RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16115
(258 letters)
>gnl|CDD|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 271 bits (695), Expect = 1e-89
Identities = 85/151 (56%), Positives = 103/151 (68%), Gaps = 13/151 (8%)
Query: 98 SLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK 157
+KR+TDVM GK V+CGYG+VGKGC QSL+G G + +TEIDPICALQA MDGF VV
Sbjct: 196 GIKRATDVMIAGKVAVVCGYGDVGKGCAQSLRGQGARVIVTEIDPICALQAAMDGFEVVT 255
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRT-PDLTWEK 216
+ EV DI VT TGNK+V+TREHM MK+G +VCN+GH + EIDV SLR P L WE
Sbjct: 256 MEEVAPQADIFVTTTGNKDVITREHMRAMKDGAIVCNIGHFDNEIDVASLRNNPGLKWEN 315
Query: 217 VRSQVDHVIWPD------------VNLKNNT 235
++ QVDH+ +PD VNL T
Sbjct: 316 IKPQVDHITFPDGKRIILLAEGRLVNLGCAT 346
Score = 129 bits (327), Expect = 4e-35
Identities = 39/67 (58%), Positives = 48/67 (71%), Gaps = 1/67 (1%)
Query: 31 QALALIELFNAPAGRYKSDVYLLPKKMDEYVASLHLPTFDAHLTELSDEQAKYMGLNKAG 90
Q LA IELF P G+YK+ VY+LPKK+DE VA LHL A LT+L+ EQA Y+G+ G
Sbjct: 360 QVLAQIELFTKP-GKYKNGVYVLPKKLDEKVARLHLEKLGAKLTKLTKEQADYIGVPVEG 418
Query: 91 PFKPSYY 97
PFKP +Y
Sbjct: 419 PFKPDHY 425
>gnl|CDD|109716 pfam00670, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 238 bits (610), Expect = 2e-80
Identities = 76/131 (58%), Positives = 93/131 (70%)
Query: 98 SLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK 157
+KR+TDVM GK V+CGYG+VGKGC SLKG G + +TEIDPICALQA M+GF VV
Sbjct: 12 GIKRATDVMIAGKVAVVCGYGDVGKGCAASLKGQGARVIVTEIDPICALQAAMEGFQVVT 71
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 217
L EV++ DI VT TGNK+++T EHM KMKN +VCN+GH + EIDV L T WE +
Sbjct: 72 LEEVVKKADIFVTTTGNKDIITGEHMAKMKNDAIVCNIGHFDNEIDVAWLNTNGKKWENI 131
Query: 218 RSQVDHVIWPD 228
+ QVD PD
Sbjct: 132 KPQVDRYTLPD 142
>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 = 244 bits (626), Expect = 2e-79
Identities = 66/131 (50%), Positives = 89/131 (67%)
Query: 98 SLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK 157
+KR+T+V+ GK VV+ GYG VGKGC +GLG + +TE+DPICALQA MDGF V+
Sbjct: 184 GIKRATNVLIAGKVVVVAGYGWVGKGCAMRARGLGARVIVTEVDPICALQAAMDGFEVMP 243
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 217
+ E + DI VTATGNK+V+ EH +KMK+G ++CN GH + EIDV +L + ++
Sbjct: 244 MEEAAKIGDIFVTATGNKDVIRGEHFEKMKDGAILCNAGHFDVEIDVAALEELAVEKREI 303
Query: 218 RSQVDHVIWPD 228
R QVD PD
Sbjct: 304 RPQVDEYTLPD 314
Score = 90.2 bits (225), Expect = 7e-21
Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 31 QALALIELFNAPAGRYKSDVYLLPKKMDEYVASLHLPTFDAHLTELSDEQAKYMGLN 87
QALA IEL+ + + VY+LPK++DE VA L L L +L++EQA+Y+G
Sbjct: 347 QALAQIELWKNR-DKLEPGVYVLPKELDEEVARLKLEALGIKLDKLTEEQAEYLGSW 402
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 235 bits (601), Expect = 5e-79
Identities = 66/131 (50%), Positives = 88/131 (67%)
Query: 98 SLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK 157
+ R+T+V+ GK VV+ GYG+VGKG L+GLG + +TEIDPI AL+A MDGF V+K
Sbjct: 12 GILRATNVLLAGKNVVVAGYGDVGKGVAARLRGLGARVIVTEIDPIRALEAAMDGFEVMK 71
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 217
+ E + DI VTATGNK+V+TREH MK+G ++ N GH + EIDV +L + +V
Sbjct: 72 MEEAAKRADIFVTATGNKDVITREHFRAMKDGAILANAGHFDVEIDVAALEELAVEKREV 131
Query: 218 RSQVDHVIWPD 228
R QVD PD
Sbjct: 132 RPQVDEYTLPD 142
>gnl|CDD|235488 PRK05476, PRK05476, S-adenosyl-L-homocysteine hydrolase;
Provisional.
Length = 425
Score = 220 bits (564), Expect = 6e-70
Identities = 68/131 (51%), Positives = 93/131 (70%)
Query: 98 SLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK 157
+KR+T+V+ GK VV+ GYG+VGKGC Q L+GLG + +TE+DPICALQA MDGF V+
Sbjct: 201 GIKRATNVLIAGKVVVVAGYGDVGKGCAQRLRGLGARVIVTEVDPICALQAAMDGFRVMT 260
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 217
+ E DI VTATGNK+V+T EHM+ MK+G ++ N+GH + EIDV +L + W ++
Sbjct: 261 MEEAAELGDIFVTATGNKDVITAEHMEAMKDGAILANIGHFDNEIDVAALEELAVKWREI 320
Query: 218 RSQVDHVIWPD 228
+ QVD PD
Sbjct: 321 KPQVDEYTLPD 331
Score = 87.1 bits (217), Expect = 1e-19
Identities = 32/63 (50%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 31 QALALIELFNAPAGRYKSDVYLLPKKMDEYVASLHLPTFDAHLTELSDEQAKYMGLNKAG 90
QALA IELF G+ + VY+LPK++DE VA L L L EL++EQA+Y+G+ G
Sbjct: 364 QALAQIELFTNR-GKLEPGVYVLPKELDEEVARLKLKALGVKLDELTEEQAEYIGVWVEG 422
Query: 91 PFK 93
PFK
Sbjct: 423 PFK 425
>gnl|CDD|223573 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
metabolism].
Length = 420
Score = 202 bits (515), Expect = 1e-62
Identities = 65/147 (44%), Positives = 93/147 (63%)
Query: 82 KYMGLNKAGPFKPSYYSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEID 141
K + N+ G + + R+T+V+ GK VV+ GYG VG+G L+G+G + +TE+D
Sbjct: 182 KSLFDNRYGTGQSLLDGILRATNVLLAGKNVVVAGYGWVGRGIAMRLRGMGARVIVTEVD 241
Query: 142 PICALQACMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTE 201
PI AL+A MDGF V+ + E +T DI VTATGNK+V+ +EH +KMK+G ++ N GH + E
Sbjct: 242 PIRALEAAMDGFRVMTMEEAAKTGDIFVTATGNKDVIRKEHFEKMKDGAILANAGHFDVE 301
Query: 202 IDVNSLRTPDLTWEKVRSQVDHVIWPD 228
IDV L + +VR QVD PD
Sbjct: 302 IDVAGLEELAVEKREVRPQVDEYELPD 328
Score = 70.0 bits (172), Expect = 8e-14
Identities = 27/61 (44%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 31 QALALIELFNAPAGRYKSDVYLLPKKMDEYVASLHLPTFDAHLTELSDEQAKYMGLNKAG 90
QALA I L G+ + VY LPK++DE VA L L L EL++EQA+Y+G + G
Sbjct: 361 QALAQIYLV-KNHGKLEPGVYRLPKELDEEVARLKLEAMGIELDELTEEQAEYLGSWEEG 419
Query: 91 P 91
Sbjct: 420 T 420
>gnl|CDD|240258 PTZ00075, PTZ00075, Adenosylhomocysteinase; Provisional.
Length = 476
Score = 200 bits (511), Expect = 1e-61
Identities = 74/151 (49%), Positives = 100/151 (66%), Gaps = 8/151 (5%)
Query: 99 LKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKL 158
+ R+TDVM GK VV+CGYG+VGKGC Q+L+G G + +TEIDPICALQA M+G+ VV L
Sbjct: 244 IFRATDVMIAGKTVVVCGYGDVGKGCAQALRGFGARVVVTEIDPICALQAAMEGYQVVTL 303
Query: 159 NEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRT-PDLTWEKV 217
+V+ T DI VTATGNK+++T EHM +MKN +V N+GH + EI V L P + ++
Sbjct: 304 EDVVETADIFVTATGNKDIITLEHMRRMKNNAIVGNIGHFDNEIQVAELEAYPGIEIVEI 363
Query: 218 RSQVDHVIWPDVNLKNNTVIDLFRKPKSRLY 248
+ QVD +PD +I L + RL
Sbjct: 364 KPQVDRYTFPD----GKGIILL---AEGRLV 387
Score = 88.6 bits (220), Expect = 5e-20
Identities = 34/68 (50%), Positives = 47/68 (69%), Gaps = 1/68 (1%)
Query: 31 QALALIELF-NAPAGRYKSDVYLLPKKMDEYVASLHLPTFDAHLTELSDEQAKYMGLNKA 89
Q LA IEL+ N G+Y + VY LPK++DE VA LHL A LT+L+D+QA+Y+G+
Sbjct: 407 QVLAQIELWENRDTGKYPNGVYKLPKELDEKVARLHLKKLGAKLTKLTDKQAEYIGVPVD 466
Query: 90 GPFKPSYY 97
GP+K +Y
Sbjct: 467 GPYKSDHY 474
>gnl|CDD|218507 pfam05221, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 430
Score = 181 bits (462), Expect = 7e-55
Identities = 59/132 (44%), Positives = 78/132 (59%), Gaps = 1/132 (0%)
Query: 98 SLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK 157
+KR+TDVM GK V+CGYG+VGKGC SL+G G + +TEIDPICALQA M+G+ VV
Sbjct: 199 GIKRATDVMIAGKVAVVCGYGDVGKGCAASLRGQGARVIVTEIDPICALQAAMEGYQVVT 258
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLR-TPDLTWEK 216
L EV++ DI VT TG +++ H MK +VCN+GH + EIDV L
Sbjct: 259 LEEVVKDADIFVTTTGCVDIIVGRHFMNMKKDAIVCNIGHFDCEIDVGWLNYNAKKITNI 318
Query: 217 VRSQVDHVIWPD 228
+ +
Sbjct: 319 KPQVDRYTLPNG 330
Score = 115 bits (289), Expect = 8e-30
Identities = 34/68 (50%), Positives = 46/68 (67%), Gaps = 1/68 (1%)
Query: 31 QALALIELFNAP-AGRYKSDVYLLPKKMDEYVASLHLPTFDAHLTELSDEQAKYMGLNKA 89
Q LA IEL+ G+Y+ VY+LPK +DE VA LHL LT+L+D+QA+Y+G+
Sbjct: 362 QVLAQIELWTKRDTGKYEVGVYVLPKHLDEKVARLHLGKLGVKLTKLTDKQAEYIGVPVE 421
Query: 90 GPFKPSYY 97
GPFKP +Y
Sbjct: 422 GPFKPDHY 429
>gnl|CDD|178111 PLN02494, PLN02494, adenosylhomocysteinase.
Length = 477
Score = 167 bits (425), Expect = 5e-49
Identities = 65/133 (48%), Positives = 90/133 (67%), Gaps = 1/133 (0%)
Query: 99 LKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKL 158
L R+TDVM GK V+CGYG+VGKGC ++K G + +TEIDPICALQA M+G+ V+ L
Sbjct: 244 LMRATDVMIAGKVAVICGYGDVGKGCAAAMKAAGARVIVTEIDPICALQALMEGYQVLTL 303
Query: 159 NEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRT-PDLTWEKV 217
+V+ DI VT TGNK+++ +HM KMKN +VCN+GH + EID+ L T P + +
Sbjct: 304 EDVVSEADIFVTTTGNKDIIMVDHMRKMKNNAIVCNIGHFDNEIDMLGLETYPGVKRITI 363
Query: 218 RSQVDHVIWPDVN 230
+ Q D ++PD
Sbjct: 364 KPQTDRWVFPDTG 376
Score = 78.8 bits (194), Expect = 9e-17
Identities = 32/68 (47%), Positives = 47/68 (69%), Gaps = 1/68 (1%)
Query: 31 QALALIELFNAPA-GRYKSDVYLLPKKMDEYVASLHLPTFDAHLTELSDEQAKYMGLNKA 89
Q +A +EL+N G+Y+ VY+LPK +DE VA+LHL A LT+LS +QA Y+ +
Sbjct: 408 QVIAQLELWNEKKSGKYEKKVYVLPKHLDEKVAALHLGKLGAKLTKLSKDQADYINVPVE 467
Query: 90 GPFKPSYY 97
GP+KP++Y
Sbjct: 468 GPYKPAHY 475
>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 = 166 bits (421), Expect = 5e-49
Identities = 62/151 (41%), Positives = 91/151 (60%)
Query: 78 DEQAKYMGLNKAGPFKPSYYSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYI 137
D K + N+ G + + + R+T+++ GK VV+ GYG GKG +G+G + +
Sbjct: 165 DAYTKSLFDNRYGTGQSTIDGILRATNLLIAGKTVVVAGYGWCGKGIAMRARGMGARVIV 224
Query: 138 TEIDPICALQACMDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGH 197
TE+DPI AL+A MDGF V+ + E + DI +TATGNK+V+ EH + MK+G +V N+GH
Sbjct: 225 TEVDPIRALEAAMDGFRVMTMEEAAKIGDIFITATGNKDVIRGEHFENMKDGAIVANIGH 284
Query: 198 SNTEIDVNSLRTPDLTWEKVRSQVDHVIWPD 228
+ EIDV +L + VR QVD I D
Sbjct: 285 FDVEIDVKALEELAVEKVNVRPQVDEYILKD 315
Score = 59.7 bits (145), Expect = 2e-10
Identities = 23/61 (37%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 31 QALALIELFNAPAGRYKSDVYLLPKKMDEYVASLHLPTFDAHLTELSDEQAKYMGLNKAG 90
QALA L+ + + VY LPK++DE VA L L + EL++EQ +Y+G + G
Sbjct: 348 QALAAEYLWKNH-DKLEPGVYRLPKELDEMVARLKLEAMGIEIDELTEEQKEYLGSWEEG 406
Query: 91 P 91
Sbjct: 407 T 407
>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 = 79.6 bits (196), Expect = 2e-17
Identities = 33/111 (29%), Positives = 48/111 (43%), Gaps = 6/111 (5%)
Query: 106 MFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFS-VVKLNEVIRT 164
GK VV+ G G VGK Q L+GLG + IT+I+ Q G V +L E +
Sbjct: 157 DVAGKTVVVVGAGVVGKEAAQMLRGLGAQVLITDINVEALEQLEELGGKNVEELEEALAE 216
Query: 165 VDIVVTATGNKN-----VVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTP 210
D++VT T +V E +++MK G V+ N+
Sbjct: 217 ADVIVTTTLLPGKRAGILVPEELVEQMKPGSVIVNVAVGAVGCVQALHTQL 267
>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 = 2e-06
Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 8/93 (8%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQACMDGFSVVKLNEVIRTVDI 167
GK V + G G +G+ + LK G VI D +A G V L+E++ D+
Sbjct: 35 GKTVGIIGLGRIGRAVARRLKAFGMKVIA---YDRYPKAEAEALGARYVSLDELLAESDV 91
Query: 168 VVTAT----GNKNVVTREHMDKMKNGCVVCNMG 196
V ++++ E + MK G ++ N
Sbjct: 92 VSLHLPLTPETRHLINAERLALMKPGAILINTA 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 = 4e-06
Identities = 28/95 (29%), Positives = 47/95 (49%), Gaps = 13/95 (13%)
Query: 112 VVLCGYGEVGKGCCQSLKGLGCVIYITEIDP--ICALQACMDG-FSVVKLN-----EVIR 163
VV+ G G VG G + KGLG + + ++ P + L++ + F+ + E ++
Sbjct: 23 VVVIGAGVVGLGAAATAKGLGAEVTVLDVRPARLRQLESLLGARFTTLYSQAELLEEAVK 82
Query: 164 TVDIVVTA---TGNK--NVVTREHMDKMKNGCVVC 193
D+V+ A G K +VTRE + MK G V+
Sbjct: 83 EADLVIGAVLIPGAKAPKLVTREMVKSMKPGSVIV 117
>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 = 45.6 bits (109), Expect = 1e-05
Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 14/115 (12%)
Query: 88 KAGPFKPSYYSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGC--VIYITEIDPIC- 144
K G ++ YY+ + GK V + G+G +G+ + LK G ++Y DP
Sbjct: 127 KDGEWRKDYYNYDGYGPEL-RGKTVGIVGFGAIGRRVAKRLKAFGAEVLVY----DPYVD 181
Query: 145 ALQACMDGFSVVKLNEVIRTVDIV-----VTATGNKNVVTREHMDKMKNGCVVCN 194
+ DG V L E+++ D+V +T + ++ E MK N
Sbjct: 182 PEKIEADGVKKVSLEELLKRSDVVSLHARLTP-ETRGMIGAEEFALMKPTAYFIN 235
>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 = 43.7 bits (104), Expect = 1e-05
Identities = 31/105 (29%), Positives = 44/105 (41%), Gaps = 17/105 (16%)
Query: 106 MFGGKQ---VVLCGYGEVGKGCCQSLKGLGCVIYITEIDP--ICALQACMDGFSVVK--- 157
GG VV+ G G VG G + KGLG + I ++ P + L + F
Sbjct: 14 GAGGVPPAKVVVIGGGVVGLGAAATAKGLGAPVTILDVRPERLEQLDSLFAEFVETDIFS 73
Query: 158 ----LNEVIRTVDIVVTA---TGNK--NVVTREHMDKMKNGCVVC 193
L E I D+V+ G + +VTRE + MK G V+
Sbjct: 74 NCEYLAEAIAEADLVIGTVLIPGARAPKLVTREMVKTMKPGSVIV 118
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 43.1 bits (102), Expect = 6e-05
Identities = 24/93 (25%), Positives = 39/93 (41%), Gaps = 10/93 (10%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQAC--MDGFSVVKLNEVIRTV 165
GK V + G G +G+ + LK G VI DP + V L+E++
Sbjct: 142 GKTVGIIGLGRIGRAVAKRLKAFGMKVIG---YDPYSPRERAGVDGVVGVDSLDELLAEA 198
Query: 166 DIVVTAT----GNKNVVTREHMDKMKNGCVVCN 194
DI+ + ++ E + KMK G ++ N
Sbjct: 199 DILTLHLPLTPETRGLINAEELAKMKPGAILIN 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 = 9e-05
Identities = 26/93 (27%), Positives = 42/93 (45%), Gaps = 11/93 (11%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGC-VIY--ITEIDPICALQACMDGFSVVKLNEVIRTV 165
GK V + G G +G+ + L+ G V+Y T GF VV L+E++
Sbjct: 140 GKTVGIVGLGRIGQRVAKRLQAFGMKVLYYDRTRKPEPEEDL----GFRVVSLDELLAQS 195
Query: 166 DIVVTATG----NKNVVTREHMDKMKNGCVVCN 194
D+VV ++++ E + MK G V+ N
Sbjct: 196 DVVVLHLPLTPETRHLINEEELALMKPGAVLVN 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 = 1e-04
Identities = 25/104 (24%), Positives = 48/104 (46%), Gaps = 8/104 (7%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQACMDGFSVVKLNEVIRTVDI 167
GK + + G+G +G+ + + LG VI + P G V L E+++ D
Sbjct: 139 GKTLGIIGFGRIGREVAKIARALGMNVIA-YDPYPKDEQAV-ELGVKTVSLEELLKNSDF 196
Query: 168 V---VTATG-NKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSL 207
+ V T K+++ ++ ++ MK+G ++ N ID +L
Sbjct: 197 ISLHVPLTPETKHMINKKELELMKDGAIIINTSRGGV-IDEEAL 239
>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 = 3e-04
Identities = 23/94 (24%), Positives = 37/94 (39%), Gaps = 8/94 (8%)
Query: 107 FGGKQVVLCGYGEVGKGCCQSLK-GLGCVIYITEIDP-ICALQACMDGFSVVKLNEVIRT 164
GK V + GYG +G + LK G + DP + G V L E++
Sbjct: 145 LSGKTVGIIGYGNIGSRVAEILKEGFNAKVLAY--DPYVSEEVIKKKGAKPVSLEELLAE 202
Query: 165 VDIVV----TATGNKNVVTREHMDKMKNGCVVCN 194
DI+ +++ + KMK G ++ N
Sbjct: 203 SDIISLHAPLTEETYHMINEKAFSKMKKGVILVN 236
>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 = 41.0 bits (97), Expect = 3e-04
Identities = 23/94 (24%), Positives = 41/94 (43%), Gaps = 8/94 (8%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 168
GK V++ G G++G+ + K G + A + ++ +L+E++ D V
Sbjct: 134 GKTVLIVGLGDIGREIARRAKAFGMRVIGVRRSGRPAPPVVDEVYTPDELDELLPEADYV 193
Query: 169 VTA------TGNKNVVTREHMDKMKNGCVVCNMG 196
V A T + + E MK G V+ N+G
Sbjct: 194 VNALPLTPET--RGLFNAERFAAMKPGAVLINVG 225
>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 = 40.7 bits (96), Expect = 4e-04
Identities = 26/113 (23%), Positives = 46/113 (40%), Gaps = 7/113 (6%)
Query: 88 KAGPFKPSYYSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQ 147
+ G + S ++ GK V + GYG +G+ + LK G + P
Sbjct: 118 RRGIWHGRAGEEPESKEL--RGKTVGILGYGHIGREIARLLKAFGMRVIGVSRSPKEDEG 175
Query: 148 ACMDGFSVVKLNEVIRTVDIVVTAT----GNKNVVTREHMDKMKNGCVVCNMG 196
A G + L+E + D+VV A + ++ + MK G ++ N+G
Sbjct: 176 ADFVGT-LSDLDEALEQADVVVVALPLTKQTRGLIGAAELAAMKPGAILVNVG 227
>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 = 40.3 bits (95), Expect = 4e-04
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 4/92 (4%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 168
GK V + G G +G+ + L G G + + P+ + V+L+E++ + D +
Sbjct: 144 GKTVGILGMGALGRAIARRLSGFGATLLYYDPHPLDQAEEQALNLRRVELDELLESSDFL 203
Query: 169 VTAT----GNKNVVTREHMDKMKNGCVVCNMG 196
V A +++ E + KMK G ++ N
Sbjct: 204 VLALPLTPDTLHLINAEALAKMKPGALLVNPC 235
>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 = 38.7 bits (91), Expect = 5e-04
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 112 VVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLN----EV-----I 162
+++ GYG VG+ + L+ G + + + DP + +G VV + EV I
Sbjct: 1 IIIIGYGRVGRSLAEELREGGPDVVVIDKDPERVEELREEGVPVVVGDATDEEVLEEAGI 60
Query: 163 RTVDIVVTATGN 174
D VV ATG+
Sbjct: 61 EEADAVVAATGD 72
>gnl|CDD|234592 PRK00045, hemA, glutamyl-tRNA reductase; Reviewed.
Length = 423
Score = 40.6 bits (96), Expect = 5e-04
Identities = 19/85 (22%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 107 FGGKQVVLCGYGEVGKGCCQSLKGLGCV-IYIT----EIDPICALQACMDGFSVVKLNEV 161
GK+V++ G GE+G+ + L G I + E A + + + +L E
Sbjct: 180 LSGKKVLVIGAGEMGELVAKHLAEKGVRKITVANRTLERAEELAEEFGGEAIPLDELPEA 239
Query: 162 IRTVDIVVTATGNKN-VVTREHMDK 185
+ DIV+++TG + ++ + +++
Sbjct: 240 LAEADIVISSTGAPHPIIGKGMVER 264
>gnl|CDD|215501 PLN02928, PLN02928, oxidoreductase family protein.
Length = 347
Score = 40.4 bits (95), Expect = 5e-04
Identities = 23/104 (22%), Positives = 37/104 (35%), Gaps = 16/104 (15%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYIT------EIDPICALQACMDGFSVVK----- 157
GK V + GYG +G + L+ G + T E + + V +
Sbjct: 159 GKTVFILGYGAIGIELAKRLRPFGVKLLATRRSWTSEPEDGLLIPNGDVDDLVDEKGGHE 218
Query: 158 -LNEVIRTVDIVVTA----TGNKNVVTREHMDKMKNGCVVCNMG 196
+ 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 = 39.1 bits (92), Expect = 0.001
Identities = 27/109 (24%), Positives = 48/109 (44%), Gaps = 11/109 (10%)
Query: 97 YSLKRSTDVMFG----GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDG 152
+SL D + G GK + + G G +G+ + LKG G + + P + G
Sbjct: 130 WSLSGGPDPLLGFDLRGKTLGIIGLGRIGQAVARRLKGFGMKVLYYDRSPNPEAEK-ELG 188
Query: 153 FSVVKLNEVIRTVDIVV-----TATGNKNVVTREHMDKMKNGCVVCNMG 196
V L+E++ DI+ T ++++ E + KMK G ++ N
Sbjct: 189 ARYVDLDELLAESDIISLHCPLTPE-TRHLINAEELAKMKPGAILVNTA 236
>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 = 38.7 bits (91), Expect = 0.002
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 6/93 (6%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVI--YITEIDPICALQACMDGFSVVKLNEVIRTVD 166
GK + + G G +G+ + LG + Y + A + ++ V L E++ T D
Sbjct: 135 GKTLGVIGLGNIGRLVANAALALGMKVIGYDPYLSVEAAWKLSVEVQRVTSLEELLATAD 194
Query: 167 IV---VTAT-GNKNVVTREHMDKMKNGCVVCNM 195
+ V T + ++ E + KMK G ++ N
Sbjct: 195 YITLHVPLTDETRGLINAELLAKMKPGAILLNF 227
>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 = 38.7 bits (91), Expect = 0.002
Identities = 25/103 (24%), Positives = 43/103 (41%), Gaps = 18/103 (17%)
Query: 105 VMFGGKQVVLCGYGEVGKGCCQSLKGLGC-VIYIT-----EIDPICALQACMDGFSVVKL 158
GK V + G G +G+ + L+G G VIY E + G V+L
Sbjct: 138 RELSGKTVGIVGLGNIGRAVARRLRGFGVEVIYYDRFRDPEAEEKDL------GVRYVEL 191
Query: 159 NEVIRTVDIVV-----TATGNKNVVTREHMDKMKNGCVVCNMG 196
+E++ D+V T ++++ E + MK G ++ N
Sbjct: 192 DELLAESDVVSLHVPLTPE-TRHLIGAEELAAMKPGAILINTA 233
>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 = 0.004
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 107 FGGKQVVLCGYGEVGKGCCQSLKGLG-CVIYITEIDPICALQ-ACMDGFSVVKLNEV--- 161
GK+V++ G GE+G+ + L G I I A + A G + V L+E+
Sbjct: 176 LKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELAKELGGNAVPLDELLEL 235
Query: 162 IRTVDIVVTATG 173
+ D+V++ATG
Sbjct: 236 LNEADVVISATG 247
>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 = 0.005
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 10/92 (10%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 168
GK V + G G++G+ + LKG GC + + P L G V L+E++ DI+
Sbjct: 144 GKTVGVIGTGKIGQAFARILKGFGCRVLAYDPYPNPELAK--LGVEYVDLDELLAESDII 201
Query: 169 ------VTATGNKNVVTREHMDKMKNGCVVCN 194
T +++ E + KMK+G ++ N
Sbjct: 202 SLHCPLTPET--HHLINAETIAKMKDGVMLIN 231
>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 = 0.006
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 8/85 (9%)
Query: 107 FGGKQVVLCGYGEVGKGCCQSLKGLGC-VIYIT-----EIDPICA-LQACMDGFSVVKLN 159
GK+V+L G GE+ + + L G I I + + + + +L
Sbjct: 10 LKGKKVLLIGAGEMARLAAKHLLSKGAKKITIANRTLEKAKELAEEFPVGGEALPLDELE 69
Query: 160 EVIRTVDIVVTATGNKN-VVTREHM 183
E++ DIV++AT ++T+E +
Sbjct: 70 ELLAEADIVISATSAPTPIITKEMV 94
>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 = 36.0 bits (84), Expect = 0.007
Identities = 25/99 (25%), Positives = 37/99 (37%), Gaps = 17/99 (17%)
Query: 99 LKRSTDVMFGGKQVVLCGYGE-VGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK 157
L + + GK+VV+ G VGK L +C +
Sbjct: 34 LLKRYGIDLAGKKVVVVGRSNIVGKPLAALLLNRNA------TVTVCHSKT-------KN 80
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 196
L E + DIV+ A G +V D +K G VV ++G
Sbjct: 81 LKEHTKQADIVIVAVGKPGLVKG---DMVKPGAVVIDVG 116
>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
Length = 335
Score = 36.3 bits (83), Expect = 0.011
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 95 SYYSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQ-ACMDGF 153
+YY K + + GK V + GYG G Q+L+ G V + + P + + A DGF
Sbjct: 3 TYYE-KDANVELLQGKTVAVIGYGSQGHAQAQNLRDSG-VEVVVGVRPGKSFEVAKADGF 60
Query: 154 SVVKLNEVIRTVDIV 168
V+ ++E +RT +V
Sbjct: 61 EVMSVSEAVRTAQVV 75
>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 = 0.013
Identities = 23/87 (26%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 107 FGGKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQACMDGFSVVKLNEVIRTV 165
GK V + GYG G +L+ G VI +A DGF V + E I
Sbjct: 1 LKGKTVAIIGYGSQGHAQALNLRDSGLNVIVGLRKGGASWKKATEDGFKVGTVEEAIPQA 60
Query: 166 DIVVTATGNK---NVVTREHMDKMKNG 189
D+++ ++ V E +K G
Sbjct: 61 DLIMNLLPDEVQHEVYEAEIQPLLKEG 87
Score = 27.3 bits (61), Expect = 8.8
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 67 PTFDAHLTELSDEQAKYMGLNKAGPFKPSYYSLKRSTDVMFGGKQVVLCG 116
PT +A L+ AK +G +AG + ++ K T+ G+Q VLCG
Sbjct: 143 PTGEAMAIALA--YAKAIGGGRAGVLETTF---KEETESDLFGEQAVLCG 187
>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 = 0.013
Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 9/92 (9%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEI--DPICALQACMDGFSVVKLNEVIRTVD 166
GK + + G G +GK + L G G + + D A + G V L E+++ D
Sbjct: 142 GKTLGIIGLGRIGKAVARRLSGFGMKVLAYDPYPDEEFAKEH---GVEFVSLEELLKESD 198
Query: 167 IV---VTAT-GNKNVVTREHMDKMKNGCVVCN 194
+ + T ++++ + MK G ++ N
Sbjct: 199 FISLHLPLTPETRHLINAAELALMKPGAILIN 230
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 36.1 bits (84), Expect = 0.013
Identities = 23/98 (23%), Positives = 42/98 (42%), Gaps = 20/98 (20%)
Query: 97 YSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSL--KGLGCVIYITEIDPIC------ALQ- 147
L + K+V++ G GE+G+ + L KG+ + I A +
Sbjct: 166 VELAKRIFGSLKDKKVLVIGAGEMGELVAKHLAEKGVKKIT-------IANRTLERAEEL 218
Query: 148 ACMDGFSVVKLNEV---IRTVDIVVTATGNKN-VVTRE 181
A G V L E+ + D+V+++T + ++TRE
Sbjct: 219 AKKLGAEAVALEELLEALAEADVVISSTSAPHPIITRE 256
>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 = 35.7 bits (83), Expect = 0.014
Identities = 29/115 (25%), Positives = 45/115 (39%), Gaps = 15/115 (13%)
Query: 88 KAGPFKPSYYSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGC-VI-YITEIDPICA 145
K + + + D G + G G++G+ Q KG G VI Y DP
Sbjct: 127 KNQDLQDAGVIGRELEDQTVG-----VVGTGKIGRAVAQRAKGFGMKVIAY----DPFRN 177
Query: 146 LQACMDGFSVVKLNEVIRTVDIV---VTAT-GNKNVVTREHMDKMKNGCVVCNMG 196
+ G V L E+ + DI+ V T N +++ E MK G ++ N
Sbjct: 178 PELEDKGVKYVSLEELFKNSDIISLHVPLTPENHHMINEEAFKLMKKGVIIINTA 232
>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 = 35.5 bits (83), Expect = 0.021
Identities = 28/106 (26%), Positives = 45/106 (42%), Gaps = 22/106 (20%)
Query: 112 VVLCGYGEVGKGCCQSLKGLGCVIYITEIDP--ICALQACMDG------FSVVKLNEVIR 163
VV+ G G VG+ + GLG + + +I+ + L G + L E ++
Sbjct: 171 VVILGAGVVGENAARVALGLGAEVTVLDINLERLRYLDDIFGGRVTTLYSNPANLEEALK 230
Query: 164 TVDIVVTA---TGNK--NVVTREHMDKMKNGCVVCNMGHSNTEIDV 204
D+V+ A G K +VT E + MK G V+ +DV
Sbjct: 231 EADLVIGAVLIPGAKAPKLVTEEMVKTMKPGSVI---------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 = 33.7 bits (77), Expect = 0.049
Identities = 18/76 (23%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 137 ITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTATGN---KNVVTREHMDKMKNGCVVC 193
I+EI+P ++A + + +++ + DIV A N K ++ ++K K+ ++
Sbjct: 83 ISEINPYTEIEAYDEKITEENIDKFFKDADIVCEAFDNAEAKAMLVNAVLEKYKDKYLIA 142
Query: 194 NMGHSNTEIDVNSLRT 209
G + + D NS++T
Sbjct: 143 ASGLAGYD-DANSIKT 157
>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 = 0.050
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 152 GFSVVKLNEVIRTVDIV---VTAT-GNKNVVTREHMDKMKNGCVVCN 194
GF V L E+++ DI+ V T +++ RE+ MK G V+ N
Sbjct: 181 GFRYVSLEELLQESDIISLHVPYTPQTHHLINRENFALMKPGAVLIN 227
>gnl|CDD|173781 cd03361, TOPRIM_TopoIA_RevGyr, TopoIA_RevGyr : The
topoisomerase-primase (TORPIM) domain found in members
of the type IA family of DNA topoisomerases (Topo IA)
similar to the ATP-dependent reverse gyrase found in
archaea and thermophilic bacteria. Type IA DNA
topoisomerases remove (relax) negative supercoils in the
DNA by: cleaving one strand of the DNA duplex,
covalently linking to the 5' phosphoryl end of the DNA
break and, allowing the other strand of the duplex to
pass through the gap. Reverse gyrase is also able to
insert positive supercoils in the presence of ATP and
negative supercoils in the presence of AMPPNP. The
TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). For topoisomerases the
conserved glutamate is believed to act as a general base
in strand joining and, as a general acid in strand
cleavage. The DXD motif may co-ordinate Mg2+, a cofactor
required for full catalytic function.
Length = 170
Score = 33.4 bits (77), Expect = 0.054
Identities = 22/102 (21%), Positives = 35/102 (34%), Gaps = 26/102 (25%)
Query: 72 HLTELSDEQAKYMGLNKAGPFKPSYYSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGL 131
H+ +L ++ + + G + P Y S+KR D G Q C
Sbjct: 50 HVYDLVTKEGGHGVVEDDGRYVPVYDSIKRCRD---CGYQFTE------DSDKC------ 94
Query: 132 GCVIYITEIDPICALQACMDGFSVVK-LNEVIRTVDIVVTAT 172
P C + D ++ L E+ VD V+ AT
Sbjct: 95 ----------PRCGSENIDDKLETLEALRELALEVDEVLIAT 126
>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 = 0.092
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 196
L + R DI+V A G N++ E +K G VV ++G
Sbjct: 195 LASITREADILVAAAGRPNLIGAEM---VKPGAVVVDVG 230
>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 = 32.6 bits (75), Expect = 0.12
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 9/80 (11%)
Query: 96 YYSLKRSTDVMFG-----GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACM 150
+ +K + + + G GK V + G G+VG + L G + + +I+ +A
Sbjct: 10 FLGMKAAAEHLLGTDSLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEAVARAA- 68
Query: 151 DGFSV--VKLNEVIRT-VDI 167
+ F V E+ D+
Sbjct: 69 ELFGATVVAPEEIYSVDADV 88
>gnl|CDD|224626 COG1712, COG1712, Predicted dinucleotide-utilizing enzyme [General
function prediction only].
Length = 255
Score = 32.8 bits (75), Expect = 0.13
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 112 VVLCGYGEVGKGCCQSLK-GLGCV----IYITEIDPICALQACMDGFSVVKLNEVIRTVD 166
V + G G +GK + ++ G +Y + + L+A + V ++E+I VD
Sbjct: 3 VGIVGCGAIGKFLLELVRDGRVDFELVAVYDRDEEKAKELEASVGRRCVSDIDELIAEVD 62
Query: 167 IVVTATGNKNVVTREHMDK-MKNGC 190
+VV A + V RE++ K +K G
Sbjct: 63 LVVEAASPEAV--REYVPKILKAGI 85
>gnl|CDD|217267 pfam02882, THF_DHG_CYH_C, Tetrahydrofolate
dehydrogenase/cyclohydrolase, NAD(P)-binding domain.
Length = 160
Score = 32.0 bits (74), Expect = 0.14
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHS 198
L E+ R DIVV A G ++ + +K G VV ++G +
Sbjct: 73 LAEITREADIVVVAVGKPGLIKADW---VKPGAVVIDVGIN 110
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 33.1 bits (76), Expect = 0.15
Identities = 24/102 (23%), Positives = 37/102 (36%), Gaps = 26/102 (25%)
Query: 72 HLTELSDEQAKYMGLNKAGPFKPSYYSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGL 131
H+ +L E + L K G + P Y ++KR D G+Q V + C
Sbjct: 667 HVFDLVTEPGVHGVLVKDGKYVPVYDTIKRCRD---CGEQFV-----DSEDKC------- 711
Query: 132 GCVIYITEIDPICALQACMDGFSVVK-LNEVIRTVDIVVTAT 172
P C + D V+ L E+ VD ++ T
Sbjct: 712 ----------PRCGSRNVEDKTETVEALRELALEVDEILIGT 743
>gnl|CDD|181414 PRK08410, PRK08410, 2-hydroxyacid dehydrogenase; Provisional.
Length = 311
Score = 32.3 bits (74), Expect = 0.21
Identities = 23/93 (24%), Positives = 48/93 (51%), Gaps = 10/93 (10%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQACMDGFSVVKLNEVIRTVDI 167
GK+ + G G +GK + + G V+Y + + + + + V L E+++T DI
Sbjct: 145 GKKWGIIGLGTIGKRVAKIAQAFGAKVVYYST-----SGKNKNEEYERVSLEELLKTSDI 199
Query: 168 V-VTATGN---KNVVTREHMDKMKNGCVVCNMG 196
+ + A N KN++ + + +K+G ++ N+G
Sbjct: 200 ISIHAPLNEKTKNLIAYKELKLLKDGAILINVG 232
Score = 28.4 bits (64), Expect = 3.7
Identities = 11/47 (23%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 160 EVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNS 206
E I+ +I++T NK V+ +E + ++ N ++C +D+
Sbjct: 38 ERIKDANIIIT---NKVVIDKEVLSQLPNLKLICITATGTNNVDIEY 81
>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 = 0.25
Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 14/94 (14%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYI---TEIDPICALQACMDGFSVVKLNEVIRTV 165
GK V + G G +G + K GC + +E + AL G V L+E++
Sbjct: 144 GKTVGIVGTGAIGLRVARLFKAFGCKVLAYSRSEKEEAKAL-----GIEYVSLDELLAES 198
Query: 166 DIV-----VTATGNKNVVTREHMDKMKNGCVVCN 194
DIV + K ++ +E + MK ++ N
Sbjct: 199 DIVSLHLPLND-ETKGLIGKEKLALMKESAILIN 231
>gnl|CDD|223643 COG0569, TrkA, K+ transport systems, NAD-binding component
[Inorganic ion transport and metabolism].
Length = 225
Score = 31.9 bits (73), Expect = 0.27
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 11/79 (13%)
Query: 110 KQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDP------ICALQACM----DGFSVVKLN 159
++++ G G VG+ + L G + + + D + D L
Sbjct: 1 MKIIIIGAGRVGRSVARELSEEGHNVVLIDRDEERVEEFLADELDTHVVIGDATDEDVLE 60
Query: 160 EV-IRTVDIVVTATGNKNV 177
E I D VV ATGN V
Sbjct: 61 EAGIDDADAVVAATGNDEV 79
>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 = 32.0 bits (73), Expect = 0.30
Identities = 26/114 (22%), Positives = 44/114 (38%), Gaps = 17/114 (14%)
Query: 96 YYSLKRS-TDVMFGGK-----QVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQAC 149
Y L R M G +V++ G G VG G + K LG + + +I
Sbjct: 143 AYELARIQGGRMGGAGGVPPAKVLIIGAGVVGLGAAKIAKKLGANVLVYDIKEEKLKGVE 202
Query: 150 MDGFSVVK------LNEVIRTVDIVVTATGNKN-----VVTREHMDKMKNGCVV 192
G S ++ L + ++ DI++ A ++ E + MK G V+
Sbjct: 203 TLGGSRLRYSQKEELEKELKQTDILINAILVDGPRAPILIMEELVGPMKRGAVI 256
>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 = 0.31
Identities = 22/104 (21%), Positives = 44/104 (42%), Gaps = 11/104 (10%)
Query: 100 KRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGC--VIYITEIDP-ICALQACMDGFSVV 156
R G+ V + G+G +G+ + L+ G ++Y DP + A +A G +V
Sbjct: 141 TRRGGRGLYGRTVGIVGFGRIGRAVVELLRPFGLRVLVY----DPYLPAAEAAALGVELV 196
Query: 157 KLNEVIRTVDIVVTATG----NKNVVTREHMDKMKNGCVVCNMG 196
L+E++ D+V + ++ + M++G N
Sbjct: 197 SLDELLARSDVVSLHAPLTPETRGMIDARLLALMRDGATFINTA 240
>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 = 0.34
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 163 RTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 196
R DIVV A G +NV+T D +K G V ++G
Sbjct: 200 RQADIVVAAVGKRNVLT---ADMVKPGATVIDVG 230
>gnl|CDD|172660 PRK14172, PRK14172, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 278
Score = 31.3 bits (71), Expect = 0.41
Identities = 47/171 (27%), Positives = 71/171 (41%), Gaps = 29/171 (16%)
Query: 53 LPKKMDE-YVASLHLPTFDAHLTELSDEQAK--YMGLNKAGPFKP-SYYSLKRSTDVMFG 108
LPK +DE + + D + L+ Y G P P S +L +S ++
Sbjct: 100 LPKHLDEKKITNKIDANKD--IDCLTFISVGKFYKGEKCFLPCTPNSVITLIKSLNIDIE 157
Query: 109 GKQVVLCGYGE-VGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK-LNEVIRTVD 166
GK+VV+ G VGK Q L + I S K L EV + D
Sbjct: 158 GKEVVVIGRSNIVGKPVAQLLLNENATVTICH--------------SKTKNLKEVCKKAD 203
Query: 167 IVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 217
I+V A G + E+ +K G +V ++G S+ VN T D+ ++KV
Sbjct: 204 ILVVAIGRPKFIDEEY---VKEGAIVIDVGTSS----VNGKITGDVNFDKV 247
>gnl|CDD|234662 PRK00141, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 473
Score = 31.3 bits (71), Expect = 0.54
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 112 VVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQ-ACMDGFSVVKLNEVIRTVD---I 167
V++ G G G+G L LGC + + + + + + G + + E +D +
Sbjct: 18 VLVAGAGVSGRGIAAMLSELGCDVVVADDNETARHKLIEVTGVADISTAEASDQLDSFSL 77
Query: 168 VVTATG 173
VVT+ G
Sbjct: 78 VVTSPG 83
>gnl|CDD|184552 PRK14175, PRK14175, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 286
Score = 30.7 bits (69), Expect = 0.59
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 217
+ ++ D++V+A G +VT+ D +K G V+ ++G++ D N D+ ++ V
Sbjct: 195 MASYLKDADVIVSAVGKPGLVTK---DVVKEGAVIIDVGNT---PDENGKLKGDVDYDAV 248
Query: 218 R 218
+
Sbjct: 249 K 249
>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 = 0.74
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTE 201
L E R D + A G VT D +K G VV ++G + T+
Sbjct: 198 LAEECREADFLFVAIGRPRFVTA---DMVKPGAVVVDVGINRTD 238
>gnl|CDD|188459 TIGR03944, dehyd_SbnB_fam, 2,3-diaminopropionate biosynthesis
protein SbnB. Members of this protein family are
probable NAD-dependent dehydrogenases related to the
alanine dehydrogenase of Archaeoglobus fulgidus (see
TIGR02371, PDB structure 1OMO and PMID:15313611) and
more distantly to ornithine cyclodeaminase. Members
include the staphylobactin biosynthesis protein SbnB and
tend to occur in contexts suggesting non-ribosomal
peptide synthesis, always adjacent to (occasionally
fused with) a pyridoxal phosphate-dependent enzyme,
SbnA. The pair appears to provide 2,3-diaminopropionate
for biosynthesis of siderophores or other secondary
metabolites [Cellular processes, Biosynthesis of natural
products].
Length = 327
Score = 30.7 bits (70), Expect = 0.76
Identities = 23/89 (25%), Positives = 34/89 (38%), Gaps = 31/89 (34%)
Query: 160 EVIRTVDIVVTATGNKNVVTREHMDK---MKNGCVVCNMGHSNTEIDVNSLRTPDLTWE- 215
+R D+VVTAT V ++D + G +V N+ SLR DL E
Sbjct: 194 AALRQADLVVTAT----VAGTPYIDDPAWFQPGALVLNI----------SLR--DLAPEV 237
Query: 216 -----KVRSQVDHVIWPDVNLKNNTVIDL 239
+ +HV + NT + L
Sbjct: 238 ILKADNIVDDWEHV------CRANTSLHL 260
>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 = 0.78
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 160 EVIRTVDIVVTATGNKNVVTREHMDK-MKNGCVV 192
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 = 30.3 bits (69), Expect = 0.79
Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 21/97 (21%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 168
+V + G+G +G ++LK G +T + + E + DI+
Sbjct: 154 QTKVAVLGFGNTARGAIRALKLGG--ADVT----VY------TRRTEALFKEELSEYDII 201
Query: 169 VTAT-----GNKNVVTREHMDKMKNGC----VVCNMG 196
V +++ E + ++K G V C+ G
Sbjct: 202 VNCILQDTDRPDHIIYEEDLKRLKPGALIIDVSCDEG 238
>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 = 0.89
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 8/84 (9%)
Query: 116 GYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTAT--- 172
G G +G + KGLG + +I P A + D + V L+E+++ DI+
Sbjct: 152 GTGRIGLTAAKLFKGLGAKVIGYDIYPSDAAK---DVVTFVSLDELLKKSDIISLHVPYI 208
Query: 173 --GNKNVVTREHMDKMKNGCVVCN 194
N ++ +E + KMK+G ++ N
Sbjct: 209 KGKNDKLINKEFISKMKDGAILIN 232
>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 = 30.0 bits (68), Expect = 1.1
Identities = 9/33 (27%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 157 KLNEVIRTVDIVVTATGNKN-VVTREHMDKMKN 188
L E + DIV+++TG + +V++E +++
Sbjct: 233 DLEEYLAEADIVISSTGAPHPIVSKEDVERALR 265
>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 = 29.9 bits (68), Expect = 1.2
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 11/95 (11%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYI-TEIDPICALQACMDGFSVVKLNEVIRTVD 166
GK ++ G G +G+ + LK G VI + T + C + + +L+EV++ D
Sbjct: 135 GKTILFLGTGSIGQEIAKRLKAFGMKVIGVNTSGRDVEYFDKC---YPLEELDEVLKEAD 191
Query: 167 IVV-----TATGNKNVVTREHMDKMKNGCVVCNMG 196
IVV T ++ ++MK G + N+G
Sbjct: 192 IVVNVLPLTEE-THHLFDEAFFEQMKKGALFINVG 225
>gnl|CDD|223137 COG0059, IlvC, Ketol-acid reductoisomerase [Amino acid transport
and metabolism / Coenzyme metabolism].
Length = 338
Score = 29.9 bits (68), Expect = 1.3
Identities = 25/86 (29%), Positives = 37/86 (43%), Gaps = 6/86 (6%)
Query: 109 GKQVVLCGYGEVGKGCCQSLK--GLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVD 166
GK+V + GYG G +L+ GL VI +A DGF V + E + D
Sbjct: 18 GKKVAIIGYGSQGHAQALNLRDSGLN-VIIGLRKGSSSWKKAKEDGFKVYTVEEAAKRAD 76
Query: 167 IVVTATGN---KNVVTREHMDKMKNG 189
+V+ + K V +E +K G
Sbjct: 77 VVMILLPDEQQKEVYEKEIAPNLKEG 102
>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 = 30.2 bits (68), Expect = 1.4
Identities = 24/102 (23%), Positives = 37/102 (36%), Gaps = 26/102 (25%)
Query: 72 HLTELSDEQAKYMGLNKAGPFKPSYYSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGL 131
H+ +L ++ + L + G + P Y S+KR D CGY
Sbjct: 651 HVFDLVTDKGFHGVLVENGRYVPVYTSIKRCRD----------CGYQFTED--------- 691
Query: 132 GCVIYITEIDPICALQACMDGFSVVK-LNEVIRTVDIVVTAT 172
E P C + D S+++ L E+ VD V T
Sbjct: 692 ------RESCPKCGSENIEDSKSIIEILRELAHEVDEVFIGT 727
>gnl|CDD|223758 COG0686, Ald, Alanine dehydrogenase [Amino acid transport and
metabolism].
Length = 371
Score = 29.6 bits (67), Expect = 1.5
Identities = 31/108 (28%), Positives = 50/108 (46%), Gaps = 21/108 (19%)
Query: 105 VMFGG------KQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGF----- 153
V+ GG +VV+ G G VG + GLG + I +++ I L+ D F
Sbjct: 158 VLLGGVPGVLPAKVVVLGGGVVGTNAAKIAIGLGADVTILDLN-IDRLRQLDDLFGGRVH 216
Query: 154 ----SVVKLNEVIRTVDIVVTA---TGNK--NVVTREHMDKMKNGCVV 192
+ + E ++ D+V+ A G K +VTRE + +MK G V+
Sbjct: 217 TLYSTPSNIEEAVKKADLVIGAVLIPGAKAPKLVTREMVKQMKPGSVI 264
>gnl|CDD|178684 PLN03139, PLN03139, formate dehydrogenase; Provisional.
Length = 386
Score = 29.8 bits (67), Expect = 1.5
Identities = 25/93 (26%), Positives = 42/93 (45%), Gaps = 9/93 (9%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYI--TEIDPICALQACMDGFSVVKLNEVIRTV 165
GK V G G +G+ Q LK C ++Y ++DP L+ L+ ++
Sbjct: 199 GKTVGTVGAGRIGRLLLQRLKPFNCNLLYHDRLKMDP--ELEKETGAKFEEDLDAMLPKC 256
Query: 166 DIVVTAT----GNKNVVTREHMDKMKNGCVVCN 194
D+VV T + + +E + KMK G ++ N
Sbjct: 257 DVVVINTPLTEKTRGMFNKERIAKMKKGVLIVN 289
>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 = 1.7
Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 4/94 (4%)
Query: 102 STDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYI---TEIDPICALQACMDGFSVVKL 158
TD G V++ G+G G ++ LG +++ + D + + F + KL
Sbjct: 144 HTDFTIHGSNVMVLGFGRTGMTIARTFSALGARVFVGARSSADLARITEMGLIPFPLNKL 203
Query: 159 NEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVV 192
E + +DIV+ T V+T + + K+ V+
Sbjct: 204 EEKVAEIDIVIN-TIPALVLTADVLSKLPKHAVI 236
>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 = 1.8
Identities = 25/91 (27%), Positives = 39/91 (42%), Gaps = 7/91 (7%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 168
GK + + GYG +G + LG + +I L V L E++ D V
Sbjct: 140 GKTLGIIGYGHIGSQLSVLAEALGMRVIFYDIAEKLPLGNAR---QVSSLEELLAEADFV 196
Query: 169 ---VTAT-GNKNVVTREHMDKMKNGCVVCNM 195
V AT KN++ E + +MK G ++ N
Sbjct: 197 TLHVPATPSTKNMIGAEEIAQMKKGAILINA 227
>gnl|CDD|133449 cd05191, NAD_bind_amino_acid_DH, NAD(P) binding domain of amino
acid dehydrogenase-like proteins. Amino acid
dehydrogenase(DH)-like NAD(P)-binding domains are
members of the Rossmann fold superfamily and are found
in glutamate, leucine, and phenylalanine DHs (DHs),
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 86
Score = 27.7 bits (62), Expect = 1.9
Identities = 29/102 (28%), Positives = 37/102 (36%), Gaps = 29/102 (28%)
Query: 95 SYYSLKRSTDVMFG---GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMD 151
+ LK + V GK VV+ G GEVGKG + L G
Sbjct: 6 AVALLKAAGKVTNKSLKGKTVVVLGAGEVGKGIAKLLADEGG------------------ 47
Query: 152 GFSVVKLNEVIRT-VDIVVTATGNKNVVTREHMDKMKNGCVV 192
+V+ DI+VTAT V E K+ G VV
Sbjct: 48 -------KKVVLCDRDILVTATPAGVPVLEEATAKINEGAVV 82
>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 = 29.2 bits (66), Expect = 2.3
Identities = 26/116 (22%), Positives = 45/116 (38%), Gaps = 20/116 (17%)
Query: 107 FGGKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEI-DPICALQACMDG----FSVVKLNE 160
G V + G G +G+ L G VI + P+ +G +L+E
Sbjct: 123 LRGSTVAIVGAGGIGRALIPLLAPFGAKVIAVNRSGRPV-------EGADETVPADRLDE 175
Query: 161 VIRTVDIVVTATG----NKNVVTREHMDKMKNGCVVCNMG---HSNTEIDVNSLRT 209
V D VV A +++V + MK + N+ +T+ V++LR+
Sbjct: 176 VWPDADHVVLAAPLTPETRHLVDAAALAAMKPHAWLVNVARGPLVDTDALVDALRS 231
>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 = 28.3 bits (64), Expect = 2.4
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 4/88 (4%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGC-VIYITEIDPICALQACMDGFSVVKLNEVIRTVDI 167
GK++ + GYG G +L+ G VI +A DGF V + E ++ D+
Sbjct: 4 GKKIAVIGYGSQGHAHALNLRDSGVNVIVGLRPGSKSWEKAKKDGFEVYTVAEAVKKADV 63
Query: 168 VVTATGN---KNVVTREHMDKMKNGCVV 192
V+ + V +E +K G +
Sbjct: 64 VMILLPDEVQAEVYEKEIAPNLKEGAAL 91
>gnl|CDD|133446 cd01078, NAD_bind_H4MPT_DH, NADP binding domain of methylene
tetrahydromethanopterin dehydrogenase. Methylene
Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP
binding domain. NADP-dependent H4MPT DH catalyzes the
dehydrogenation of methylene- H4MPT and
methylene-tetrahydrofolate (H4F) with NADP+ as cofactor.
H4F and H4MPT are both cofactors that carry the
one-carbon units between the formyl and methyl oxidation
level. H4F and H4MPT are structurally analogous to each
other with respect to the pterin moiety, but each has
distinct side chain. H4MPT is present only in anaerobic
methanogenic archaea and aerobic methylotrophic
proteobacteria. H4MPT seems to have evolved
independently from H4F and functions as a distinct
carrier in C1 metabolism. Amino acid DH-like
NAD(P)-binding domains are members of the Rossmann fold
superfamily and include glutamate, leucine, and
phenylalanine DHs, methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 194
Score = 28.5 bits (64), Expect = 2.5
Identities = 24/126 (19%), Positives = 36/126 (28%), Gaps = 25/126 (19%)
Query: 100 KRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQAC---------- 149
D+ G VVL G G VG+ L G + + D A +A
Sbjct: 21 LMGKDLK-GKTAVVLGGTGPVGQRAAVLLAREGARVVLVGRDLERAQKAADSLRARFGEG 79
Query: 150 ---MDGFSVVKLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNS 206
++ I+ D+V A + + K V DVN
Sbjct: 80 VGAVETSDDAARAAAIKGADVVFAAGAAGVELLEKLAWAPKPLAVAA---------DVN- 129
Query: 207 LRTPDL 212
P +
Sbjct: 130 -AVPPV 134
>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 = 28.7 bits (65), Expect = 2.9
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 116 GYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIVVTAT--- 172
G G +G+ ++L G GC I + P ++ V L+ + + DI+ T
Sbjct: 150 GTGRIGQAVIKNLSGFGCKILAYDPYPNEEVK---KYAEYVDLDTLYKESDIITLHTPLT 206
Query: 173 -GNKNVVTREHMDKMKNGCVVCN 194
+++ +E + KMK+G ++ N
Sbjct: 207 EETYHLINKESIAKMKDGVIIIN 229
>gnl|CDD|133450 cd05211, NAD_bind_Glu_Leu_Phe_Val, NAD(P) binding domain of
glutamate dehydrogenase, leucine dehydrogenase,
phenylalanine dehydrogenase, and valine dehydrogenase.
Amino acid dehydrogenase (DH) is a widely distributed
family of enzymes that catalyzes the oxidative
deamination of an amino acid to its keto acid and
ammonia with concomitant reduction of NAD(P)+. This
subfamily includes glutamate, leucine, phenylalanine,
and valine DHs. Glutamate DH is a multi-domain enzyme
that catalyzes the reaction from glutamate to
2-oxyoglutarate and ammonia in the presence of NAD or
NADP. It is present in all organisms. Enzymes involved
in ammonia assimilation are typically NADP+-dependent,
while those involved in glutamate catabolism are
generally NAD+-dependent. As in other NAD+-dependent
DHs, monomers in this family have 2 domains separated by
a deep cleft. Here the c-terminal domain contains a
modified NAD-binding Rossmann fold with 7 rather than
the usual 6 beta strands and one strand anti-parrallel
to the others. Amino acid DH-like NAD(P)-binding domains
are members of the Rossmann fold superfamily and include
glutamate, leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 217
Score = 28.3 bits (63), Expect = 3.2
Identities = 27/121 (22%), Positives = 41/121 (33%), Gaps = 25/121 (20%)
Query: 95 SYYSLKRSTDVMFG---GKQVVLCGYGEVGKGCCQSLKGLGC----------VIYITEID 141
++K + + G V + G G VG G + L G IY I
Sbjct: 6 VVVAMKAAMKHLGDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIYDPGIT 65
Query: 142 PICALQAC--MDGFSVVKLNEVIR-------TVDIVV-TATGNKNVVTREHMDKMKNGCV 191
+ + G + VK+ + VDI A G NV+ E+ K+K V
Sbjct: 66 TEELINYAVALGGSARVKVQDYFPGEAILGLDVDIFAPCALG--NVIDLENAKKLKAKVV 123
Query: 192 V 192
Sbjct: 124 A 124
>gnl|CDD|236064 PRK07589, PRK07589, ornithine cyclodeaminase; Validated.
Length = 346
Score = 28.7 bits (65), Expect = 3.2
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 9/49 (18%)
Query: 135 IYITEIDPICALQACMD-----GFSVVKLN---EVIRTVDIVVTATGNK 175
I + +IDP A G +V E + DI+ T T +K
Sbjct: 157 IRLYDIDP-AATAKLARNLAGPGLRIVACRSVAEAVEGADIITTVTADK 204
>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 = 3.3
Identities = 20/63 (31%), Positives = 25/63 (39%), Gaps = 14/63 (22%)
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDV--NSLRTPDLTWE 215
L V R DI+V A G +V D +K G V IDV N + P+
Sbjct: 195 LPAVCRRADILVAAVGRPEMVKG---DWIKPGATV---------IDVGINRIPAPEKGEG 242
Query: 216 KVR 218
K R
Sbjct: 243 KTR 245
>gnl|CDD|223268 COG0190, FolD, 5,10-methylene-tetrahydrofolate
dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase
[Coenzyme metabolism].
Length = 283
Score = 28.3 bits (64), Expect = 4.0
Identities = 27/114 (23%), Positives = 37/114 (32%), Gaps = 26/114 (22%)
Query: 99 LKRSTDVMFGGKQVVLCGYGE-VGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK 157
L + GK VV+ G VGK L + + D
Sbjct: 146 LLEEYGIDLRGKNVVVVGRSNIVGKPLALLLLNANATVTVCHSR-------TKD------ 192
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPD 211
L + + DIVV A G + + + +K G VV IDV R D
Sbjct: 193 LASITKNADIVVVAVGKPHFIKADM---VKPGAVV---------IDVGINRVND 234
>gnl|CDD|240656 cd12179, 2-Hacid_dh_14, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 306
Score = 28.0 bits (63), Expect = 4.2
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 4/60 (6%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 168
GK V + GYG +GK + L G GC + + V L + + DI+
Sbjct: 138 GKTVGIIGYGNMGKAFAKRLSGFGCKVIAYDKYKNFGDAYA----EQVSLETLFKEADIL 193
>gnl|CDD|184560 PRK14190, PRK14190, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 284
Score = 28.1 bits (63), Expect = 4.4
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 196
L E+ + DI++ A G ++T + +K G VV ++G
Sbjct: 195 LAELTKQADILIVAVGKPKLITADM---VKEGAVVIDVG 230
>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 = 4.4
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 217
L EV R DI+V A G + VT+E +K G VV ++G + D N D+ +++V
Sbjct: 195 LAEVARKADILVVAIGRGHFVTKEF---VKEGAVVIDVGMNR---DENGKLIGDVDFDEV 248
Query: 218 RSQVDHVIWP 227
++V I P
Sbjct: 249 -AEVASYITP 257
>gnl|CDD|178485 PLN02897, PLN02897, tetrahydrofolate dehydrogenase/cyclohydrolase,
putative.
Length = 345
Score = 28.0 bits (62), Expect = 5.0
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 159 NEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTE 201
++ R DIV+ A G N+V R +K G VV ++G + E
Sbjct: 252 EQITRKADIVIAAAGIPNLV-RGSW--LKPGAVVIDVGTTPVE 291
>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 = 28.0 bits (63), Expect = 5.1
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 152 GFSVVKLNEVIRTVDIVVTATGNKNVVT--REHMDKMKNGCVVCN 194
G + LNE+++TVD++ T KNV+ E + + +G ++ N
Sbjct: 179 GIRYLPLNELLKTVDVICTCL-PKNVILLGEEEFELLGDGKILFN 222
>gnl|CDD|234450 TIGR04056, OMP_RagA_SusC, TonB-linked outer membrane protein,
SusC/RagA family. This model describes a distinctive
clade among the TonB-linked outer membrane proteins
(OMP). Members of this family are restricted to the
Bacteriodetes lineage (except for Gemmatimonas
aurantiaca T-27 from the novel phylum Gemmatimonadetes)
and occur in high copy numbers, with over 100 members
from Bacteroides thetaiotaomicron VPI-5482 alone.
Published descriptions of members of this family are
available for RagA from Porphyromonas gingivalis, SusC
from Bacteroides thetaiotaomicron, and OmpW from
Bacteroides caccae. Members form pairs with members of
the SusD/RagB family (pfam07980). Transporter complexes
including these outer membrane proteins are likely to
import large degradation products of proteins (e.g.
RagA) or carbohydrates (e.g. SusC) as nutrients, rather
than siderophores [Transport and binding proteins,
Unknown substrate].
Length = 982
Score = 28.3 bits (64), Expect = 5.1
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 5/54 (9%)
Query: 172 TGNKNVVTR-EHMDKMKNGCVVCNMGHSNTE----IDVNSLRTPDLTWEKVRSQ 220
GN N+ R ++ G N G +N I + L P+L WEK +
Sbjct: 608 VGNDNIGDRYPYLSLYNLGDSGYNFGTNNGTSVTGITESRLGNPNLKWEKTKKW 661
>gnl|CDD|188426 TIGR03911, pyrrolys_PylD, pyrrolysine biosynthesis protein PylD.
This protein is PylD, part of a three-gene cassette that
is sufficient to direct the biosynthesis of pyrrolysine,
the twenty-second amino acid, incorporated in some
species at a UAG canonical stop codon [Amino acid
biosynthesis, Other].
Length = 266
Score = 27.8 bits (62), Expect = 5.4
Identities = 19/88 (21%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 102 STDVMFGG---KQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSV--- 155
+ D + GG K V++ G G VG+ L G +Y+ + + + + D S+
Sbjct: 135 ALDCLTGGLKSKDVLVIGLGPVGRAAAFHLVDKGFHVYVYDKNLEVSEKLAQDLCSIGIE 194
Query: 156 VKLNEVIRTVDIVVTATGNKNVVTREHM 183
+L+E + + AT + +H+
Sbjct: 195 RELDEAMHKFSAIFEATPEAGTIREDHL 222
>gnl|CDD|184556 PRK14185, PRK14185, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 293
Score = 27.9 bits (62), Expect = 5.5
Identities = 18/56 (32%), Positives = 23/56 (41%), Gaps = 12/56 (21%)
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLT 213
L + DI++ A G V D +K G VV IDV + R PD T
Sbjct: 198 LKKECLEADIIIAALGQPEFVKA---DMVKEGAVV---------IDVGTTRVPDAT 241
>gnl|CDD|240639 cd12162, 2-Hacid_dh_4, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine yydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 307
Score = 27.8 bits (63), Expect = 5.8
Identities = 21/93 (22%), Positives = 40/93 (43%), Gaps = 11/93 (11%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 168
GK + + GYG +G+ + + G + E A V L+E++ D++
Sbjct: 147 GKTLGIIGYGNIGQAVARIARAFGMKVLFAERKG-----APPLREGYVSLDELLAQSDVI 201
Query: 169 -----VTATGNKNVVTREHMDKMKNGCVVCNMG 196
+T +N++ E + KMK G ++ N
Sbjct: 202 SLHCPLTPE-TRNLINAEELAKMKPGAILINTA 233
Score = 27.4 bits (62), Expect = 8.6
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 162 IRTVDIVVTATGNKNVVTREHMDKMKN 188
I+ DIV+T NK V+ E + ++ N
Sbjct: 42 IKDADIVIT---NKVVLDAEVLAQLPN 65
>gnl|CDD|240635 cd12158, ErythrP_dh, D-Erythronate-4-Phosphate Dehydrogenase
NAD-binding and catalytic domains.
D-Erythronate-4-phosphate Dehydrogenase (E. coli gene
PdxB), a D-specific 2-hydroxyacid dehydrogenase family
member, catalyzes the NAD-dependent oxidation of
erythronate-4-phosphate, which is followed by
transamination to form 4-hydroxy-L-threonine-4-phosphate
within the de novo biosynthesis pathway of vitamin B6.
D-Erythronate-4-phosphate dehydrogenase has the common
architecture shared with D-isomer specific 2-hydroxyacid
dehydrogenases but contains an additional C-terminal
dimerization domain in addition to an NAD-binding domain
and the "lid" domain. The lid domain corresponds to the
catalytic domain of phosphoglycerate dehydrogenase and
other proteins of the D-isomer specific 2-hydroxyacid
dehydrogenase family, which 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 = 343
Score = 27.9 bits (63), Expect = 5.9
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 116 GYGEVGKGCCQSLKGLG--CVIYITEIDPICALQACMDGFSVVKLNEVIRTVDIV 168
G G VG + L+ LG ++ DP A GF V L E++ DI+
Sbjct: 122 GVGNVGSRLARRLEALGMNVLLC----DPPRAEAEGDPGF--VSLEELLAEADII 170
>gnl|CDD|220630 pfam10209, DUF2340, Uncharacterized conserved protein (DUF2340).
This is a family of small proteins of approximately 150
amino acids of unknown function.
Length = 122
Score = 26.9 bits (60), Expect = 5.9
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 221 VDHVIWPDVNLKNNTVIDLFRKPKSRL 247
V +V++ D++LK+ T DL K+ +
Sbjct: 14 VKNVVFHDIDLKDTTAKDLLEDVKADI 40
>gnl|CDD|215332 PLN02616, PLN02616, tetrahydrofolate dehydrogenase/cyclohydrolase,
putative.
Length = 364
Score = 27.7 bits (61), Expect = 7.0
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 160 EVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLR 208
E+ R DI+++A G N+V +K G VV ++G + E D +S R
Sbjct: 270 EITREADIIISAVGQPNMV---RGSWIKPGAVVIDVGINPVE-DASSPR 314
>gnl|CDD|234703 PRK00258, aroE, shikimate 5-dehydrogenase; Reviewed.
Length = 278
Score = 27.5 bits (62), Expect = 7.0
Identities = 25/132 (18%), Positives = 45/132 (34%), Gaps = 22/132 (16%)
Query: 96 YYSLKRSTDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCV-IYITEIDP------ICALQA 148
+L+ V GK++++ G G + L LG I I A
Sbjct: 110 VRALEERLGVDLKGKRILILGAGGAARAVILPLLDLGVAEITIVNRTVERAEELAKLFGA 169
Query: 149 CMDGFSVVKLNEVIRTVDIVVTATG----NKNVVTREHMDKMKNGCVVCNMGHSNTEIDV 204
++L E + D+++ AT + + + ++ G +V D+
Sbjct: 170 LGKAELDLELQEELADFDLIINATSAGMSGELPLPPLPLSLLRPGTIVY---------DM 220
Query: 205 --NSLRTPDLTW 214
L TP L W
Sbjct: 221 IYGPLPTPFLAW 232
>gnl|CDD|180749 PRK06920, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1107
Score = 27.8 bits (62), Expect = 7.3
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 157 KLNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVC-NMGHSNTEIDVNSLRTPDL 212
KL E V+I V AT + + + D + + C++ G T+ D L+T
Sbjct: 175 KLPEFSNRVNIPVVATNDVRYINQS--DALVHECLLSVESGTKMTDPDRPRLKTDQY 229
>gnl|CDD|223247 COG0169, AroE, Shikimate 5-dehydrogenase [Amino acid transport and
metabolism].
Length = 283
Score = 27.2 bits (61), Expect = 8.9
Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 12/88 (13%)
Query: 96 YYSLKRS-TDVMFGGKQVVLCGYGEVGKGCCQSLKGLGCV-IYITEIDP---------IC 144
+LK V GK+V++ G G + +L G I +
Sbjct: 112 LRALKEFGLPVDVTGKRVLILGAGGAARAVAFALAEAGAKRITVVNRTRERAEELADLFG 171
Query: 145 ALQACMDGFSVVKLNEVIRTVDIVVTAT 172
L A ++ + + E + D+++ AT
Sbjct: 172 ELGAAVEAAA-LADLEGLEEADLLINAT 198
>gnl|CDD|176188 cd05285, sorbitol_DH, Sorbitol dehydrogenase. Sorbitol and aldose
reductase are NAD(+) binding proteins of the polyol
pathway, which interconverts glucose and fructose.
Sorbitol dehydrogenase is tetrameric and has a single
catalytic zinc per subunit. Aldose reductase catalyzes
the NADP(H)-dependent conversion of glucose to sorbital,
and SDH uses NAD(H) in the conversion of sorbitol to
fructose. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 343
Score = 27.1 bits (61), Expect = 9.0
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCV-IYITEIDP 142
G V++ G G +G K G + +T+IDP
Sbjct: 163 GDTVLVFGAGPIGLLTAAVAKAFGATKVVVTDIDP 197
>gnl|CDD|172679 PRK14191, PRK14191, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 285
Score = 27.0 bits (60), Expect = 9.0
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMG 196
L+ + DIV G +++ +K G VV ++G
Sbjct: 194 LSFYTQNADIVCVGVGKPDLIK---ASMVKKGAVVVDIG 229
>gnl|CDD|225019 COG2108, COG2108, Uncharacterized conserved protein related to
pyruvate formate-lyase activating enzyme [General
function prediction only].
Length = 353
Score = 27.4 bits (61), Expect = 9.3
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 117 YGEVGKGCCQSLKGLGCVIYITEIDPI----CALQACMDGFSVVKLNEV-IRTV-DIV 168
+G++ KGC + G V+++T + C + G V+ NE +++V DI+
Sbjct: 14 FGKLPKGCRLCVLGGKLVLFVTGLCNRSCFYCPVSDERKGKDVIYANERPVKSVEDII 71
>gnl|CDD|172675 PRK14187, PRK14187, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 294
Score = 27.1 bits (60), Expect = 9.6
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 158 LNEVIRTVDIVVTATGNKNVVTREHMDKMKNGCVVCNMGHSNTEIDVNSLRTPDLTWEKV 217
L + DI+V A G N V +K G +V ++G ++ E D+ + +V
Sbjct: 197 LADYCSKADILVAAVGIPNFV---KYSWIKKGAIVIDVGINSIEEGGVKKFVGDVDFAEV 253
Query: 218 RSQV 221
+ +
Sbjct: 254 KKKA 257
>gnl|CDD|222002 pfam13241, NAD_binding_7, Putative NAD(P)-binding. This domain is
found in fungi, plants, archaea and bacteria.
Length = 104
Score = 25.9 bits (58), Expect = 9.7
Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 109 GKQVVLCGYGEVGKGCCQSLKGLGCVIYITEIDPICALQACMDGFSVVK---LNEVIRTV 165
GK+V++ G GEV ++L G + + + P + +++ +
Sbjct: 7 GKRVLVVGGGEVALRKIRALLEAGAKVTV--VSP--EILEAEGLVRLIQREFEPGDLDGA 62
Query: 166 DIVVTATGNKNV 177
D+V+ AT + +
Sbjct: 63 DLVIAATDDPEL 74
>gnl|CDD|191413 pfam05970, PIF1, PIF1-like helicase. This family includes
homologues of the PIF1 helicase, which inhibits
telomerase activity and is cell cycle regulated. This
family includes a large number of largely
uncharacterized plant proteins. This family includes a
P-loop motif that is involved in nucleotide binding.
Length = 364
Score = 27.3 bits (61), Expect = 9.9
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 104 DVMFGGKQVVLCG 116
D FGGK VVL G
Sbjct: 136 DKPFGGKTVVLGG 148
>gnl|CDD|215640 PLN03232, PLN03232, ABC transporter C family member; Provisional.
Length = 1495
Score = 27.2 bits (60), Expect = 10.0
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 124 CCQSLKGLGCVIYITEIDP 142
CCQ+L G+ ++YI E+DP
Sbjct: 182 CCQALFGILLLVYIPELDP 200
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.138 0.424
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: 12,844,004
Number of extensions: 1176479
Number of successful extensions: 1160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1123
Number of HSP's successfully gapped: 128
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (25.9 bits)