALKFPAINVNDSVTKSKFDNRYGTGESLLDGIKRATNVLIAGKVVVVAGYGDVGKGC 227
Query: 93 CQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMD 152
Q L+GLG + +TE+DPICALQA MDGF V+ + E DI VTATGNK+V+T EHM+
Sbjct: 228 AQRLRGLGARVIVTEVDPICALQAAMDGFRVMTMEEAAELGDIFVTATGNKDVITAEHME 287
Query: 153 KMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLS 212
MK+G ++ N+GH + EIDV +L + W +++ QVD PDGKRI+LLAEGRLVNL
Sbjct: 288 AMKDGAILANIGHFDNEIDVAALEELAVKWREIKPQVDEYTLPDGKRIILLAEGRLVNLG 347
Query: 213 CSS-LPSFVVSITACTQALALIELFNAPSGRYKSDVYLLPKKMDEYVASLHLPTFDAHLT 271
++ PS V+ ++ QALA IELF G+ + VY+LPK++DE VA L L L
Sbjct: 348 AATGHPSEVMDMSFANQALAQIELFTNR-GKLEPGVYVLPKELDEEVARLKLKALGVKLD 406
Query: 272 ELSDEQAKYMGLNKAGPFK 290
EL++EQA+Y+G+ GPFK
Sbjct: 407 ELTEEQAEYIGVWVEGPFK 425
Score = 184 bits (469), Expect = 1e-52
Identities = 58/104 (55%), Positives = 77/104 (74%)
Query: 438 GLPVFAWRGETEEDFWWCIDKCVNSWQPNMILDDGGDATHWMLKKYPTMFKAIKGIVEES 497
G+PVFAW+GET E++W CI++ ++ PNMILDDGGD T + + P + IKG+ EE+
Sbjct: 97 GIPVFAWKGETLEEYWECIERALDGHGPNMILDDGGDLTLLVHTERPELLANIKGVTEET 156
Query: 498 LTGVHRLYQLSKAGKLTVPAMNVNDSVTKTKFDNLYMCRESIID 541
TGVHRLY ++K G L PA+NVNDSVTK+KFDN Y ES++D
Sbjct: 157 TTGVHRLYAMAKDGALKFPAINVNDSVTKSKFDNRYGTGESLLD 200
Score = 166 bits (424), Expect = 4e-46
Identities = 54/108 (50%), Positives = 75/108 (69%), Gaps = 1/108 (0%)
Query: 296 MDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRT 355
MDGF V+ + E DI VTATGNK+V+T EHM+ MK+G ++ N+GH + EIDV +L
Sbjct: 253 MDGFRVMTMEEAAELGDIFVTATGNKDVITAEHMEAMKDGAILANIGHFDNEIDVAALEE 312
Query: 356 PDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSS-LPSFVVSIT 402
+ W +++ QVD PDGKRI+LLAEGRLVNL ++ PS V+ ++
Sbjct: 313 LAVKWREIKPQVDEYTLPDGKRIILLAEGRLVNLGAATGHPSEVMDMS 360
Score = 56.3 bits (137), Expect = 2e-08
Identities = 19/33 (57%), Positives = 24/33 (72%)
Query: 1 MPGIMALRKRAGDDKPLKNARIVGCTHINAQTA 33
MPG+MA+R+ +KPLK ARI GC H+ QTA
Sbjct: 30 MPGLMAIREEFAAEKPLKGARIAGCLHMTIQTA 62
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 394 bits (1013), Expect = e-133
Identities = 139/264 (52%), Positives = 182/264 (68%), Gaps = 2/264 (0%)
Query: 33 AAGKLTVPAMNVNDSVTKTKFDNLYMCRESIIDSLKRSTDVMFGGKQVVLCGYGEVGKGC 92
GKL PA+NVNDSVTK+KFDNLY CRES+ D +KR+TDVM GK V+CGYG+VGKGC
Sbjct: 166 KKGKLLFPAINVNDSVTKSKFDNLYGCRESLPDGIKRATDVMIAGKVAVVCGYGDVGKGC 225
Query: 93 CQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMD 152
SL+G G + +TEIDPICALQA M+G+ VV L EV++ DI VT TG +++ H
Sbjct: 226 AASLRGQGARVIVTEIDPICALQAAMEGYQVVTLEEVVKDADIFVTTTGCVDIIVGRHFM 285
Query: 153 KMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLS 212
MK +VCN+GH + EIDV L ++ QVD P+G+RI+LLAEGRL+NL
Sbjct: 286 NMKKDAIVCNIGHFDCEIDVGWLNYNAKKITNIKPQVDRYTLPNGRRIILLAEGRLLNLG 345
Query: 213 CSS-LPSFVVSITACTQALALIELFNAP-SGRYKSDVYLLPKKMDEYVASLHLPTFDAHL 270
C++ PSFV+S + Q LA IEL+ +G+Y+ VY+LPK +DE VA LHL L
Sbjct: 346 CATGHPSFVMSNSFTNQVLAQIELWTKRDTGKYEVGVYVLPKHLDEKVARLHLGKLGVKL 405
Query: 271 TELSDEQAKYMGLNKAGPFKPSYY 294
T+L+D+QA+Y+G+ GPFKP +Y
Sbjct: 406 TKLTDKQAEYIGVPVEGPFKPDHY 429
Score = 194 bits (495), Expect = 2e-56
Identities = 66/108 (61%), Positives = 83/108 (76%), Gaps = 3/108 (2%)
Query: 437 TGLPVFAWRGETEEDFWWCIDKCV---NSWQPNMILDDGGDATHWMLKKYPTMFKAIKGI 493
G+PVFAW+GET E++WWCI++ + + PNMILDDGGDAT + KKYP I+G+
Sbjct: 91 AGVPVFAWKGETLEEYWWCIERALTFKDGQGPNMILDDGGDATLLIHKKYPQYLAGIRGV 150
Query: 494 VEESLTGVHRLYQLSKAGKLTVPAMNVNDSVTKTKFDNLYMCRESIID 541
EE+ TGVHRLY++ K GKL PA+NVNDSVTK+KFDNLY CRES+ D
Sbjct: 151 SEETTTGVHRLYKMLKKGKLLFPAINVNDSVTKSKFDNLYGCRESLPD 198
Score = 123 bits (310), Expect = 2e-30
Identities = 49/113 (43%), Positives = 70/113 (61%), Gaps = 1/113 (0%)
Query: 295 SMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLR 354
+M+G+ VV L EV++ DI VT TG +++ H MK +VCN+GH + EIDV L
Sbjct: 250 AMEGYQVVTLEEVVKDADIFVTTTGCVDIIVGRHFMNMKKDAIVCNIGHFDCEIDVGWLN 309
Query: 355 TPDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSS-LPSFVVSITACTQ 406
++ QVD P+G+RI+LLAEGRL+NL C++ PSFV+S + Q
Sbjct: 310 YNAKKITNIKPQVDRYTLPNGRRIILLAEGRLLNLGCATGHPSFVMSNSFTNQ 362
Score = 66.3 bits (162), Expect = 1e-11
Identities = 20/33 (60%), Positives = 24/33 (72%)
Query: 1 MPGIMALRKRAGDDKPLKNARIVGCTHINAQTA 33
MPG+MALR+ G +PLK ARI GC H+ QTA
Sbjct: 25 MPGLMALREEYGPSQPLKGARIAGCLHMTVQTA 57
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 387 bits (995), Expect = e-130
Identities = 146/274 (53%), Positives = 195/274 (71%), Gaps = 3/274 (1%)
Query: 24 GCTHINAQTAAGKLTVPAMNVNDSVTKTKFDNLYMCRESIIDSLKRSTDVMFGGKQVVLC 83
G + G+L PA+NVNDSVTK+KFDN+Y CR S+ID + R+TDVM GK VV+C
Sbjct: 201 GVHRLYKMLKKGELLFPAINVNDSVTKSKFDNIYGCRHSLIDGIFRATDVMIAGKTVVVC 260
Query: 84 GYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTATGNK 143
GYG+VGKGC Q+L+G G + +TEIDPICALQA M+G+ VV L +V+ T DI VTATGNK
Sbjct: 261 GYGDVGKGCAQALRGFGARVVVTEIDPICALQAAMEGYQVVTLEDVVETADIFVTATGNK 320
Query: 144 NVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRT-PDLTWEKVRSQVDHVIWPDGKRIVL 202
+++T EHM +MKN +V N+GH + EI V L P + +++ QVD +PDGK I+L
Sbjct: 321 DIITLEHMRRMKNNAIVGNIGHFDNEIQVAELEAYPGIEIVEIKPQVDRYTFPDGKGIIL 380
Query: 203 LAEGRLVNLSCSS-LPSFVVSITACTQALALIELF-NAPSGRYKSDVYLLPKKMDEYVAS 260
LAEGRLVNL C++ PSFV+S + Q LA IEL+ N +G+Y + VY LPK++DE VA
Sbjct: 381 LAEGRLVNLGCATGHPSFVMSNSFTNQVLAQIELWENRDTGKYPNGVYKLPKELDEKVAR 440
Query: 261 LHLPTFDAHLTELSDEQAKYMGLNKAGPFKPSYY 294
LHL A LT+L+D+QA+Y+G+ GP+K +Y
Sbjct: 441 LHLKKLGAKLTKLTDKQAEYIGVPVDGPYKSDHY 474
Score = 141 bits (358), Expect = 1e-36
Identities = 61/147 (41%), Positives = 81/147 (55%), Gaps = 46/147 (31%)
Query: 440 PVFAWRGETEEDFWWCIDKCVNSWQ----PNMILDDGGDAT---HWMLK----------- 481
PVFAW+GET E++WWC ++ + W PN+I+DDGGDAT H +K
Sbjct: 97 PVFAWKGETLEEYWWCTEQALK-WPNGDGPNLIVDDGGDATLLVHEGVKAEKLYEEKGIL 155
Query: 482 ---------------------------KYPTMFKAIKGIVEESLTGVHRLYQLSKAGKLT 514
K+ + K I G+ EE+ TGVHRLY++ K G+L
Sbjct: 156 PDPLDPSNEDEKCLLTVLKKLLTKNPDKWTNLVKKIVGVSEETTTGVHRLYKMLKKGELL 215
Query: 515 VPAMNVNDSVTKTKFDNLYMCRESIID 541
PA+NVNDSVTK+KFDN+Y CR S+ID
Sbjct: 216 FPAINVNDSVTKSKFDNIYGCRHSLID 242
Score = 141 bits (358), Expect = 1e-36
Identities = 57/114 (50%), Positives = 79/114 (69%), Gaps = 2/114 (1%)
Query: 295 SMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLR 354
+M+G+ VV L +V+ T DI VTATGNK+++T EHM +MKN +V N+GH + EI V L
Sbjct: 294 AMEGYQVVTLEDVVETADIFVTATGNKDIITLEHMRRMKNNAIVGNIGHFDNEIQVAELE 353
Query: 355 T-PDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSS-LPSFVVSITACTQ 406
P + +++ QVD +PDGK I+LLAEGRLVNL C++ PSFV+S + Q
Sbjct: 354 AYPGIEIVEIKPQVDRYTFPDGKGIILLAEGRLVNLGCATGHPSFVMSNSFTNQ 407
Score = 54.3 bits (131), Expect = 9e-08
Identities = 21/33 (63%), Positives = 24/33 (72%)
Query: 1 MPGIMALRKRAGDDKPLKNARIVGCTHINAQTA 33
MPG+MALR+ G KPLK ARI GC H+ QTA
Sbjct: 27 MPGLMALREEYGPSKPLKGARITGCLHMTVQTA 59
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 355 bits (912), Expect = e-118
Identities = 124/257 (48%), Positives = 170/257 (66%), Gaps = 2/257 (0%)
Query: 33 AAGKLTVPAMNVNDSVTKTKFDNLYMCRESIIDSLKRSTDVMFGGKQVVLCGYGEVGKGC 92
G L PA+NVNDSVTK+ FDN Y +S++D + R+T+V+ GK VV+ GYG VG+G
Sbjct: 165 KDGVLKFPAINVNDSVTKSLFDNRYGTGQSLLDGILRATNVLLAGKNVVVAGYGWVGRGI 224
Query: 93 CQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMD 152
L+G+G + +TE+DPI AL+A MDGF V+ + E +T DI VTATGNK+V+ +EH +
Sbjct: 225 AMRLRGMGARVIVTEVDPIRALEAAMDGFRVMTMEEAAKTGDIFVTATGNKDVIRKEHFE 284
Query: 153 KMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLS 212
KMK+G ++ N GH + EIDV L + +VR QVD PDGKRI+LLAEGRLVNL+
Sbjct: 285 KMKDGAILANAGHFDVEIDVAGLEELAVEKREVRPQVDEYELPDGKRIILLAEGRLVNLA 344
Query: 213 CSS-LPSFVVSITACTQALALIELFNAPSGRYKSDVYLLPKKMDEYVASLHLPTFDAHLT 271
++ PS V+ ++ QALA I L G+ + VY LPK++DE VA L L L
Sbjct: 345 AATGHPSEVMDMSFANQALAQIYLVKNH-GKLEPGVYRLPKELDEEVARLKLEAMGIELD 403
Query: 272 ELSDEQAKYMGLNKAGP 288
EL++EQA+Y+G + G
Sbjct: 404 ELTEEQAEYLGSWEEGT 420
Score = 161 bits (410), Expect = 3e-44
Identities = 55/104 (52%), Positives = 74/104 (71%), Gaps = 1/104 (0%)
Query: 438 GLPVFAWRGETEEDFWWCIDKCVNSWQPNMILDDGGDATHWMLKKYPTMFKAIKGIVEES 497
G+PVFAW+GET E+++ ID+ V W+PN+I+DDGGD T + + P + AIKG EE+
Sbjct: 95 GIPVFAWKGETLEEYYEAIDQ-VLDWEPNIIIDDGGDLTKLVHLERPELLDAIKGGTEET 153
Query: 498 LTGVHRLYQLSKAGKLTVPAMNVNDSVTKTKFDNLYMCRESIID 541
TGVHRL + K G L PA+NVNDSVTK+ FDN Y +S++D
Sbjct: 154 TTGVHRLRAMEKDGVLKFPAINVNDSVTKSLFDNRYGTGQSLLD 197
Score = 155 bits (394), Expect = 4e-42
Identities = 55/108 (50%), Positives = 75/108 (69%), Gaps = 1/108 (0%)
Query: 296 MDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRT 355
MDGF V+ + E +T DI VTATGNK+V+ +EH +KMK+G ++ N GH + EIDV L
Sbjct: 250 MDGFRVMTMEEAAKTGDIFVTATGNKDVIRKEHFEKMKDGAILANAGHFDVEIDVAGLEE 309
Query: 356 PDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSS-LPSFVVSIT 402
+ +VR QVD PDGKRI+LLAEGRLVNL+ ++ PS V+ ++
Sbjct: 310 LAVEKREVRPQVDEYELPDGKRIILLAEGRLVNLAAATGHPSEVMDMS 357
Score = 52.3 bits (126), Expect = 4e-07
Identities = 18/34 (52%), Positives = 25/34 (73%)
Query: 1 MPGIMALRKRAGDDKPLKNARIVGCTHINAQTAA 34
MP +MA+R+ ++KPLK ARI GC H+ A+TA
Sbjct: 27 MPVLMAIREEFAEEKPLKGARIAGCLHMTAKTAV 60
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 317 bits (814), Expect = e-103
Identities = 135/266 (50%), Positives = 185/266 (69%), Gaps = 4/266 (1%)
Query: 33 AAGKLTVPAMNVNDSVTKTKFDNLYMCRESIIDSLKRSTDVMFGGKQVVLCGYGEVGKGC 92
G L PA+NVNDSVTK+KFDNLY CR S+ D L R+TDVM GK V+CGYG+VGKGC
Sbjct: 210 KNGTLLFPAINVNDSVTKSKFDNLYGCRHSLPDGLMRATDVMIAGKVAVICGYGDVGKGC 269
Query: 93 CQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMD 152
++K G + +TEIDPICALQA M+G+ V+ L +V+ DI VT TGNK+++ +HM
Sbjct: 270 AAAMKAAGARVIVTEIDPICALQALMEGYQVLTLEDVVSEADIFVTTTGNKDIIMVDHMR 329
Query: 153 KMKNGCVVCNMGHSNTEIDVNSLRT-PDLTWEKVRSQVDHVIWPDGKR-IVLLAEGRLVN 210
KMKN +VCN+GH + EID+ L T P + ++ Q D ++PD I++LAEGRL+N
Sbjct: 330 KMKNNAIVCNIGHFDNEIDMLGLETYPGVKRITIKPQTDRWVFPDTGSGIIVLAEGRLMN 389
Query: 211 LSCSS-LPSFVVSITACTQALALIELFNA-PSGRYKSDVYLLPKKMDEYVASLHLPTFDA 268
L C++ PSFV+S + Q +A +EL+N SG+Y+ VY+LPK +DE VA+LHL A
Sbjct: 390 LGCATGHPSFVMSCSFTNQVIAQLELWNEKKSGKYEKKVYVLPKHLDEKVAALHLGKLGA 449
Query: 269 HLTELSDEQAKYMGLNKAGPFKPSYY 294
LT+LS +QA Y+ + GP+KP++Y
Sbjct: 450 KLTKLSKDQADYINVPVEGPYKPAHY 475
Score = 114 bits (286), Expect = 3e-27
Identities = 58/146 (39%), Positives = 78/146 (53%), Gaps = 46/146 (31%)
Query: 441 VFAWRGETEEDFWWCIDKCVNSWQ----PNMILDDGGDAT---HWMLK------------ 481
VFAW+GET +++WWC ++ ++ W P++I+DDGGDAT H +K
Sbjct: 98 VFAWKGETLQEYWWCTERALD-WGPGGGPDLIVDDGGDATLLIHEGVKAEEEFEKDGTLP 156
Query: 482 --------------------------KYPTMFKAIKGIVEESLTGVHRLYQLSKAGKLTV 515
KY M + + G+ EE+ TGV RLYQ+ K G L
Sbjct: 157 DPTSTDNAEFKIVLTIIKDGLKVDPKKYHKMKERLVGVSEETTTGVKRLYQMQKNGTLLF 216
Query: 516 PAMNVNDSVTKTKFDNLYMCRESIID 541
PA+NVNDSVTK+KFDNLY CR S+ D
Sbjct: 217 PAINVNDSVTKSKFDNLYGCRHSLPD 242
Score = 110 bits (277), Expect = 5e-26
Identities = 50/114 (43%), Positives = 75/114 (65%), Gaps = 3/114 (2%)
Query: 296 MDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRT 355
M+G+ V+ L +V+ DI VT TGNK+++ +HM KMKN +VCN+GH + EID+ L T
Sbjct: 295 MEGYQVLTLEDVVSEADIFVTTTGNKDIIMVDHMRKMKNNAIVCNIGHFDNEIDMLGLET 354
Query: 356 -PDLTWEKVRSQVDHVIWPDGKR-IVLLAEGRLVNLSCSS-LPSFVVSITACTQ 406
P + ++ Q D ++PD I++LAEGRL+NL C++ PSFV+S + Q
Sbjct: 355 YPGVKRITIKPQTDRWVFPDTGSGIIVLAEGRLMNLGCATGHPSFVMSCSFTNQ 408
Score = 41.8 bits (98), Expect = 7e-04
Identities = 17/33 (51%), Positives = 20/33 (60%)
Query: 1 MPGIMALRKRAGDDKPLKNARIVGCTHINAQTA 33
MPG+MA R G +P K ARI G H+ QTA
Sbjct: 28 MPGLMACRTEFGPSQPFKGARITGSLHMTIQTA 60
>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 = 308 bits (792), Expect = e-100
Identities = 117/266 (43%), Positives = 164/266 (61%), Gaps = 2/266 (0%)
Query: 24 GCTHINAQTAAGKLTVPAMNVNDSVTKTKFDNLYMCRESIIDSLKRSTDVMFGGKQVVLC 83
G + A A G L PA+NVND+ TK+ FDN Y +S ID + R+T+++ GK VV+
Sbjct: 143 GVIRLRAMEAEGVLKFPAINVNDAYTKSLFDNRYGTGQSTIDGILRATNLLIAGKTVVVA 202
Query: 84 GYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTATGNK 143
GYG GKG +G+G + +TE+DPI AL+A MDGF V+ + E + DI +TATGNK
Sbjct: 203 GYGWCGKGIAMRARGMGARVIVTEVDPIRALEAAMDGFRVMTMEEAAKIGDIFITATGNK 262
Query: 144 NVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKVRSQVDHVIWPDGKRIVLL 203
+V+ EH + MK+G +V N+GH + EIDV +L + VR QVD I DG+RI LL
Sbjct: 263 DVIRGEHFENMKDGAIVANIGHFDVEIDVKALEELAVEKVNVRPQVDEYILKDGRRIYLL 322
Query: 204 AEGRLVNLSCSS-LPSFVVSITACTQALALIELFNAPSGRYKSDVYLLPKKMDEYVASLH 262
AEGRLVNL+ + PS V+ ++ QALA L+ + + VY LPK++DE VA L
Sbjct: 323 AEGRLVNLAAAEGHPSEVMDMSFANQALAAEYLWKNH-DKLEPGVYRLPKELDEMVARLK 381
Query: 263 LPTFDAHLTELSDEQAKYMGLNKAGP 288
L + EL++EQ +Y+G + G
Sbjct: 382 LEAMGIEIDELTEEQKEYLGSWEEGT 407
Score = 148 bits (375), Expect = 2e-39
Identities = 47/106 (44%), Positives = 68/106 (64%), Gaps = 1/106 (0%)
Query: 436 YTGLPVFAWRGETEEDFWWCIDKCVNSWQPNMILDDGGDATHWMLKKYPTMFKAIKGIVE 495
G+PVFAWRGET E+++W I++ ++ +PN+I+DDG D + + P + + I G E
Sbjct: 80 GAGIPVFAWRGETNEEYYWAIEQVLDH-EPNIIIDDGADLIFLLHTERPELLEKIIGGSE 138
Query: 496 ESLTGVHRLYQLSKAGKLTVPAMNVNDSVTKTKFDNLYMCRESIID 541
E+ TGV RL + G L PA+NVND+ TK+ FDN Y +S ID
Sbjct: 139 ETTTGVIRLRAMEAEGVLKFPAINVNDAYTKSLFDNRYGTGQSTID 184
Score = 128 bits (323), Expect = 2e-32
Identities = 53/112 (47%), Positives = 72/112 (64%), Gaps = 1/112 (0%)
Query: 296 MDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRT 355
MDGF V+ + E + DI +TATGNK+V+ EH + MK+G +V N+GH + EIDV +L
Sbjct: 237 MDGFRVMTMEEAAKIGDIFITATGNKDVIRGEHFENMKDGAIVANIGHFDVEIDVKALEE 296
Query: 356 PDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSS-LPSFVVSITACTQ 406
+ VR QVD I DG+RI LLAEGRLVNL+ + PS V+ ++ Q
Sbjct: 297 LAVEKVNVRPQVDEYILKDGRRIYLLAEGRLVNLAAAEGHPSEVMDMSFANQ 348
Score = 50.9 bits (122), Expect = 1e-06
Identities = 16/33 (48%), Positives = 23/33 (69%)
Query: 1 MPGIMALRKRAGDDKPLKNARIVGCTHINAQTA 33
MP +M +R+R ++KPLK ARI C H+ +TA
Sbjct: 14 MPVLMRIRERFSEEKPLKGARIAACLHVTVETA 46
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 295 bits (756), Expect = 2e-98
Identities = 99/161 (61%), Positives = 120/161 (74%)
Query: 55 NLYMCRESIIDSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICAL 114
NLY CRES+ID +KR+TDVM GK V+CGYG+VGKGC SLKG G + +TEIDPICAL
Sbjct: 1 NLYGCRESLIDGIKRATDVMIAGKVAVVCGYGDVGKGCAASLKGQGARVIVTEIDPICAL 60
Query: 115 QACMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNS 174
QA M+GF VV L EV++ DI VT TGNK+++T EHM KMKN +VCN+GH + EIDV
Sbjct: 61 QAAMEGFQVVTLEEVVKKADIFVTTTGNKDIITGEHMAKMKNDAIVCNIGHFDNEIDVAW 120
Query: 175 LRTPDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSS 215
L T WE ++ QVD PDGK I+LLAEGRLVNL C++
Sbjct: 121 LNTNGKKWENIKPQVDRYTLPDGKHIILLAEGRLVNLGCAT 161
Score = 170 bits (434), Expect = 1e-50
Identities = 56/99 (56%), Positives = 71/99 (71%)
Query: 295 SMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLR 354
+M+GF VV L EV++ DI VT TGNK+++T EHM KMKN +VCN+GH + EIDV L
Sbjct: 63 AMEGFQVVTLEEVVKKADIFVTTTGNKDIITGEHMAKMKNDAIVCNIGHFDNEIDVAWLN 122
Query: 355 TPDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSS 393
T WE ++ QVD PDGK I+LLAEGRLVNL C++
Sbjct: 123 TNGKKWENIKPQVDRYTLPDGKHIILLAEGRLVNLGCAT 161
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 291 bits (747), Expect = 4e-97
Identities = 85/160 (53%), Positives = 111/160 (69%)
Query: 55 NLYMCRESIIDSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICAL 114
N Y ES++D + R+T+V+ GK VV+ GYG+VGKG L+GLG + +TEIDPI AL
Sbjct: 1 NRYGTGESLLDGILRATNVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVTEIDPIRAL 60
Query: 115 QACMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNS 174
+A MDGF V+K+ E + DI VTATGNK+V+TREH MK+G ++ N GH + EIDV +
Sbjct: 61 EAAMDGFEVMKMEEAAKRADIFVTATGNKDVITREHFRAMKDGAILANAGHFDVEIDVAA 120
Query: 175 LRTPDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCS 214
L + +VR QVD PDGKRI LLAEGRLVNL+ +
Sbjct: 121 LEELAVEKREVRPQVDEYTLPDGKRIYLLAEGRLVNLAAA 160
Score = 174 bits (443), Expect = 5e-52
Identities = 53/97 (54%), Positives = 67/97 (69%)
Query: 296 MDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRT 355
MDGF V+K+ E + DI VTATGNK+V+TREH MK+G ++ N GH + EIDV +L
Sbjct: 64 MDGFEVMKMEEAAKRADIFVTATGNKDVITREHFRAMKDGAILANAGHFDVEIDVAALEE 123
Query: 356 PDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCS 392
+ +VR QVD PDGKRI LLAEGRLVNL+ +
Sbjct: 124 LAVEKREVRPQVDEYTLPDGKRIYLLAEGRLVNLAAA 160
>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 = 122 bits (308), Expect = 3e-31
Identities = 52/229 (22%), Positives = 81/229 (35%), Gaps = 32/229 (13%)
Query: 24 GCTHINAQTAAGKLTVPAMNVNDSVTKTKFDNLYMCRESIIDSLKRSTDVMFGG------ 77
G H + A + + A+ V N E + + R +V G
Sbjct: 97 GADHRDLTEALARAGLTAIAVEGVELPLLTSNSIGAGELSVQFIARFLEVQQPGRLGGAP 156
Query: 78 ----KQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFS-VVKLNEVIRT 132
K VV+ G G VGK Q L+GLG + IT+I+ Q G V +L E +
Sbjct: 157 DVAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDINVEALEQLEELGGKNVEELEEALAE 216
Query: 133 VDIVVTATGNKN-----VVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKVRS 187
D++VT T +V E +++MK G V+ N+ L E
Sbjct: 217 ADVIVTTTLLPGKRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALH--TQLLEE---- 270
Query: 188 QVDHVIWPDGKRIVLLAEGRLVNLSCSS-LPSFVVSITACTQALALIEL 235
G +V + + C+ +P A AL++L
Sbjct: 271 ---------GHGVVHYGDVNMPGPGCAMGVPWDATLRLAANTLPALVKL 310
Score = 52.2 bits (125), Expect = 3e-07
Identities = 10/83 (12%), Positives = 26/83 (31%), Gaps = 9/83 (10%)
Query: 463 WQPNMILDDGGDATHW---MLKKYPTMFKAIKGIVEESLTGVHRLYQLSKAGKLTVPAMN 519
W +++L T+ +++K + + ++ HR + + + A+
Sbjct: 63 WSLDVVLKVKEPLTNAEYALIQKLG-----DRLLFTYTIGADHRDLTEA-LARAGLTAIA 116
Query: 520 VNDSVTKTKFDNLYMCRESIIDR 542
V N E +
Sbjct: 117 VEGVELPLLTSNSIGAGELSVQF 139
Score = 41.4 bits (97), Expect = 7e-04
Identities = 20/112 (17%), Positives = 34/112 (30%), Gaps = 21/112 (18%)
Query: 288 PFKPSYYSMDGFS-VVKLNEVIRTVDIVVTATGNKN-----VVTREHMDKMKNGCVVCNM 341
G V +L E + D++VT T +V E +++MK G V+ N+
Sbjct: 193 VEALEQLEELGGKNVEELEEALAEADVIVTTTLLPGKRAGILVPEELVEQMKPGSVIVNV 252
Query: 342 GHSNTEIDVNSLRTPDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSS 393
L E G +V + + C+
Sbjct: 253 AVGAVGCVQALH--TQLLEE-------------GHGVVHYGDVNMPGPGCAM 289
>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 = 46.3 bits (111), Expect = 6e-06
Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 8/93 (8%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQACMDGFSVVKLNEVIRTVDI 135
GK V + G G +G+ + LK G VI D +A G V L+E++ D+
Sbjct: 35 GKTVGIIGLGRIGRAVARRLKAFGMKVIA---YDRYPKAEAEALGARYVSLDELLAESDV 91
Query: 136 VVTAT----GNKNVVTREHMDKMKNGCVVCNMG 164
V ++++ E + MK G ++ N
Sbjct: 92 VSLHLPLTPETRHLINAERLALMKPGAILINTA 124
Score = 34.4 bits (80), Expect = 0.067
Identities = 11/59 (18%), Positives = 24/59 (40%), Gaps = 4/59 (6%)
Query: 288 PFKPSYYSMDGFSVVKLNEVIRTVDIVVTAT----GNKNVVTREHMDKMKNGCVVCNMG 342
+ + G V L+E++ D+V ++++ E + MK G ++ N
Sbjct: 66 RYPKAEAEALGARYVSLDELLAESDVVSLHLPLTPETRHLINAERLALMKPGAILINTA 124
>gnl|CDD|214966 smart01002, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. Alanine dehydrogenase catalyzes the
NAD-dependent reversible reductive amination of pyruvate
into alanine.
Length = 149
Score = 45.2 bits (108), Expect = 1e-05
Identities = 28/95 (29%), Positives = 47/95 (49%), Gaps = 13/95 (13%)
Query: 80 VVLCGYGEVGKGCCQSLKGLGCVIYITEIDP--ICALQACMDG-FSVVKLN-----EVIR 131
VV+ G G VG G + KGLG + + ++ P + L++ + F+ + E ++
Sbjct: 23 VVVIGAGVVGLGAAATAKGLGAEVTVLDVRPARLRQLESLLGARFTTLYSQAELLEEAVK 82
Query: 132 TVDIVVTA---TGNK--NVVTREHMDKMKNGCVVC 161
D+V+ A G K +VTRE + MK G V+
Sbjct: 83 EADLVIGAVLIPGAKAPKLVTREMVKSMKPGSVIV 117
Score = 36.3 bits (85), Expect = 0.012
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 10/58 (17%)
Query: 287 GPFKPSYYSMDGFSVVKLNEVIRTVDIVVTA---TGNK--NVVTREHMDKMKNGCVVC 339
F Y + E ++ D+V+ A G K +VTRE + MK G V+
Sbjct: 65 ARFTTLYSQAELLE-----EAVKEADLVIGAVLIPGAKAPKLVTREMVKSMKPGSVIV 117
>gnl|CDD|216396 pfam01262, AlaDh_PNT_C, Alanine dehydrogenase/PNT, C-terminal
domain. This family now also contains the lysine
2-oxoglutarate reductases.
Length = 150
Score = 44.1 bits (105), Expect = 3e-05
Identities = 31/105 (29%), Positives = 44/105 (41%), Gaps = 17/105 (16%)
Query: 74 MFGGKQ---VVLCGYGEVGKGCCQSLKGLGCVIYITEIDP--ICALQACMDGFSVVK--- 125
GG VV+ G G VG G + KGLG + I ++ P + L + F
Sbjct: 14 GAGGVPPAKVVVIGGGVVGLGAAATAKGLGAPVTILDVRPERLEQLDSLFAEFVETDIFS 73
Query: 126 ----LNEVIRTVDIVVTA---TGNK--NVVTREHMDKMKNGCVVC 161
L E I D+V+ G + +VTRE + MK G V+
Sbjct: 74 NCEYLAEAIAEADLVIGTVLIPGARAPKLVTREMVKTMKPGSVIV 118
Score = 31.0 bits (71), Expect = 0.73
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 304 LNEVIRTVDIVVTA---TGNK--NVVTREHMDKMKNGCVVC 339
L E I D+V+ G + +VTRE + MK G V+
Sbjct: 78 LAEAIAEADLVIGTVLIPGARAPKLVTREMVKTMKPGSVIV 118
>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 = 44.8 bits (107), Expect = 5e-05
Identities = 24/95 (25%), Positives = 40/95 (42%), Gaps = 13/95 (13%)
Query: 76 GGKQVVLCGYGEVGKGCCQSLKGLGC--VIYITEIDPIC-ALQACMDGFSVVKLNEVIRT 132
GK V + G+G +G+ + LK G ++Y DP + DG V L E+++
Sbjct: 146 RGKTVGIVGFGAIGRRVAKRLKAFGAEVLVY----DPYVDPEKIEADGVKKVSLEELLKR 201
Query: 133 VDIV-----VTATGNKNVVTREHMDKMKNGCVVCN 162
D+V +T + ++ E MK N
Sbjct: 202 SDVVSLHARLTP-ETRGMIGAEEFALMKPTAYFIN 235
Score = 29.4 bits (67), Expect = 5.0
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 6/50 (12%)
Query: 296 MDGFSVVKLNEVIRTVDIV-----VTATGNKNVVTREHMDKMKNGCVVCN 340
DG V L E+++ D+V +T + ++ E MK N
Sbjct: 187 ADGVKKVSLEELLKRSDVVSLHARLTP-ETRGMIGAEEFALMKPTAYFIN 235
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 43.1 bits (102), Expect = 2e-04
Identities = 24/93 (25%), Positives = 39/93 (41%), Gaps = 10/93 (10%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQAC--MDGFSVVKLNEVIRTV 133
GK V + G G +G+ + LK G VI DP + V L+E++
Sbjct: 142 GKTVGIIGLGRIGRAVAKRLKAFGMKVIG---YDPYSPRERAGVDGVVGVDSLDELLAEA 198
Query: 134 DIVVTAT----GNKNVVTREHMDKMKNGCVVCN 162
DI+ + ++ E + KMK G ++ N
Sbjct: 199 DILTLHLPLTPETRGLINAEELAKMKPGAILIN 231
Score = 29.2 bits (66), Expect = 6.0
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 290 KPSYYSMDGFSVVKLNEVIRTVDIVVTAT----GNKNVVTREHMDKMKNGCVVCN 340
+ V L+E++ DI+ + ++ E + KMK G ++ N
Sbjct: 177 RERAGVDGVVGVDSLDELLAEADILTLHLPLTPETRGLINAEELAKMKPGAILIN 231
>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 = 42.6 bits (101), Expect = 3e-04
Identities = 26/93 (27%), Positives = 42/93 (45%), Gaps = 11/93 (11%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGC-VIY--ITEIDPICALQACMDGFSVVKLNEVIRTV 133
GK V + G G +G+ + L+ G V+Y T GF VV L+E++
Sbjct: 140 GKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRTRKPEPEEDL----GFRVVSLDELLAQS 195
Query: 134 DIVVTATG----NKNVVTREHMDKMKNGCVVCN 162
D+VV ++++ E + MK G V+ N
Sbjct: 196 DVVVLHLPLTPETRHLINEEELALMKPGAVLVN 228
Score = 28.4 bits (64), Expect = 8.7
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 298 GFSVVKLNEVIRTVDIVVTATG----NKNVVTREHMDKMKNGCVVCN 340
GF VV L+E++ D+VV ++++ E + MK G V+ N
Sbjct: 182 GFRVVSLDELLAQSDVVVLHLPLTPETRHLINEEELALMKPGAVLVN 228
>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 = 42.5 bits (101), Expect = 3e-04
Identities = 25/104 (24%), Positives = 48/104 (46%), Gaps = 8/104 (7%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQACMDGFSVVKLNEVIRTVDI 135
GK + + G+G +G+ + + LG VI + P G V L E+++ D
Sbjct: 139 GKTLGIIGFGRIGREVAKIARALGMNVIA-YDPYPKDEQAV-ELGVKTVSLEELLKNSDF 196
Query: 136 V---VTATG-NKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSL 175
+ V T K+++ ++ ++ MK+G ++ N ID +L
Sbjct: 197 ISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGV-IDEEAL 239
Score = 32.9 bits (76), Expect = 0.32
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 297 DGFSVVKLNEVIRTVDIV---VTATG-NKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNS 352
G V L E+++ D + V T K+++ ++ ++ MK+G ++ N ID +
Sbjct: 180 LGVKTVSLEELLKNSDFISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGV-IDEEA 238
Query: 353 L 353
L
Sbjct: 239 L 239
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 41.7 bits (99), Expect = 8e-04
Identities = 21/99 (21%), Positives = 44/99 (44%), Gaps = 14/99 (14%)
Query: 61 ESIIDSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCV-IYIT----EIDPICALQ 115
+ I L GK+V++ G GE+G+ + L G I + E A +
Sbjct: 174 KQIFGDLS--------GKKVLVIGAGEMGELVAKHLAEKGVRKITVANRTLERAEELAEE 225
Query: 116 ACMDGFSVVKLNEVIRTVDIVVTATGNKN-VVTREHMDK 153
+ + +L E + DIV+++TG + ++ + +++
Sbjct: 226 FGGEAIPLDELPEALAEADIVISSTGAPHPIIGKGMVER 264
Score = 30.9 bits (71), Expect = 1.7
Identities = 7/30 (23%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 303 KLNEVIRTVDIVVTATGNKN-VVTREHMDK 331
+L E + DIV+++TG + ++ + +++
Sbjct: 235 ELPEALAEADIVISSTGAPHPIIGKGMVER 264
>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 = 41.4 bits (98), Expect = 9e-04
Identities = 23/94 (24%), Positives = 41/94 (43%), Gaps = 8/94 (8%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 136
GK V++ G G++G+ + K G + A + ++ +L+E++ D V
Sbjct: 134 GKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVDEVYTPDELDELLPEADYV 193
Query: 137 VTA------TGNKNVVTREHMDKMKNGCVVCNMG 164
V A T + + E MK G V+ N+G
Sbjct: 194 VNALPLTPET--RGLFNAERFAAMKPGAVLINVG 225
Score = 29.8 bits (68), Expect = 3.4
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 17/71 (23%)
Query: 282 GLNKAGPFKPSY----YSMDGFSVVKLNEVIRTVDIVVTA------TGNKNVVTREHMDK 331
G+ ++G P Y+ D +L+E++ D VV A T + + E
Sbjct: 162 GVRRSGRPAPPVVDEVYTPD-----ELDELLPEADYVVNALPLTPET--RGLFNAERFAA 214
Query: 332 MKNGCVVCNMG 342
MK G V+ N+G
Sbjct: 215 MKPGAVLINVG 225
>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 = 41.2 bits (97), Expect = 9e-04
Identities = 23/94 (24%), Positives = 37/94 (39%), Gaps = 8/94 (8%)
Query: 75 FGGKQVVLCGYGEVGKGCCQSLK-GLGCVIYITEIDP-ICALQACMDGFSVVKLNEVIRT 132
GK V + GYG +G + LK G + DP + G V L E++
Sbjct: 145 LSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAY--DPYVSEEVIKKKGAKPVSLEELLAE 202
Query: 133 VDIVV----TATGNKNVVTREHMDKMKNGCVVCN 162
DI+ +++ + KMK G ++ N
Sbjct: 203 SDIISLHAPLTEETYHMINEKAFSKMKKGVILVN 236
Score = 31.1 bits (71), Expect = 1.4
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 5/58 (8%)
Query: 288 PFKP-SYYSMDGFSVVKLNEVIRTVDIVV----TATGNKNVVTREHMDKMKNGCVVCN 340
P+ G V L E++ DI+ +++ + KMK G ++ N
Sbjct: 179 PYVSEEVIKKKGAKPVSLEELLAESDIISLHAPLTEETYHMINEKAFSKMKKGVILVN 236
>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 = 38.3 bits (90), Expect = 0.001
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 80 VVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLN----EV-----I 130
+++ GYG VG+ + L+ G + + + DP + +G VV + EV I
Sbjct: 1 IIIIGYGRVGRSLAEELREGGPDVVVIDKDPERVEELREEGVPVVVGDATDEEVLEEAGI 60
Query: 131 RTVDIVVTATGN 142
D VV ATG+
Sbjct: 61 EEADAVVAATGD 72
>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 = 40.7 bits (96), Expect = 0.001
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 4/92 (4%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 136
GK V + G G +G+ + L G G + + P+ + V+L+E++ + D +
Sbjct: 144 GKTVGILGMGALGRAIARRLSGFGATLLYYDPHPLDQAEEQALNLRRVELDELLESSDFL 203
Query: 137 VTAT----GNKNVVTREHMDKMKNGCVVCNMG 164
V A +++ E + KMK G ++ N
Sbjct: 204 VLALPLTPDTLHLINAEALAKMKPGALLVNPC 235
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 40.4 bits (95), Expect = 0.002
Identities = 23/104 (22%), Positives = 37/104 (35%), Gaps = 16/104 (15%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVIYIT------EIDPICALQACMDGFSVVK----- 125
GK V + GYG +G + L+ G + T E + + V +
Sbjct: 159 GKTVFILGYGAIGIELAKRLRPFGVKLLATRRSWTSEPEDGLLIPNGDVDDLVDEKGGHE 218
Query: 126 -LNEVIRTVDIVVTA----TGNKNVVTREHMDKMKNGCVVCNMG 164
+ E DIVV +V E + MK G ++ N+
Sbjct: 219 DIYEFAGEADIVVLCCTLTKETAGIVNDEFLSSMKKGALLVNIA 262
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 38.8 bits (91), Expect = 0.005
Identities = 23/93 (24%), Positives = 42/93 (45%), Gaps = 7/93 (7%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 136
GK + + G G +G+ + LKG G + + P + G V L+E++ DI+
Sbjct: 146 GKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNPEAEK-ELGARYVDLDELLAESDII 204
Query: 137 V-----TATGNKNVVTREHMDKMKNGCVVCNMG 164
T ++++ E + KMK G ++ N
Sbjct: 205 SLHCPLTPE-TRHLINAEELAKMKPGAILVNTA 236
Score = 29.1 bits (66), Expect = 6.4
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 298 GFSVVKLNEVIRTVDIVV-----TATGNKNVVTREHMDKMKNGCVVCNMG 342
G V L+E++ DI+ T ++++ E + KMK G ++ N
Sbjct: 188 GARYVDLDELLAESDIISLHCPLTPE-TRHLINAEELAKMKPGAILVNTA 236
>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 = 38.3 bits (90), Expect = 0.006
Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 16/102 (15%)
Query: 73 VMFGGKQVVLCGYGEVGKGCCQSLKGLGC-VIYIT-----EIDPICALQACMDGFSVVKL 126
GK V + G G +G+ + L+G G VIY E + G V+L
Sbjct: 138 RELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEAEEKDL------GVRYVEL 191
Query: 127 NEVIRTVDIVVTAT----GNKNVVTREHMDKMKNGCVVCNMG 164
+E++ D+V ++++ E + MK G ++ N
Sbjct: 192 DELLAESDVVSLHVPLTPETRHLIGAEELAAMKPGAILINTA 233
>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 = 38.3 bits (90), Expect = 0.006
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 6/93 (6%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVI--YITEIDPICALQACMDGFSVVKLNEVIRTVD 134
GK + + G G +G+ + LG + Y + A + ++ V L E++ T D
Sbjct: 135 GKTLGVIGLGNIGRLVANAALALGMKVIGYDPYLSVEAAWKLSVEVQRVTSLEELLATAD 194
Query: 135 IV---VTAT-GNKNVVTREHMDKMKNGCVVCNM 163
+ V T + ++ E + KMK G ++ N
Sbjct: 195 YITLHVPLTDETRGLINAELLAKMKPGAILLNF 227
Score = 29.5 bits (67), Expect = 4.2
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 301 VVKLNEVIRTVDIV---VTAT-GNKNVVTREHMDKMKNGCVVCNM 341
V L E++ T D + V T + ++ E + KMK G ++ N
Sbjct: 183 VTSLEELLATADYITLHVPLTDETRGLINAELLAKMKPGAILLNF 227
>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 = 38.0 bits (89), Expect = 0.009
Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 5/96 (5%)
Query: 73 VMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRT 132
GK V + GYG +G+ + LK G + P A G + L+E +
Sbjct: 133 KELRGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPKEDEGADFVGT-LSDLDEALEQ 191
Query: 133 VDIVVTAT----GNKNVVTREHMDKMKNGCVVCNMG 164
D+VV A + ++ + MK G ++ N+G
Sbjct: 192 ADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVG 227
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(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 = 311
Score = 37.6 bits (88), Expect = 0.012
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 75 FGGKQVVLCGYGEVGKGCCQSLKGLG-CVIYITEIDPICALQ-ACMDGFSVVKLNEV--- 129
GK+V++ G GE+G+ + L G I I A + A G + V L+E+
Sbjct: 176 LKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELAKELGGNAVPLDELLEL 235
Query: 130 IRTVDIVVTATG 141
+ D+V++ATG
Sbjct: 236 LNEADVVISATG 247
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 37.6 bits (88), Expect = 0.013
Identities = 24/102 (23%), Positives = 43/102 (42%), Gaps = 20/102 (19%)
Query: 61 ESIIDSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSL--KGLGCVIYITEIDPIC------ 112
S L + K+V++ G GE+G+ + L KG+ + I
Sbjct: 162 SSAAVELAKRIFGSLKDKKVLVIGAGEMGELVAKHLAEKGVKKIT-------IANRTLER 214
Query: 113 ALQ-ACMDGFSVVKLNEV---IRTVDIVVTATGNKN-VVTRE 149
A + A G V L E+ + D+V+++T + ++TRE
Sbjct: 215 AEELAKKLGAEAVALEELLEALAEADVVISSTSAPHPIITRE 256
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 35.7 bits (83), Expect = 0.013
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 8/85 (9%)
Query: 75 FGGKQVVLCGYGEVGKGCCQSLKGLGC-VIYIT-----EIDPICA-LQACMDGFSVVKLN 127
GK+V+L G GE+ + + L G I I + + + + +L
Sbjct: 10 LKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRTLEKAKELAEEFPVGGEALPLDELE 69
Query: 128 EVIRTVDIVVTATGNKN-VVTREHM 151
E++ DIV++AT ++T+E +
Sbjct: 70 ELLAEADIVISATSAPTPIITKEMV 94
Score = 28.0 bits (63), Expect = 6.0
Identities = 9/28 (32%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 303 KLNEVIRTVDIVVTATGNKN-VVTREHM 329
+L E++ DIV++AT ++T+E +
Sbjct: 67 ELEELLAEADIVISATSAPTPIITKEMV 94
>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 = 37.4 bits (88), Expect = 0.015
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 10/92 (10%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 136
GK V + G G++G+ + LKG GC + + P L G V L+E++ DI+
Sbjct: 144 GKTVGVIGTGKIGQAFARILKGFGCRVLAYDPYPNPELAK--LGVEYVDLDELLAESDII 201
Query: 137 ------VTATGNKNVVTREHMDKMKNGCVVCN 162
T +++ E + KMK+G ++ N
Sbjct: 202 SLHCPLTPET--HHLINAETIAKMKDGVMLIN 231
>gnl|CDD|133448 cd01080, NAD_bind_m-THF_DH_Cyclohyd, NADP binding domain of
methylene-tetrahydrofolate dehydrogenase/cyclohydrolase.
NADP binding domain of the Methylene-Tetrahydrofolate
Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase)
bifunctional enzyme. Tetrahydrofolate is a versatile
carrier of activated one-carbon units. The major
one-carbon folate donors are N-5 methyltetrahydrofolate,
N5,N10-m-THF, and N10-formayltetrahydrofolate. The
oxidation of metabolic intermediate m-THF to m-THF
requires the enzyme m-THF DH. In addition, most DHs also
have an associated cyclohydrolase activity which
catalyzes its hydrolysis to N10-formyltetrahydrofolate.
m-THF DH is typically found as part of a multifunctional
protein in eukaryotes. NADP-dependent m-THF DH in
mammals, birds and yeast are components of a
trifunctional enzyme with DH, cyclohydrolase, and
synthetase activities. Certain eukaryotic cells also
contain homodimeric bifunctional DH/cyclodrolase form.
In bacteria, monofucntional DH, as well as bifunctional
m-THF m-THF DHm-THF DHDH/cyclodrolase are found. In
addition, yeast (S. cerevisiae) also express an
monofunctional DH. This family contains the bifunctional
DH/cyclohydrolase. M-THF DH, like other amino acid
DH-like NAD(P)-binding domains, is a member of the
Rossmann fold superfamily which includes glutamate,
leucine, and phenylalanine DHs, m-THF DH,
methylene-tetrahydromethanopterin DH, m-THF
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.
Length = 168
Score = 36.4 bits (85), Expect = 0.016
Identities = 25/99 (25%), Positives = 37/99 (37%), Gaps = 17/99 (17%)
Query: 67 LKRSTDVMFGGKQVVLCGYGE-VGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK 125
L + + GK+VV+ G VGK L +C +
Sbjct: 34 LLKRYGIDLAGKKVVVVGRSNIVGKPLAALLLNRNA------TVTVCHSKT-------KN 80
Query: 126 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 164
L E + DIV+ A G +V D +K G VV ++G
Sbjct: 81 LKEHTKQADIVIVAVGKPGLVKG---DMVKPGAVVIDVG 116
Score = 31.0 bits (71), Expect = 0.79
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 303 KLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 342
L E + DIV+ A G +V D +K G VV ++G
Sbjct: 80 NLKEHTKQADIVIVAVGKPGLVKG---DMVKPGAVVIDVG 116
>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 = 36.2 bits (84), Expect = 0.034
Identities = 23/87 (26%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 75 FGGKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQACMDGFSVVKLNEVIRTV 133
GK V + GYG G +L+ G VI +A DGF V + E I
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGASWKKATEDGFKVGTVEEAIPQA 60
Query: 134 DIVVTATGNK---NVVTREHMDKMKNG 157
D+++ ++ V E +K G
Sbjct: 61 DLIMNLLPDEVQHEVYEAEIQPLLKEG 87
>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 = 36.1 bits (84), Expect = 0.038
Identities = 27/95 (28%), Positives = 41/95 (43%), Gaps = 10/95 (10%)
Query: 76 GGKQVVLCGYGEVGKGCCQSLKGLGC-VI-YITEIDPICALQACMDGFSVVKLNEVIRTV 133
+ V + G G++G+ Q KG G VI Y DP + G V L E+ +
Sbjct: 142 EDQTVGVVGTGKIGRAVAQRAKGFGMKVIAY----DPFRNPELEDKGVKYVSLEELFKNS 197
Query: 134 DIV---VTAT-GNKNVVTREHMDKMKNGCVVCNMG 164
DI+ V T N +++ E MK G ++ N
Sbjct: 198 DIISLHVPLTPENHHMINEEAFKLMKKGVIIINTA 232
Score = 28.4 bits (64), Expect = 9.2
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 288 PFKPSYYSMDGFSVVKLNEVIRTVDIV---VTAT-GNKNVVTREHMDKMKNGCVVCNMG 342
PF+ G V L E+ + DI+ V T N +++ E MK G ++ N
Sbjct: 174 PFRNPELEDKGVKYVSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTA 232
>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 = 35.9 bits (84), Expect = 0.044
Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 9/92 (9%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEI--DPICALQACMDGFSVVKLNEVIRTVD 134
GK + + G G +GK + L G G + + D A + G V L E+++ D
Sbjct: 142 GKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYPDEEFAKEH---GVEFVSLEELLKESD 198
Query: 135 IV---VTAT-GNKNVVTREHMDKMKNGCVVCN 162
+ + T ++++ + MK G ++ N
Sbjct: 199 FISLHLPLTPETRHLINAAELALMKPGAILIN 230
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 35.9 bits (82), Expect = 0.044
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 74 MFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQ-ACMDGFSVVKLNEVIRT 132
+ GK V + GYG G Q+L+ G V + + P + + A DGF V+ ++E +RT
Sbjct: 13 LLQGKTVAVIGYGSQGHAQAQNLRDSG-VEVVVGVRPGKSFEVAKADGFEVMSVSEAVRT 71
Query: 133 VDIV 136
+V
Sbjct: 72 AQVV 75
>gnl|CDD|240630 cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic
domains. Alanine dehydrogenase (L-AlaDH) catalyzes the
NAD-dependent conversion of pyruvate to L-alanine via
reductive amination. Like formate dehydrogenase and
related enzymes, L-AlaDH is comprised of 2 domains
connected by a long alpha helical stretch, each
resembling a Rossmann fold NAD-binding domain. The
NAD-binding domain is inserted within the linear
sequence of the more divergent catalytic domain. Ligand
binding and active site residues are found in the cleft
between the subdomains. L-AlaDH is typically hexameric
and is critical in carbon and nitrogen metabolism in
micro-organisms.
Length = 359
Score = 35.8 bits (84), Expect = 0.054
Identities = 28/106 (26%), Positives = 45/106 (42%), Gaps = 22/106 (20%)
Query: 80 VVLCGYGEVGKGCCQSLKGLGCVIYITEIDP--ICALQACMDG------FSVVKLNEVIR 131
VV+ G G VG+ + GLG + + +I+ + L G + L E ++
Sbjct: 171 VVILGAGVVGENAARVALGLGAEVTVLDINLERLRYLDDIFGGRVTTLYSNPANLEEALK 230
Query: 132 TVDIVVTA---TGNK--NVVTREHMDKMKNGCVVCNMGHSNTEIDV 172
D+V+ A G K +VT E + MK G V+ +DV
Sbjct: 231 EADLVIGAVLIPGAKAPKLVTEEMVKTMKPGSVI---------VDV 267
Score = 32.0 bits (74), Expect = 0.74
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 14/52 (26%)
Query: 304 LNEVIRTVDIVVTA---TGNK--NVVTREHMDKMKNGCVVCNMGHSNTEIDV 350
L E ++ D+V+ A G K +VT E + MK G V+ +DV
Sbjct: 225 LEEALKEADLVIGAVLIPGAKAPKLVTEEMVKTMKPGSVI---------VDV 267
>gnl|CDD|162819 TIGR02354, thiF_fam2, thiamine biosynthesis protein ThiF, family 2.
Members of the HesA/MoeB/ThiF family of proteins
(pfam00899) include a number of members encoded in the
midst of thiamine biosynthetic operons. This mix of
known and putative ThiF proteins shows a deep split in
phylogenetic trees, with one the E. coli ThiF and the E.
coli MoeB proteins seemingly more closely related than
E. coli ThiF and Campylobacter (for example) ThiF. This
model represents the divergent clade of putative ThiF
proteins such found in Campylobacter [Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine].
Length = 200
Score = 34.8 bits (80), Expect = 0.067
Identities = 29/134 (21%), Positives = 57/134 (42%), Gaps = 20/134 (14%)
Query: 105 ITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTATGN---KNVVTREHMDKMKNGCVVC 161
I+EI+P ++A + + +++ + DIV A N K ++ ++K K+ ++
Sbjct: 83 ISEINPYTEIEAYDEKITEENIDKFFKDADIVCEAFDNAEAKAMLVNAVLEKYKDKYLIA 142
Query: 162 NMGHSNTEIDVNSLRTPDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSSLPSFVV 221
G + + D NS++T ++ K L +G+ L + V
Sbjct: 143 ASGLAGYD-DANSIKTRKIS----------------KHFYLCGDGKSDAKQGLGLMAPRV 185
Query: 222 SITACTQALALIEL 235
I A QA ++EL
Sbjct: 186 QICAAHQANLVLEL 199
>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 = 0.13
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 120 GFSVVKLNEVIRTVDIV---VTAT-GNKNVVTREHMDKMKNGCVVCN 162
GF V L E+++ DI+ V T +++ RE+ MK G V+ N
Sbjct: 181 GFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLIN 227
Score = 34.2 bits (79), Expect = 0.13
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 298 GFSVVKLNEVIRTVDIV---VTAT-GNKNVVTREHMDKMKNGCVVCN 340
GF V L E+++ DI+ V T +++ RE+ MK G V+ N
Sbjct: 181 GFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLIN 227
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 34.2 bits (79), Expect = 0.14
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 10/63 (15%)
Query: 290 KPSYYSMDG------FSVVKLNEVIRTVDIV-VTATGN---KNVVTREHMDKMKNGCVVC 339
K YYS G + V L E+++T DI+ + A N KN++ + + +K+G ++
Sbjct: 170 KVVYYSTSGKNKNEEYERVSLEELLKTSDIISIHAPLNEKTKNLIAYKELKLLKDGAILI 229
Query: 340 NMG 342
N+G
Sbjct: 230 NVG 232
Score = 32.3 bits (74), Expect = 0.59
Identities = 23/93 (24%), Positives = 48/93 (51%), Gaps = 10/93 (10%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQACMDGFSVVKLNEVIRTVDI 135
GK+ + G G +GK + + G V+Y + + + + + V L E+++T DI
Sbjct: 145 GKKWGIIGLGTIGKRVAKIAQAFGAKVVYYST-----SGKNKNEEYERVSLEELLKTSDI 199
Query: 136 V-VTATGN---KNVVTREHMDKMKNGCVVCNMG 164
+ + A N KN++ + + +K+G ++ N+G
Sbjct: 200 ISIHAPLNEKTKNLIAYKELKLLKDGAILINVG 232
Score = 28.4 bits (64), Expect = 9.7
Identities = 11/47 (23%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 128 EVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNS 174
E I+ +I++T NK V+ +E + ++ N ++C +D+
Sbjct: 38 ERIKDANIIIT---NKVVIDKEVLSQLPNLKLICITATGTNNVDIEY 81
Score = 28.4 bits (64), Expect = 9.7
Identities = 11/47 (23%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 306 EVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNS 352
E I+ +I++T NK V+ +E + ++ N ++C +D+
Sbjct: 38 ERIKDANIIIT---NKVVIDKEVLSQLPNLKLICITATGTNNVDIEY 81
>gnl|CDD|237636 PRK14186, PRK14186, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 297
Score = 33.5 bits (77), Expect = 0.22
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 126 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 164
L + R DI+V A G N++ E +K G VV ++G
Sbjct: 195 LASITREADILVAAAGRPNLIGAEM---VKPGAVVVDVG 230
Score = 33.5 bits (77), Expect = 0.22
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 304 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 342
L + R DI+V A G N++ E +K G VV ++G
Sbjct: 195 LASITREADILVAAAGRPNLIGAEM---VKPGAVVVDVG 230
>gnl|CDD|217267 pfam02882, THF_DHG_CYH_C, Tetrahydrofolate
dehydrogenase/cyclohydrolase, NAD(P)-binding domain.
Length = 160
Score = 32.0 bits (74), Expect = 0.32
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 126 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHS 166
L E+ R DIVV A G ++ + +K G VV ++G +
Sbjct: 73 LAEITREADIVVVAVGKPGLIKADW---VKPGAVVIDVGIN 110
Score = 32.0 bits (74), Expect = 0.32
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 304 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHS 344
L E+ R DIVV A G ++ + +K G VV ++G +
Sbjct: 73 LAEITREADIVVVAVGKPGLIKADW---VKPGAVVIDVGIN 110
>gnl|CDD|240621 cd01620, Ala_dh_like, Alanine dehydrogenase and related
dehydrogenases. Alanine dehydrogenase/Transhydrogenase,
such as the hexameric L-alanine dehydrogenase of
Phormidium lapideum, contain 2 Rossmann fold-like
domains linked by an alpha helical region. Related
proteins include Saccharopine Dehydrogenase (SDH),
bifunctional lysine ketoglutarate reductase
/saccharopine dehydrogenase enzyme,
N(5)-(carboxyethyl)ornithine synthase, and Rubrum
transdehydrogenase. Alanine dehydrogenase (L-AlaDH)
catalyzes the NAD-dependent conversion of pyrucate to
L-alanine via reductive amination. Transhydrogenases
found in bacterial and inner mitochondrial membranes
link NAD(P)(H)-dependent redox reactions to proton
translocation. The energy of the proton electrochemical
gradient (delta-p), generated by the respiratory
electron transport chain, is consumed by
transhydrogenase in NAD(P)+ reduction. Transhydrogenase
is likely involved in the regulation of the citric acid
cycle. Rubrum transhydrogenase has 3 components, dI,
dII, and dIII. dII spans the membrane while dI and dIII
protrude on the cytoplasmic/matirx side. DI contains 2
domains with Rossmann folds, linked by a long alpha
helix, and contains a NAD binding site. Two dI
polypeptides (represented in this sub-family)
spontaneously form a heterotrimer with one dIII in the
absence of dII. In the heterotrimer, both dI chains may
bind NAD, but only one is well-ordered. dIII also binds
a well-ordered NADP, but in a different orientation than
classical Rossmann domains.
Length = 317
Score = 32.8 bits (75), Expect = 0.39
Identities = 29/148 (19%), Positives = 53/148 (35%), Gaps = 22/148 (14%)
Query: 35 GKLTVPAMNV--NDSVTKTKFDNLYMCRESIIDSL----KRSTDVMFGGK-----QVVLC 83
KLT A+ ND + ++ + + M G +V++
Sbjct: 109 KKLTAYALEDLENDFRPRLAPNSNIAGYAGVQLGAYELARIQGGRMGGAGGVPPAKVLII 168
Query: 84 GYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK------LNEVIRTVDIVV 137
G G VG G + K LG + + +I G S ++ L + ++ DI++
Sbjct: 169 GAGVVGLGAAKIAKKLGANVLVYDIKEEKLKGVETLGGSRLRYSQKEELEKELKQTDILI 228
Query: 138 TATGNKN-----VVTREHMDKMKNGCVV 160
A ++ E + MK G V+
Sbjct: 229 NAILVDGPRAPILIMEELVGPMKRGAVI 256
>gnl|CDD|224626 COG1712, COG1712, Predicted dinucleotide-utilizing enzyme [General
function prediction only].
Length = 255
Score = 32.8 bits (75), Expect = 0.39
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 80 VVLCGYGEVGKGCCQSLK-GLGCV----IYITEIDPICALQACMDGFSVVKLNEVIRTVD 134
V + G G +GK + ++ G +Y + + L+A + V ++E+I VD
Sbjct: 3 VGIVGCGAIGKFLLELVRDGRVDFELVAVYDRDEEKAKELEASVGRRCVSDIDELIAEVD 62
Query: 135 IVVTATGNKNVVTREHMDK-MKNGC 158
+VV A + V RE++ K +K G
Sbjct: 63 LVVEAASPEAV--REYVPKILKAGI 85
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 31.9 bits (73), Expect = 0.67
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 11/79 (13%)
Query: 78 KQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDP------ICALQACM----DGFSVVKLN 127
++++ G G VG+ + L G + + + D + D L
Sbjct: 1 MKIIIIGAGRVGRSVARELSEEGHNVVLIDRDEERVEEFLADELDTHVVIGDATDEDVLE 60
Query: 128 EV-IRTVDIVVTATGNKNV 145
E I D VV ATGN V
Sbjct: 61 EAGIDDADAVVAATGNDEV 79
>gnl|CDD|240638 cd12161, GDH_like_1, Putative glycerate dehydrogenase and related
proteins of the D-specific 2-hydroxy dehydrogenase
family. This group contains a variety of proteins
variously identified as glycerate dehydrogenase (GDH,
aka Hydroxypyruvate Reductase) and other enzymes of the
2-hydroxyacid dehydrogenase family. GDH catalyzes the
reversible reaction of (R)-glycerate + NAD+ to
hydroxypyruvate + NADH + H+. 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 = 315
Score = 32.2 bits (74), Expect = 0.68
Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 14/94 (14%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVIYI---TEIDPICALQACMDGFSVVKLNEVIRTV 133
GK V + G G +G + K GC + +E + AL G V L+E++
Sbjct: 144 GKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRSEKEEAKAL-----GIEYVSLDELLAES 198
Query: 134 DIV-----VTATGNKNVVTREHMDKMKNGCVVCN 162
DIV + K ++ +E + MK ++ N
Sbjct: 199 DIVSLHLPLND-ETKGLIGKEKLALMKESAILIN 231
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 32.4 bits (74), Expect = 0.82
Identities = 26/131 (19%), Positives = 53/131 (40%), Gaps = 16/131 (12%)
Query: 167 NTEIDVNSLRTPDLTWEKVRSQVDHVIWPDGKRIVLLAEGRLVNLSCSSLPSFVVSITAC 226
EI+ + ++ E++ ++D D +R+ + EG+L + + + ++ + +
Sbjct: 573 FIEIEFKEIS--EVDLEELLREIDE----DRERVRRVLEGKLKEETKDLVKTALMIVESP 626
Query: 227 TQALALIELFNAPSGRY--KSDVYLLP--KKMDEYVASLHLPTFDAHLTELSDEQAKYMG 282
+A + F PS R VY + + AS H+ +L E +
Sbjct: 627 NKARTIASFFGRPSVRRLGGGVVYEVAIGDLVLTITASG------GHVFDLVTEPGVHGV 680
Query: 283 LNKAGPFKPSY 293
L K G + P Y
Sbjct: 681 LVKDGKYVPVY 691
>gnl|CDD|240661 cd12185, HGDH_LDH_like, Putative Lactate dehydrogenase and
(R)-2-Hydroxyglutarate Dehydrogenase-like proteins,
NAD-binding and catalytic domains. This group contains
various putative dehydrogenases related to D-lactate
dehydrogenase (LDH), (R)-2-hydroxyglutarate
dehydrogenase (HGDH), and related enzymes, members of
the 2-hydroxyacid dehydrogenases family. LDH catalyzes
the interconversion of pyruvate and lactate, and HGDH
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. Despite often low sequence
identity within this 2-hydroxyacid dehydrogenase family,
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 = 322
Score = 31.8 bits (73), Expect = 0.95
Identities = 39/159 (24%), Positives = 67/159 (42%), Gaps = 21/159 (13%)
Query: 21 RIVGCTHINAQTAAGKLTVPAMNVN---DSVTKTKFDNLYMCRESIIDSLKRS--TDVMF 75
R +G HI+ AA +L + NV +SV + M +KR+ D
Sbjct: 75 RSIGYDHIDL-DAAKELGIKVSNVTYSPNSVADYTVMLMLMALRKYKQIMKRAEVNDYSL 133
Query: 76 GGKQ--------VVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLN 127
GG Q V + G G +G+ ++L G GC I + P ++ V L+
Sbjct: 134 GGLQGRELRNLTVGVIGTGRIGQAVIKNLSGFGCKILAYDPYPNEEVK---KYAEYVDLD 190
Query: 128 EVIRTVDIVVTAT----GNKNVVTREHMDKMKNGCVVCN 162
+ + DI+ T +++ +E + KMK+G ++ N
Sbjct: 191 TLYKESDIITLHTPLTEETYHLINKESIAKMKDGVIIIN 229
>gnl|CDD|184559 PRK14189, PRK14189, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 285
Score = 31.6 bits (72), Expect = 0.98
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 131 RTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 164
R DIVV A G +NV+T D +K G V ++G
Sbjct: 200 RQADIVVAAVGKRNVLT---ADMVKPGATVIDVG 230
Score = 31.6 bits (72), Expect = 0.98
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 309 RTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 342
R DIVV A G +NV+T D +K G V ++G
Sbjct: 200 RQADIVVAAVGKRNVLT---ADMVKPGATVIDVG 230
>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 = 31.8 bits (73), Expect = 1.0
Identities = 22/104 (21%), Positives = 44/104 (42%), Gaps = 11/104 (10%)
Query: 68 KRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGC--VIYITEIDP-ICALQACMDGFSVV 124
R G+ V + G+G +G+ + L+ G ++Y DP + A +A G +V
Sbjct: 141 TRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVY----DPYLPAAEAAALGVELV 196
Query: 125 KLNEVIRTVDIVVTATG----NKNVVTREHMDKMKNGCVVCNMG 164
L+E++ D+V + ++ + M++G N
Sbjct: 197 SLDELLARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTA 240
>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 = 31.0 bits (71), Expect = 1.1
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 4/62 (6%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSV--VKLNEVIRT-V 133
GK V + G G+VG + L G + + +I+ +A + F V E+
Sbjct: 28 GKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEAVARAA-ELFGATVVAPEEIYSVDA 86
Query: 134 DI 135
D+
Sbjct: 87 DV 88
>gnl|CDD|212086 cd11517, SLC6sbd_B0AT3, glycine transporter, B0AT3; solute-binding
domain. B0AT3 (also called Xtrp2, XT2) transports
glycine. Human B0AT3 is encoded by the SLC6A18 gene.
B0AT3 is expressed in the kidney. Mutations in the
SLC6A18 gene may contribute to the autosomal recessive
disorder iminoglycinuria and its related disorder
hyperglycinuria. SLC6A18 or its neighboring genes are
associated with increased susceptibility to myocardial
infarction. This subgroup belongs to the solute carrier
6 (SLC6) transporter family.
Length = 576
Score = 31.7 bits (72), Expect = 1.1
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 428 LLNSLTSSYTGLPVFAWRG-ETEEDFWWCIDK 458
L+NS+TS Y +PVF+ G + D+ C+D+
Sbjct: 278 LVNSMTSLYASIPVFSVLGFKATNDYEHCLDR 309
>gnl|CDD|165280 PHA02976, PHA02976, hypothetical protein; Provisional.
Length = 181
Score = 30.8 bits (69), Expect = 1.4
Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 2/88 (2%)
Query: 208 LVNLSCSSLPSFVVSITACTQALALIELFNAPSGRYKSDVY--LLPKKMDEYVASLHLPT 265
+ N+ + + C Q + E N G Y+ + Y L +DE+ ++
Sbjct: 59 IFNIFIGCFHDDIEYSSGCFQYITRDEFLNMTDGSYEEEFYIEKLNSPLDEFCLAIAPLV 118
Query: 266 FDAHLTELSDEQAKYMGLNKAGPFKPSY 293
+ E ++ K +N FKP+Y
Sbjct: 119 INEDDIEHLNDDEKCKNVNDEEMFKPTY 146
>gnl|CDD|184552 PRK14175, PRK14175, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 286
Score = 31.0 bits (70), Expect = 1.4
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 126 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 185
+ ++ D++V+A G +VT+ D +K G V+ ++G++ D N D+ ++ V
Sbjct: 195 MASYLKDADVIVSAVGKPGLVTK---DVVKEGAVIIDVGNT---PDENGKLKGDVDYDAV 248
Query: 186 R 186
+
Sbjct: 249 K 249
Score = 31.0 bits (70), Expect = 1.4
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 304 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 363
+ ++ D++V+A G +VT+ D +K G V+ ++G++ D N D+ ++ V
Sbjct: 195 MASYLKDADVIVSAVGKPGLVTK---DVVKEGAVIIDVGNT---PDENGKLKGDVDYDAV 248
Query: 364 R 364
+
Sbjct: 249 K 249
Score = 28.3 bits (63), Expect = 8.7
Identities = 19/64 (29%), Positives = 30/64 (46%)
Query: 3 GIMALRKRAGDDKPLKNARIVGCTHINAQTAAGKLTVPAMNVNDSVTKTKFDNLYMCRES 62
GIM + K A D KNA ++G +HI Q + L +V +++K Y+
Sbjct: 144 GIMEILKHADIDLEGKNAVVIGRSHIVGQPVSKLLLQKNASVTILHSRSKDMASYLKDAD 203
Query: 63 IIDS 66
+I S
Sbjct: 204 VIVS 207
>gnl|CDD|240647 cd12170, 2-Hacid_dh_9, 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 = 294
Score = 30.7 bits (70), Expect = 1.6
Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 21/90 (23%)
Query: 271 TELSDEQAKYMGLNKAG--------PF--KPSYYS--------MDGFSVVKLNEVIRTVD 312
EL+ + +GL G F YYS G + LNE+++TVD
Sbjct: 134 RELTGLKVGIIGLGTTGQMIADALSFFGADVYYYSRTRKPDAEAKGIRYLPLNELLKTVD 193
Query: 313 IVVTATGNKNVVT--REHMDKMKNGCVVCN 340
++ T KNV+ E + + +G ++ N
Sbjct: 194 VICTCL-PKNVILLGEEEFELLGDGKILFN 222
>gnl|CDD|234662 PRK00141, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 473
Score = 30.9 bits (70), Expect = 1.7
Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 6/84 (7%)
Query: 62 SIIDSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQ-ACMDG 120
SI+ L + G +V++ G G G+G L LGC + + + + + + G
Sbjct: 2 SILVPLSALPQELSG--RVLVAGAGVSGRGIAAMLSELGCDVVVADDNETARHKLIEVTG 59
Query: 121 FSVVKLNEVIRTVD---IVVTATG 141
+ + E +D +VVT+ G
Sbjct: 60 VADISTAEASDQLDSFSLVVTSPG 83
>gnl|CDD|237635 PRK14184, PRK14184, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 286
Score = 30.5 bits (69), Expect = 1.8
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 126 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTE 169
L E R D + A G VT D +K G VV ++G + T+
Sbjct: 198 LAEECREADFLFVAIGRPRFVTA---DMVKPGAVVVDVGINRTD 238
Score = 30.5 bits (69), Expect = 1.8
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 304 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTE 347
L E R D + A G VT D +K G VV ++G + T+
Sbjct: 198 LAEECREADFLFVAIGRPRFVTA---DMVKPGAVVVDVGINRTD 238
>gnl|CDD|201603 pfam01118, Semialdhyde_dh, Semialdehyde dehydrogenase, NAD binding
domain. This Pfam entry contains the following members:
N-acetyl-glutamine semialdehyde dehydrogenase (AgrC)
Aspartate-semialdehyde dehydrogenase.
Length = 121
Score = 29.4 bits (67), Expect = 1.8
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 128 EVIRTVDIVVTATGNKNVVTREHMDK-MKNGCVV 160
E ++ VDIV A V++E K ++ G VV
Sbjct: 62 EDLKDVDIVFLALPAG--VSKELAPKLLEAGAVV 93
Score = 29.4 bits (67), Expect = 1.8
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 306 EVIRTVDIVVTATGNKNVVTREHMDK-MKNGCVV 338
E ++ VDIV A V++E K ++ G VV
Sbjct: 62 EDLKDVDIVFLALPAG--VSKELAPKLLEAGAVV 93
>gnl|CDD|240658 cd12181, ceo_syn, N(5)-(carboxyethyl)ornithine synthase.
N(5)-(carboxyethyl)ornithine synthase (ceo_syn)
catalyzes the NADP-dependent conversion of
N5-(L-1-carboxyethyl)-L-ornithine to L-ornithine +
pyruvate. Ornithine plays a key role in the urea cycle,
which in mammals is used in arginine biosynthesis, and
is a precursor in polyamine synthesis. ceo_syn is
related to the NAD-dependent L-alanine dehydrogenases.
Like formate dehydrogenase and related enzymes, ceo_syn
is comprised of 2 domains connected by a long alpha
helical stretch, each resembling a Rossmann fold
NAD-binding domain. The NAD-binding domain is inserted
within the linear sequence of the more divergent
catalytic domain. These ceo_syn proteins have a
partially conserved NAD-binding motif and active site
residues that are characteristic of related enzymes such
as Saccharopine Dehydrogenase.
Length = 295
Score = 30.7 bits (70), Expect = 1.9
Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 21/97 (21%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 136
+V + G+G +G ++LK G +T + + E + DI+
Sbjct: 154 QTKVAVLGFGNTARGAIRALKLGG--ADVT----VY------TRRTEALFKEELSEYDII 201
Query: 137 VTAT-----GNKNVVTREHMDKMKNGC----VVCNMG 164
V +++ E + ++K G V C+ G
Sbjct: 202 VNCILQDTDRPDHIIYEEDLKRLKPGALIIDVSCDEG 238
>gnl|CDD|177458 PHA02676, PHA02676, A-type inclusion protein; Provisional.
Length = 520
Score = 30.7 bits (69), Expect = 2.1
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 415 CY-HLRFASNLAKYLLNSLTSSYTGLPVFAWRGETEEDFWWCIDKCVNSWQP 465
CY L + LA N + Y G+P++ W G + + ++ N++
Sbjct: 151 CYDFLNYMGTLASQYKN--KAIYIGVPMYWWYGVDVKSVYLKLETHWNNYDT 200
>gnl|CDD|226383 COG3865, COG3865, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 151
Score = 29.7 bits (67), Expect = 2.1
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 5/41 (12%)
Query: 446 GETEEDFWWCIDKCVNSWQ---PNM--ILDDGGDATHWMLK 481
G E W DK SWQ + ++ DG A M+
Sbjct: 102 GGEAEACGWLKDKFGVSWQIVPRVLGELMADGDRAFEAMMA 142
>gnl|CDD|233242 TIGR01035, hemA, glutamyl-tRNA reductase. This enzyme, together
with glutamate-1-semialdehyde-2,1-aminomutase
(TIGR00713), leads to the production of
delta-amino-levulinic acid from Glu-tRNA [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 417
Score = 30.8 bits (70), Expect = 2.2
Identities = 27/102 (26%), Positives = 48/102 (47%), Gaps = 14/102 (13%)
Query: 61 ESIIDSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSL--KGLGCVIYIT---EIDPICALQ 115
E I SLK GK+ +L G GE+G+ + L KG+G ++ E A +
Sbjct: 172 ERIFGSLK--------GKKALLIGAGEMGELVAKHLLRKGVGKILIANRTYERAEDLAKE 223
Query: 116 ACMDGFSVVKLNEVIRTVDIVVTATGNKN-VVTREHMDKMKN 156
+ L E + DIV+++TG + +V++E +++
Sbjct: 224 LGGEAVKFEDLEEYLAEADIVISSTGAPHPIVSKEDVERALR 265
Score = 30.0 bits (68), Expect = 2.9
Identities = 9/33 (27%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 303 KLNEVIRTVDIVVTATGNKN-VVTREHMDKMKN 334
L E + DIV+++TG + +V++E +++
Sbjct: 233 DLEEYLAEADIVISSTGAPHPIVSKEDVERALR 265
>gnl|CDD|240660 cd12184, HGDH_like, (R)-2-Hydroxyglutarate Dehydrogenase and
related dehydrogenases, NAD-binding and catalytic
domains. (R)-2-hydroxyglutarate dehydrogenase (HGDH)
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. HGDH is a member of the
D-2-hydroxyacid NAD(+)-dependent dehydrogenase family;
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 = 330
Score = 30.3 bits (69), Expect = 2.3
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 8/84 (9%)
Query: 84 GYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTAT--- 140
G G +G + KGLG + +I P A + D + V L+E+++ DI+
Sbjct: 152 GTGRIGLTAAKLFKGLGAKVIGYDIYPSDAAK---DVVTFVSLDELLKKSDIISLHVPYI 208
Query: 141 --GNKNVVTREHMDKMKNGCVVCN 162
N ++ +E + KMK+G ++ N
Sbjct: 209 KGKNDKLINKEFISKMKDGAILIN 232
>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 = 30.2 bits (69), Expect = 2.9
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 11/95 (11%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYI-TEIDPICALQACMDGFSVVKLNEVIRTVD 134
GK ++ G G +G+ + LK G VI + T + C + + +L+EV++ D
Sbjct: 135 GKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTSGRDVEYFDKC---YPLEELDEVLKEAD 191
Query: 135 IVV-----TATGNKNVVTREHMDKMKNGCVVCNMG 164
IVV T ++ ++MK G + N+G
Sbjct: 192 IVVNVLPLTEE-THHLFDEAFFEQMKKGALFINVG 225
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 30.0 bits (68), Expect = 3.2
Identities = 31/108 (28%), Positives = 50/108 (46%), Gaps = 21/108 (19%)
Query: 73 VMFGG------KQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGF----- 121
V+ GG +VV+ G G VG + GLG + I +++ I L+ D F
Sbjct: 158 VLLGGVPGVLPAKVVVLGGGVVGTNAAKIAIGLGADVTILDLN-IDRLRQLDDLFGGRVH 216
Query: 122 ----SVVKLNEVIRTVDIVVTA---TGNK--NVVTREHMDKMKNGCVV 160
+ + E ++ D+V+ A G K +VTRE + +MK G V+
Sbjct: 217 TLYSTPSNIEEAVKKADLVIGAVLIPGAKAPKLVTREMVKQMKPGSVI 264
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 29.9 bits (68), Expect = 3.2
Identities = 25/86 (29%), Positives = 37/86 (43%), Gaps = 6/86 (6%)
Query: 77 GKQVVLCGYGEVGKGCCQSLK--GLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVD 134
GK+V + GYG G +L+ GL VI +A DGF V + E + D
Sbjct: 18 GKKVAIIGYGSQGHAQALNLRDSGLN-VIIGLRKGSSSWKKAKEDGFKVYTVEEAAKRAD 76
Query: 135 IVVTATGN---KNVVTREHMDKMKNG 157
+V+ + K V +E +K G
Sbjct: 77 VVMILLPDEQQKEVYEKEIAPNLKEG 102
>gnl|CDD|172658 PRK14170, PRK14170, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 29.7 bits (66), Expect = 3.8
Identities = 30/117 (25%), Positives = 46/117 (39%), Gaps = 17/117 (14%)
Query: 54 DNLYMCRESIIDSLKRSTDVMFGGKQVVLCGYGE-VGKGCCQSLKGLGCVIYITEIDPIC 112
D+ C + I L +ST GK+ V+ G VGK Q L + I
Sbjct: 134 DSFVPCTPAGIIELIKSTGTQIEGKRAVVIGRSNIVGKPVAQLLLNENATVTIAHS---- 189
Query: 113 ALQACMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTE 169
L +V + DI+V ATG V +++ +K G +V ++G E
Sbjct: 190 ---------RTKDLPQVAKEADILVVATGLAKFVKKDY---IKPGAIVIDVGMDRDE 234
>gnl|CDD|218237 pfam04738, Lant_dehyd_C, Lantibiotic dehydratase, C terminus.
Lantibiotics are ribosomally synthesised antimicrobial
agents derived from ribosomally synthesised peptides.
They are produced by bacteria of the Firmicutes phylum,
and include mutacin, subtilin, and nisin. Lantibiotic
peptides contain thioether bridges termed lanthionines
that are thought to be generated by dehydration of
serine and threonine residues followed by addition of
cysteine residues. This family constitutes the
C-terminus of the enzyme proposed to catalyze the
dehydration step.
Length = 500
Score = 29.6 bits (67), Expect = 4.4
Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 12/81 (14%)
Query: 248 YLLPKKMDEYVASLHLPTFDAHLTELSDEQAKYMGLNKAG------PFKPSYY-SMDGFS 300
+ ++++E +A+L A +LS ++ N+ G P Y S+ S
Sbjct: 284 HPERERLEEELAALPHKLAGAVPVQLS-----FVPRNRRGKNVTRTPRLLGYVISLGEHS 338
Query: 301 VVKLNEVIRTVDIVVTATGNK 321
N VI D+ V A ++
Sbjct: 339 DKSDNRVIPLADLYVGAEDDR 359
>gnl|CDD|131900 TIGR02853, spore_dpaA, dipicolinic acid synthetase, A subunit.
This predicted Rossman fold-containing protein is the A
subunit of dipicolinic acid synthetase as found in most,
though not all, endospore-forming low-GC Gram-positive
bacteria; it is absent in Clostridium. The B subunit is
represented by TIGR02852. This protein is also known as
SpoVFA [Cellular processes, Sporulation and
germination].
Length = 287
Score = 29.3 bits (66), Expect = 4.4
Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 4/94 (4%)
Query: 70 STDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYI---TEIDPICALQACMDGFSVVKL 126
TD G V++ G+G G ++ LG +++ + D + + F + KL
Sbjct: 144 HTDFTIHGSNVMVLGFGRTGMTIARTFSALGARVFVGARSSADLARITEMGLIPFPLNKL 203
Query: 127 NEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVV 160
E + +DIV+ T V+T + + K+ V+
Sbjct: 204 EEKVAEIDIVIN-TIPALVLTADVLSKLPKHAVI 236
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 29.4 bits (66), Expect = 4.6
Identities = 25/93 (26%), Positives = 42/93 (45%), Gaps = 9/93 (9%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYI--TEIDPICALQACMDGFSVVKLNEVIRTV 133
GK V G G +G+ Q LK C ++Y ++DP L+ L+ ++
Sbjct: 199 GKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDRLKMDP--ELEKETGAKFEEDLDAMLPKC 256
Query: 134 DIVVTAT----GNKNVVTREHMDKMKNGCVVCN 162
D+VV T + + +E + KMK G ++ N
Sbjct: 257 DVVVINTPLTEKTRGMFNKERIAKMKKGVLIVN 289
>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 = 29.5 bits (67), Expect = 5.1
Identities = 25/91 (27%), Positives = 39/91 (42%), Gaps = 7/91 (7%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 136
GK + + GYG +G + LG + +I L V L E++ D V
Sbjct: 140 GKTLGIIGYGHIGSQLSVLAEALGMRVIFYDIAEKLPLGNAR---QVSSLEELLAEADFV 196
Query: 137 ---VTAT-GNKNVVTREHMDKMKNGCVVCNM 163
V AT KN++ E + +MK G ++ N
Sbjct: 197 TLHVPATPSTKNMIGAEEIAQMKKGAILINA 227
Score = 28.7 bits (65), Expect = 8.0
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 304 LNEVIRTVDIV---VTAT-GNKNVVTREHMDKMKNGCVVCNM 341
L E++ D V V AT KN++ E + +MK G ++ N
Sbjct: 186 LEELLAEADFVTLHVPATPSTKNMIGAEEIAQMKKGAILINA 227
>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 = 28.7 bits (65), Expect = 5.2
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 4/88 (4%)
Query: 77 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQACMDGFSVVKLNEVIRTVDI 135
GK++ + GYG G +L+ G VI +A DGF V + E ++ D+
Sbjct: 4 GKKIAVIGYGSQGHAHALNLRDSGVNVIVGLRPGSKSWEKAKKDGFEVYTVAEAVKKADV 63
Query: 136 VVTATGN---KNVVTREHMDKMKNGCVV 160
V+ + V +E +K G +
Sbjct: 64 VMILLPDEVQAEVYEKEIAPNLKEGAAL 91
>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 = 27.3 bits (61), Expect = 5.9
Identities = 29/98 (29%), Positives = 36/98 (36%), Gaps = 29/98 (29%)
Query: 67 LKRSTDVMFG---GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSV 123
LK + V GK VV+ G GEVGKG + L G
Sbjct: 10 LKAAGKVTNKSLKGKTVVVLGAGEVGKGIAKLLADEGG---------------------- 47
Query: 124 VKLNEVIRT-VDIVVTATGNKNVVTREHMDKMKNGCVV 160
+V+ DI+VTAT V E K+ G VV
Sbjct: 48 ---KKVVLCDRDILVTATPAGVPVLEEATAKINEGAVV 82
>gnl|CDD|223268 COG0190, FolD, 5,10-methylene-tetrahydrofolate
dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase
[Coenzyme metabolism].
Length = 283
Score = 29.1 bits (66), Expect = 6.0
Identities = 28/117 (23%), Positives = 39/117 (33%), Gaps = 26/117 (22%)
Query: 64 IDSLKRSTDVMFGGKQVVLCGYGE-VGKGCCQSLKGLGCVIYITEIDPICALQACMDGFS 122
I +L + GK VV+ G VGK L + + D
Sbjct: 143 IMTLLEEYGIDLRGKNVVVVGRSNIVGKPLALLLLNANATVTVCHSR-------TKD--- 192
Query: 123 VVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPD 179
L + + DIVV A G + + + +K G VV IDV R D
Sbjct: 193 ---LASITKNADIVVVAVGKPHFIKADM---VKPGAVV---------IDVGINRVND 234
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 29.4 bits (66), Expect = 7.0
Identities = 38/186 (20%), Positives = 68/186 (36%), Gaps = 52/186 (27%)
Query: 167 NTEIDVNSLRTPDLTWEKVRSQVDHVIWPDGKRI-VLLAEGRLVNLSCSSLPSFVVSITA 225
EI+ + DL EK+ ++D D +++ + +L ++L VV +
Sbjct: 560 TYEIEFKRIDEVDL--EKLIREIDE----DREKVRRIREGKGRKDLVKTAL--LVVE--S 609
Query: 226 CTQALALIELFNAPSGRY--KSDVYLLPKKMDEYV----ASLHLPTFDAHLTELSDEQAK 279
+A + F PS R S VY +P + + + AS H+ +L ++
Sbjct: 610 PNKARTIARFFGKPSVRKIGGSVVYEVP--VGDLILMITASG------GHVFDLVTDKGF 661
Query: 280 YMGLNKAGPFKPSYYS--------------------------MDGFSVVK-LNEVIRTVD 312
+ L + G + P Y S D S+++ L E+ VD
Sbjct: 662 HGVLVENGRYVPVYTSIKRCRDCGYQFTEDRESCPKCGSENIEDSKSIIEILRELAHEVD 721
Query: 313 IVVTAT 318
V T
Sbjct: 722 EVFIGT 727
>gnl|CDD|240636 cd12159, 2-Hacid_dh_2, 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 = 303
Score = 28.8 bits (65), Expect = 8.3
Identities = 26/116 (22%), Positives = 45/116 (38%), Gaps = 20/116 (17%)
Query: 75 FGGKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEI-DPICALQACMDG----FSVVKLNE 128
G V + G G +G+ L G VI + P+ +G +L+E
Sbjct: 123 LRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRSGRPV-------EGADETVPADRLDE 175
Query: 129 VIRTVDIVVTATG----NKNVVTREHMDKMKNGCVVCNMG---HSNTEIDVNSLRT 177
V D VV A +++V + MK + N+ +T+ V++LR+
Sbjct: 176 VWPDADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRS 231
>gnl|CDD|233354 TIGR01312, XylB, D-xylulose kinase. This model describes
D-xylulose kinases, a subfamily of the FGGY family of
carbohydrate kinases. The member from Klebsiella
pneumoniae, designated DalK (see PMID:9324246), was
annotated erroneously in GenBank as D-arabinitol kinase
but is authentic D-xylulose kinase. D-xylulose kinase
(XylB) generally is found with xylose isomerase (XylA)
and acts in xylose utilization [Energy metabolism,
Sugars].
Length = 481
Score = 28.8 bits (65), Expect = 8.9
Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 24/97 (24%)
Query: 434 SSYTGLPVF----AWRGETEEDFWWCIDKCVNSWQPNMILDDGGDATHWMLKKYPTMFKA 489
S V W + ED+W + +A +L++ M +
Sbjct: 24 SGSAPHTVISPHPGWSEQDPEDWWDATE----------------EAIKELLEQASEMGQD 67
Query: 490 IKGIVEESLTG-VHRLYQLSKAGKLTVPAMNVNDSVT 525
IKGI ++G +H L L G++ PA+ ND+ T
Sbjct: 68 IKGI---GISGQMHGLVLLDANGEVLRPAILWNDTRT 101
>gnl|CDD|184558 PRK14188, PRK14188, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 296
Score = 28.4 bits (64), Expect = 9.1
Identities = 20/63 (31%), Positives = 25/63 (39%), Gaps = 14/63 (22%)
Query: 126 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDV--NSLRTPDLTWE 183
L V R DI+V A G +V D +K G V IDV N + P+
Sbjct: 195 LPAVCRRADILVAAVGRPEMVKG---DWIKPGATV---------IDVGINRIPAPEKGEG 242
Query: 184 KVR 186
K R
Sbjct: 243 KTR 245
Score = 28.4 bits (64), Expect = 9.1
Identities = 20/63 (31%), Positives = 25/63 (39%), Gaps = 14/63 (22%)
Query: 304 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDV--NSLRTPDLTWE 361
L V R DI+V A G +V D +K G V IDV N + P+
Sbjct: 195 LPAVCRRADILVAAVGRPEMVKG---DWIKPGATV---------IDVGINRIPAPEKGEG 242
Query: 362 KVR 364
K R
Sbjct: 243 KTR 245
>gnl|CDD|237634 PRK14179, PRK14179, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 28.2 bits (63), Expect = 9.7
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 126 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 185
L EV R DI+V A G + VT+E +K G VV ++G + D N D+ +++V
Sbjct: 195 LAEVARKADILVVAIGRGHFVTKEF---VKEGAVVIDVGMNR---DENGKLIGDVDFDEV 248
Query: 186 RSQVDHVIWP 195
++V I P
Sbjct: 249 -AEVASYITP 257
Score = 28.2 bits (63), Expect = 9.7
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 304 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 363
L EV R DI+V A G + VT+E +K G VV ++G + D N D+ +++V
Sbjct: 195 LAEVARKADILVVAIGRGHFVTKEF---VKEGAVVIDVGMNR---DENGKLIGDVDFDEV 248
Query: 364 RSQVDHVIWP 373
++V I P
Sbjct: 249 -AEVASYITP 257
>gnl|CDD|184560 PRK14190, PRK14190, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 28.4 bits (64), Expect = 9.8
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 126 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 164
L E+ + DI++ A G ++T + +K G VV ++G
Sbjct: 195 LAELTKQADILIVAVGKPKLITADM---VKEGAVVIDVG 230
Score = 28.4 bits (64), Expect = 9.8
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 304 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 342
L E+ + DI++ A G ++T + +K G VV ++G
Sbjct: 195 LAELTKQADILIVAVGKPKLITADM---VKEGAVVIDVG 230
>gnl|CDD|236064 PRK07589, PRK07589, ornithine cyclodeaminase; Validated.
Length = 346
Score = 28.3 bits (64), Expect = 9.8
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 9/49 (18%)
Query: 103 IYITEIDPICALQACMD-----GFSVVKLN---EVIRTVDIVVTATGNK 143
I + +IDP A G +V E + DI+ T T +K
Sbjct: 157 IRLYDIDP-AATAKLARNLAGPGLRIVACRSVAEAVEGADIITTVTADK 204
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
0.320 0.135 0.412
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: 26,625,188
Number of extensions: 2512603
Number of successful extensions: 2533
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2467
Number of HSP's successfully gapped: 164
Length of query: 542
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 440
Effective length of database: 6,413,494
Effective search space: 2821937360
Effective search space used: 2821937360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.1 bits)