RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029791
(188 letters)
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 344 bits (883), Expect = e-120
Identities = 165/183 (90%), Positives = 179/183 (97%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
K++IGINGFGRIGRLVARV+LQRDDVELVAVNDPFITT+YMTYMFKYDSVHGQWKHHELK
Sbjct: 5 KIRIGINGFGRIGRLVARVVLQRDDVELVAVNDPFITTEYMTYMFKYDSVHGQWKHHELK 64
Query: 63 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 122
VKDDKTLLFGEKPVTVFG+RNPE+IPW E GA++VVESTGVFTDKDKAAAHLKGGAKKV+
Sbjct: 65 VKDDKTLLFGEKPVTVFGIRNPEDIPWGEAGADFVVESTGVFTDKDKAAAHLKGGAKKVV 124
Query: 123 ISAPSKDAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 182
ISAPSKDAPMFVVGVNE+EYK +L+IVSNASCTTNCLAPLAKVI+D+FGIVEGLMTTVHS
Sbjct: 125 ISAPSKDAPMFVVGVNEHEYKSDLDIVSNASCTTNCLAPLAKVINDRFGIVEGLMTTVHS 184
Query: 183 ITG 185
IT
Sbjct: 185 ITA 187
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 319 bits (818), Expect = e-109
Identities = 129/183 (70%), Positives = 147/183 (80%), Gaps = 1/183 (0%)
Query: 2 GKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHEL 61
GK KIGINGFGRIGRLV R+ RDD+E+VAVNDPFI YM YMFKYDS HG +K +
Sbjct: 84 GKTKIGINGFGRIGRLVLRIATSRDDIEVVAVNDPFIDAKYMAYMFKYDSTHGNFKGT-I 142
Query: 62 KVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKV 121
V DD TL K + V R+P EIPW + GAEYVVES+GVFT +KA+AHLKGGAKKV
Sbjct: 143 NVVDDSTLEINGKQIKVTSKRDPAEIPWGDFGAEYVVESSGVFTTVEKASAHLKGGAKKV 202
Query: 122 IISAPSKDAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVH 181
+ISAPS DAPMFVVGVNE YKP +NIVSNASCTTNCLAPLAKV+H++FGI+EGLMTTVH
Sbjct: 203 VISAPSADAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAKVVHEEFGILEGLMTTVH 262
Query: 182 SIT 184
+ T
Sbjct: 263 ATT 265
>gnl|CDD|173322 PTZ00023, PTZ00023, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 337
Score = 263 bits (674), Expect = 6e-89
Identities = 117/182 (64%), Positives = 139/182 (76%), Gaps = 3/182 (1%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKV 63
VK+GINGFGRIGRLV R L+R+DVE+VA+NDPF+T DYM Y+ KYDSVHG E+ V
Sbjct: 3 VKLGINGFGRIGRLVFRAALEREDVEVVAINDPFMTLDYMCYLLKYDSVHGSLPA-EVSV 61
Query: 64 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 123
D L+ G K V VF ++P IPW + G + V ESTGVF K+KA AHLKGGAKKVI+
Sbjct: 62 TDG-FLMIGSKKVHVFFEKDPAAIPWGKNGVDVVCESTGVFLTKEKAQAHLKGGAKKVIM 120
Query: 124 SAPSKD-APMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 182
SAP KD P++V+GVN +Y IVSNASCTTNCLAPLAKV++DKFGIVEGLMTTVH+
Sbjct: 121 SAPPKDDTPIYVMGVNHTQYDKSQRIVSNASCTTNCLAPLAKVVNDKFGIVEGLMTTVHA 180
Query: 183 IT 184
T
Sbjct: 181 ST 182
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 259 bits (665), Expect = 2e-87
Identities = 104/186 (55%), Positives = 131/186 (70%), Gaps = 6/186 (3%)
Query: 3 KVKIGINGFGRIGRLVARVILQRD-DVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHEL 61
+K+ INGFGRIGRLVAR L+RD D+E+VA+ND DY+ ++ KYDSVHG++ E+
Sbjct: 1 MIKVAINGFGRIGRLVARAALERDGDIEVVAINDL-TDPDYLAHLLKYDSVHGRFDG-EV 58
Query: 62 KVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHL-KGGAKK 120
+VKDD L+ K + V R+P +PWA+ G + VVE TG FT ++KA HL GGAKK
Sbjct: 59 EVKDD-ALVVNGKGIKVLAERDPANLPWADLGVDIVVECTGKFTGREKAEKHLKAGGAKK 117
Query: 121 VIISAPSKDA-PMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 179
V+ISAP KD V GVN N Y IVSNASCTTNCLAP+AKV++D FGI +GLMTT
Sbjct: 118 VLISAPGKDDVATVVYGVNHNYYDAGHTIVSNASCTTNCLAPVAKVLNDAFGIEKGLMTT 177
Query: 180 VHSITG 185
VH+ T
Sbjct: 178 VHAYTN 183
>gnl|CDD|233453 TIGR01534, GAPDH-I, glyceraldehyde-3-phosphate dehydrogenase, type
I. This model represents glyceraldehyde-3-phosphate
dehydrogenase (GAPDH), the enzyme responsible for the
interconversion of 1,3-diphosphoglycerate and
glyceraldehyde-3-phosphate, a central step in glycolysis
and gluconeogenesis. Forms exist which utilize NAD (EC
1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In
some species, NAD- and NADP- utilizing forms exist,
generally being responsible for reactions in the
anabolic and catabolic directions respectively. Two PFAM
models cover the two functional domains of this protein;
pfam00044 represents the N-terminal NAD(P)-binding
domain and pfam02800 represents the C-terminal catalytic
domain. An additional form of gap gene is found in gamma
proteobacteria and is responsible for the conversion of
erythrose-4-phosphate (E4P) to 4-phospho-erythronate in
the biosynthesis of pyridoxine. This pathway of
pyridoxine biosynthesis appears to be limited, however,
to a relatively small number of bacterial species
although it is prevalent among the gamma-proteobacteria.
This enzyme is described by TIGR001532. These sequences
generally score between trusted and noise to this GAPDH
model due to the close evolutionary relationship. There
exists the possiblity that some forms of GAPDH may be
bifunctional and act on E4P in species which make
pyridoxine and via hydroxythreonine and lack a separate
E4PDH enzyme (for instance, the GAPDH from Bacillus
stearothermophilus has been shown to posess a limited
E4PD activity as well as a robust GAPDH activity). There
are a great number of sequences in the databases which
score between trusted and noise to this model, nearly
all of them due to fragmentary sequences. It seems that
study of this gene has been carried out in many species
utilizing PCR probes which exclude the extreme ends of
the consenses used to define this model. The noise level
is set relative not to E4PD, but the next closest
outliers, the class II GAPDH's (found in archaea,
TIGR01546) and aspartate semialdehyde dehydrogenase
(ASADH, TIGR01296) both of which have highest-scoring
hits around -225 to the prior model [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 326
Score = 254 bits (651), Expect = 1e-85
Identities = 101/184 (54%), Positives = 132/184 (71%), Gaps = 5/184 (2%)
Query: 5 KIGINGFGRIGRLVARVILQRD--DVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
K+GINGFGRIGRLV R IL++ D+E+VA+ND +Y+ Y+ KYDSVHG+++ E+
Sbjct: 1 KVGINGFGRIGRLVLRAILEKPGNDLEVVAINDL-TDLEYLAYLLKYDSVHGRFEG-EVT 58
Query: 63 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 122
+D ++ G++ ++VF R+P ++PW G + V+E TG F DK+K HL+ GAKKV+
Sbjct: 59 ADEDGLVVNGKEVISVFSERDPSDLPWKALGVDIVIECTGKFRDKEKLEGHLEAGAKKVL 118
Query: 123 ISAPSK-DAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVH 181
ISAPSK D V GVN +EY P IVSNASCTTNCLAPLAKV+ + FGIV GLMTTVH
Sbjct: 119 ISAPSKGDVKTIVYGVNHDEYDPSERIVSNASCTTNCLAPLAKVLDEAFGIVSGLMTTVH 178
Query: 182 SITG 185
S T
Sbjct: 179 SYTN 182
>gnl|CDD|215675 pfam00044, Gp_dh_N, Glyceraldehyde 3-phosphate dehydrogenase, NAD
binding domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
N-terminal domain is a Rossmann NAD(P) binding fold.
Length = 148
Score = 219 bits (560), Expect = 4e-74
Identities = 86/151 (56%), Positives = 109/151 (72%), Gaps = 4/151 (2%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKV 63
+K+GINGFGRIGRLV R L +DD+E+VA+ND + + Y+ KYDSVHG++ E++V
Sbjct: 1 IKVGINGFGRIGRLVLRAALAQDDLEVVAINDLT-DPETLAYLLKYDSVHGRFDG-EVEV 58
Query: 64 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 123
+D L+ K + VF R+P E+PW E G + VVESTGVFT +KA AHLK GAKKVII
Sbjct: 59 DEDG-LIVNGKKIKVFAERDPAELPWGELGVDIVVESTGVFTTAEKAEAHLKAGAKKVII 117
Query: 124 SAPSKD-APMFVVGVNENEYKPELNIVSNAS 153
SAP+KD P FV GVN +Y PE +IVSNAS
Sbjct: 118 SAPAKDDDPTFVYGVNHEDYDPEDDIVSNAS 148
>gnl|CDD|214851 smart00846, Gp_dh_N, Glyceraldehyde 3-phosphate dehydrogenase, NAD
binding domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
N-terminal domain is a Rossmann NAD(P) binding fold.
Length = 149
Score = 216 bits (552), Expect = 8e-73
Identities = 86/152 (56%), Positives = 110/152 (72%), Gaps = 4/152 (2%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKV 63
+K+GINGFGRIGRLV R L+R DVE+VA+ND +Y+ Y+ KYDSVHG++ ++V
Sbjct: 1 IKVGINGFGRIGRLVLRAALERPDVEVVAINDL-TDPEYLAYLLKYDSVHGRF-PGTVEV 58
Query: 64 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 123
+ D L+ K + VF R+P +PW E G + VVE TG FT ++KA+AHLK GAKKVII
Sbjct: 59 EGD-GLVVNGKAIKVFAERDPANLPWGELGVDIVVECTGGFTTREKASAHLKAGAKKVII 117
Query: 124 SAPSKDA-PMFVVGVNENEYKPELNIVSNASC 154
SAPSKDA P FV GVN +EY E +I+SNASC
Sbjct: 118 SAPSKDADPTFVYGVNHDEYDGEDHIISNASC 149
>gnl|CDD|236079 PRK07729, PRK07729, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 343
Score = 198 bits (506), Expect = 2e-63
Identities = 84/184 (45%), Positives = 129/184 (70%), Gaps = 5/184 (2%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
K K+ INGFGRIGR+V R ++ E+VA+N + ++ + ++ KYD+VHG++ ++
Sbjct: 2 KTKVAINGFGRIGRMVFRKAIKESAFEIVAINASY-PSETLAHLIKYDTVHGKFDG-TVE 59
Query: 63 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 122
+D L+ G+K + + R+P+E+PW + G + V+E+TG F K+KA H++ GAKKVI
Sbjct: 60 AFEDHLLVDGKK-IRLLNNRDPKELPWTDLGIDIVIEATGKFNSKEKAILHVEAGAKKVI 118
Query: 123 ISAPSKDAPM-FVVGVNENEYKPELN-IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTV 180
++AP K+ + VVGVNE++ E + I+SNASCTTNCLAP+ KV+ ++FGI GLMTTV
Sbjct: 119 LTAPGKNEDVTIVVGVNEDQLDIEKHTIISNASCTTNCLAPVVKVLDEQFGIENGLMTTV 178
Query: 181 HSIT 184
H+ T
Sbjct: 179 HAYT 182
>gnl|CDD|215131 PLN02237, PLN02237, glyceraldehyde-3-phosphate dehydrogenase B.
Length = 442
Score = 193 bits (492), Expect = 3e-60
Identities = 96/188 (51%), Positives = 130/188 (69%), Gaps = 7/188 (3%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDD--VELVAVNDPFITTDYMTYMFKYDSVHGQWKHHE 60
K+K+ INGFGRIGR R R D +++V VND + +++ KYDS+ G +K +
Sbjct: 75 KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKN-ASHLLKYDSMLGTFKA-D 132
Query: 61 LKVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKK 120
+K+ DD+T+ KP+ V R+P ++PWAE G + V+E TGVF D A H++ GAKK
Sbjct: 133 VKIVDDETISVDGKPIKVVSNRDPLKLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKK 192
Query: 121 VIISAPSK--DAPMFVVGVNENEYKPEL-NIVSNASCTTNCLAPLAKVIHDKFGIVEGLM 177
VII+AP+K D P +VVGVNE++Y E+ NIVSNASCTTNCLAP KV+ ++FGIV+G M
Sbjct: 193 VIITAPAKGADIPTYVVGVNEDDYDHEVANIVSNASCTTNCLAPFVKVLDEEFGIVKGTM 252
Query: 178 TTVHSITG 185
TT HS TG
Sbjct: 253 TTTHSYTG 260
>gnl|CDD|185614 PTZ00434, PTZ00434, cytosolic glyceraldehyde 3-phosphate
dehydrogenase; Provisional.
Length = 361
Score = 188 bits (478), Expect = 4e-59
Identities = 97/198 (48%), Positives = 129/198 (65%), Gaps = 14/198 (7%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRD----DVELVAVNDPFITTDYMTYMFKYDSVHGQW 56
M +K+GINGFGRIGR+V + I + ++++VAV D +Y Y KYD+VHG+
Sbjct: 1 MAPIKVGINGFGRIGRMVFQAICDQGLIGTEIDVVAVVDMSTNAEYFAYQMKYDTVHGRP 60
Query: 57 KHHELKVK-------DDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDK 109
K+ K DD ++ G + V RNP ++PW + G +YV+ESTG+FTDK
Sbjct: 61 KYTVETTKSSPSVKTDDVLVVNGHRIKCVKAQRNPADLPWGKLGVDYVIESTGLFTDKLA 120
Query: 110 AAAHLKGGAKKVIISAP-SKDAPMFVVGVNENEYKP-ELNIVSNASCTTNCLAPLAKVI- 166
A HLKGGAKKV+ISAP S A V+GVN++EY P E ++VSNASCTTNCLAP+ V+
Sbjct: 121 AEGHLKGGAKKVVISAPASGGAKTIVMGVNQHEYSPTEHHVVSNASCTTNCLAPIVHVLT 180
Query: 167 HDKFGIVEGLMTTVHSIT 184
+ FGI GLMTT+HS T
Sbjct: 181 KEGFGIETGLMTTIHSYT 198
>gnl|CDD|180962 PRK07403, PRK07403, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 337
Score = 185 bits (470), Expect = 3e-58
Identities = 93/189 (49%), Positives = 126/189 (66%), Gaps = 12/189 (6%)
Query: 4 VKIGINGFGRIGRLVARVILQRDD--VELVAVNDPFITTDYMT--YMFKYDSVHGQWKHH 59
+++ INGFGRIGR R L R++ +ELVA+ND T+D T ++ KYDS+ G K +
Sbjct: 2 IRVAINGFGRIGRNFLRCWLGRENSQLELVAIND---TSDPRTNAHLLKYDSMLG--KLN 56
Query: 60 ELKVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAK 119
D+ ++ K + RNP +PW E G + ++ESTGVF K+ A+ H++ GAK
Sbjct: 57 ADISADENSITVNGKTIKCVSDRNPLNLPWKEWGIDLIIESTGVFVTKEGASKHIQAGAK 116
Query: 120 KVIISAPSK--DAPMFVVGVNENEYKPEL-NIVSNASCTTNCLAPLAKVIHDKFGIVEGL 176
KV+I+AP K D +VVGVN +EY E NI+SNASCTTNCLAP+AKV+HD FGI++G
Sbjct: 117 KVLITAPGKGEDIGTYVVGVNHHEYDHEDHNIISNASCTTNCLAPIAKVLHDNFGIIKGT 176
Query: 177 MTTVHSITG 185
MTT HS TG
Sbjct: 177 MTTTHSYTG 185
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 183 bits (465), Expect = 1e-57
Identities = 97/183 (53%), Positives = 130/183 (71%), Gaps = 5/183 (2%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKV 63
+K+GINGFGRIGR+V R +R D+E+VA+ND + DYM YM KYDS HG++ ++V
Sbjct: 3 IKVGINGFGRIGRIVFRAAQKRSDIEIVAIND-LLDADYMAYMLKYDSTHGRFDG-TVEV 60
Query: 64 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 123
KD ++ G+K + V R+P + W E G + V E+TG+F + A H+ GAKKV++
Sbjct: 61 KDGHLIVNGKK-IRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVM 119
Query: 124 SAPSKD-APMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHS 182
+ PSKD PMFV G N ++Y + +IVSNASCTTNCLAPLAKVI+D FGI+EGLMTTVH+
Sbjct: 120 TGPSKDNTPMFVKGANFDKYAGQ-DIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHA 178
Query: 183 ITG 185
T
Sbjct: 179 TTA 181
>gnl|CDD|215572 PLN03096, PLN03096, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 395
Score = 185 bits (470), Expect = 2e-57
Identities = 88/186 (47%), Positives = 118/186 (63%), Gaps = 5/186 (2%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDD--VELVAVNDPFITTDYMTYMFKYDSVHGQWKHHE 60
K+K+ INGFGRIGR R R D +++VA+ND +++ KYDS G + +
Sbjct: 60 KIKVAINGFGRIGRNFLRCWHGRKDSPLDVVAINDTG-GVKQASHLLKYDSTLGTFDA-D 117
Query: 61 LKVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKK 120
+K D + K + V RNP +PW E G + V+E TGVF D++ A H++ GAKK
Sbjct: 118 VKPVGDDAISVDGKVIKVVSDRNPLNLPWGELGIDLVIEGTGVFVDREGAGKHIQAGAKK 177
Query: 121 VIISAPSK-DAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 179
V+I+AP K D P +VVGVN ++YK I+SNASCTTNCLAP KV+ KFGI++G MTT
Sbjct: 178 VLITAPGKGDIPTYVVGVNADDYKHSDPIISNASCTTNCLAPFVKVLDQKFGIIKGTMTT 237
Query: 180 VHSITG 185
HS TG
Sbjct: 238 THSYTG 243
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 164 bits (416), Expect = 4e-50
Identities = 74/185 (40%), Positives = 115/185 (62%), Gaps = 7/185 (3%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
+K+GINGFGRIGRL R ++E V +NDP + ++ ++DSVHG+W HHE+
Sbjct: 2 TIKVGINGFGRIGRLALRAAWDWPELEFVQINDPAGDAATLAHLLEFDSVHGRW-HHEVT 60
Query: 63 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 122
+ D ++ K + + + W +G + V+E++GV K A+L G K+V+
Sbjct: 61 AEGD-AIVINGKRIRTTQNKAIADTDW--SGCDVVIEASGVMKTKALLQAYLDQGVKRVV 117
Query: 123 ISAPSKDAPMF--VVGVNENEYKPELN-IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT 179
++AP K+ + V+GVN++ + P ++ IV+ ASCTTNCLAP+ KVIH+K GI G MTT
Sbjct: 118 VTAPVKEEGVLNIVMGVNDHLFDPAIHPIVTAASCTTNCLAPVVKVIHEKLGIKHGSMTT 177
Query: 180 VHSIT 184
+H +T
Sbjct: 178 IHDLT 182
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 160 bits (407), Expect = 1e-48
Identities = 72/186 (38%), Positives = 114/186 (61%), Gaps = 12/186 (6%)
Query: 4 VKIGINGFGRIGRLVARVILQ---RDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHE 60
+++ INGFGRIGR V R + + R ++ +VA+N+ + M ++ KYD+ HG++
Sbjct: 2 IRVAINGFGRIGRNVLRALYESGRRAEITVVAINE-LADAEGMAHLLKYDTSHGRFAW-- 58
Query: 61 LKVKDDKTLLF-GEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAK 119
V+ ++ LF G+ + + R+ +PW E G + V++ TGV+ ++ AH+ GAK
Sbjct: 59 -DVRQERDQLFVGDDAIRLLHERDIASLPWRELGVDVVLDCTGVYGSREDGEAHIAAGAK 117
Query: 120 KVIISAPSK---DAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGL 176
KV+ S P DA + V GVN ++ + E IVSNASCTTNC+ P+ K++ D FGI G
Sbjct: 118 KVLFSHPGSNDLDATV-VYGVNHDQLRAEHRIVSNASCTTNCIIPVIKLLDDAFGIESGT 176
Query: 177 MTTVHS 182
+TT+HS
Sbjct: 177 VTTIHS 182
>gnl|CDD|130595 TIGR01532, E4PD_g-proteo, erythrose-4-phosphate dehydrogenase.
This model represents the small clade of dehydrogenases
in gamma-proteobacteria which utilize NAD+ to oxidize
erythrose-4-phosphate (E4P) to 4-phospho-erythronate, a
precursor for the de novo synthesis of pyridoxine via
4-hydroxythreonine and D-1-deoxyxylulose. This enzyme
activity appears to have evolved from
glyceraldehyde-3-phosphate dehydrogenase, whose
substrate differs only in the lack of one carbon
relative to E4P. Accordingly, this model is very close
to the corresponding models for GAPDH, and those
sequences which hit above trusted here invariably hit
between trusted and noise to the GAPDH model
(TIGR01534). Similarly, it may be found that there are
species outside of the gamma proteobacteria which
synthesize pyridoxine and have more than one aparrent
GAPDH gene of which one may have E4PD activity - this
may necessitate a readjustment of these models.
Alternatively, some of the GAPDH enzymes may prove to be
bifunctional in certain species [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pyridoxine].
Length = 325
Score = 145 bits (368), Expect = 5e-43
Identities = 72/184 (39%), Positives = 115/184 (62%), Gaps = 10/184 (5%)
Query: 5 KIGINGFGRIGRLVARVILQ---RDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHEL 61
++ INGFGRIGR V R + + R ++ +VA+N+ M ++ KYD+ HG++
Sbjct: 1 RVAINGFGRIGRNVLRALYESGRRAEITVVAINE-LADAAGMAHLLKYDTSHGRFAW--- 56
Query: 62 KVKDDKTLLF-GEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKK 120
+V+ D+ LF G+ + V R+ + +PW E G + V++ TGV+ ++ AH+ GAKK
Sbjct: 57 EVRQDRDQLFVGDDAIRVLHERSLQSLPWRELGVDLVLDCTGVYGSREHGEAHIAAGAKK 116
Query: 121 VIISAP-SKDAPMFVV-GVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMT 178
V+ S P + D +V GVN+++ + E IVSNASCTTNC+ P+ K++ D +GI G +T
Sbjct: 117 VLFSHPGASDLDATIVYGVNQDQLRAEHRIVSNASCTTNCIVPVIKLLDDAYGIESGTIT 176
Query: 179 TVHS 182
T+HS
Sbjct: 177 TIHS 180
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 124 bits (314), Expect = 7e-34
Identities = 65/190 (34%), Positives = 104/190 (54%), Gaps = 19/190 (10%)
Query: 10 GFGRIGRLVARVILQR----DDVELVAV-------NDPFITTDYMTYMFKYDSVHGQWKH 58
GFGRIGRL+AR+++++ + + L A+ D + + + DSVHG +
Sbjct: 134 GFGRIGRLLARLLIEKTGGGNGLRLRAIVVRKGSEGD----LEKRASLLRRDSVHGPFNG 189
Query: 59 HELKVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAE--YVVESTGVFTDKDKAAAHLKG 116
+++ ++ + V +PEE+ + G VV++TG + D++ + HLK
Sbjct: 190 TITVDEENNAIIANGNYIQVIYANSPEEVDYTAYGINNALVVDNTGKWRDEEGLSQHLKS 249
Query: 117 -GAKKVIISAPSK-DAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVE 174
G KV+++AP K D V GVN ++ E IVS ASCTTN + P+ K ++DK+GIV
Sbjct: 250 KGVAKVLLTAPGKGDIKNIVHGVNHSDITDEDKIVSAASCTTNAITPVLKAVNDKYGIVN 309
Query: 175 GLMTTVHSIT 184
G + TVHS T
Sbjct: 310 GHVETVHSYT 319
>gnl|CDD|173546 PTZ00353, PTZ00353, glycosomal glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 342
Score = 114 bits (288), Expect = 4e-31
Identities = 53/180 (29%), Positives = 94/180 (52%)
Query: 4 VKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKV 63
+ +GINGFG +G+ V L V +VAVND ++ Y+ Y+ + +S ++V
Sbjct: 3 ITVGINGFGPVGKAVLFASLTDPLVTVVAVNDASVSIAYIAYVLEQESPLSAPDGASIRV 62
Query: 64 KDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVII 123
++ +L G + + V + EI W + G +YVVE TG+++ + + H+ GGAK V +
Sbjct: 63 VGEQIVLNGTQKIRVSAKHDLVEIAWRDYGVQYVVECTGLYSTRSRCWGHVTGGAKGVFV 122
Query: 124 SAPSKDAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSI 183
+ S DAP + G N+ L + + LAP+ + +H+ +G+ E T +H +
Sbjct: 123 AGQSADAPTVMAGSNDERLSASLPVCCAGAPIAVALAPVIRALHEVYGVEECSYTAIHGM 182
>gnl|CDD|217235 pfam02800, Gp_dh_C, Glyceraldehyde 3-phosphate dehydrogenase,
C-terminal domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
C-terminal domain is a mixed alpha/antiparallel beta
fold.
Length = 157
Score = 57.2 bits (139), Expect = 9e-11
Identities = 19/27 (70%), Positives = 23/27 (85%)
Query: 159 LAPLAKVIHDKFGIVEGLMTTVHSITG 185
LAPLAKV++D FGI +GLMTTVH+ T
Sbjct: 1 LAPLAKVLNDNFGIEKGLMTTVHAYTA 27
>gnl|CDD|223214 COG0136, Asd, Aspartate-semialdehyde dehydrogenase [Amino acid
transport and metabolism].
Length = 334
Score = 43.0 bits (102), Expect = 3e-05
Identities = 31/127 (24%), Positives = 54/127 (42%), Gaps = 21/127 (16%)
Query: 71 FGEKPVTVFGVRNPEEIP--WAETGAEYVVESTGVFTDKDKAAAHLKGGAK--KVIISAP 126
FG K + V PE+ + + + V + G + A+ V+I
Sbjct: 47 FGGKSIGV-----PEDAADEFVFSDVDIVFFAAG----GSVSKEVEPKAAEAGCVVIDNS 97
Query: 127 S-----KDAPMFVVGVNEN---EYKPELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMT 178
S D P+ V VN +Y+ I++N +C+T L K +HD FGI +++
Sbjct: 98 SAFRMDPDVPLVVPEVNPEHLIDYQKRGFIIANPNCSTIQLVLALKPLHDAFGIKRVVVS 157
Query: 179 TVHSITG 185
T +++G
Sbjct: 158 TYQAVSG 164
>gnl|CDD|233347 TIGR01296, asd_B, aspartate-semialdehyde dehydrogenase
(peptidoglycan organisms). Two closely related families
of aspartate-semialdehyde dehydrogenase are found. They
differ by a deep split in phylogenetic and percent
identity trees and in gap patterns. This model
represents a branch more closely related to the USG-1
protein than to the other aspartate-semialdehyde
dehydrogenases represented in model TIGR00978 [Amino
acid biosynthesis, Aspartate family].
Length = 338
Score = 42.9 bits (101), Expect = 3e-05
Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 128 KDAPMFVVGVNENEYK--PELNIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSITG 185
D P+ V VN + K I++N +C+T + + K +HD+ I +++T +++G
Sbjct: 99 PDVPLVVPEVNFEDLKEFNPKGIIANPNCSTIQMVVVLKPLHDEAKIKRVVVSTYQAVSG 158
>gnl|CDD|179786 PRK04207, PRK04207, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 341
Score = 41.4 bits (98), Expect = 1e-04
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYM 46
+K+G+NG+G IG+ VA + + D+ELV V DY +
Sbjct: 1 MIKVGVNGYGTIGKRVADAVAAQPDMELVGVAK--TKPDYEARV 42
>gnl|CDD|216304 pfam01113, DapB_N, Dihydrodipicolinate reductase, N-terminus.
Dihydrodipicolinate reductase (DapB) reduces the
alpha,beta-unsaturated cyclic imine,
dihydro-dipicolinate. This reaction is the second
committed step in the biosynthesis of L-lysine and its
precursor meso-diaminopimelate, which are critical for
both protein and cell wall biosynthesis. The N-terminal
domain of DapB binds the dinucleotide NADPH.
Length = 122
Score = 39.5 bits (93), Expect = 1e-04
Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 4 VKIGINGF-GRIGRLVARVILQRDDVELVAV 33
+K+ + G GR+GR + + IL+ D ELVA
Sbjct: 1 IKVAVVGASGRMGRELIKAILEAPDFELVAA 31
>gnl|CDD|234595 PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional.
Length = 257
Score = 38.6 bits (91), Expect = 8e-04
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 3 KVKIGINGF-GRIGRLVARVILQRDDVELVAV 33
+K+ + G GR+GR + + +D+ELVA
Sbjct: 1 MIKVAVAGASGRMGRELIEAVEAAEDLELVAA 32
>gnl|CDD|223366 COG0289, DapB, Dihydrodipicolinate reductase [Amino acid
transport and metabolism].
Length = 266
Score = 38.0 bits (89), Expect = 0.001
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 3 KVKIGINGF-GRIGRLVARVILQRDDVELVAV 33
+K+ + G GR+GR + R +L+ D+ELVA
Sbjct: 2 MIKVAVAGASGRMGRTLIRAVLEAPDLELVAA 33
>gnl|CDD|233638 TIGR01921, DAP-DH, diaminopimelate dehydrogenase. This model
represents the diaminopimelate dehydrogenase enzyme
which provides an alternate (shortcut) route of lysine
buiosynthesis in Corynebacterium, Bacterioides,
Porphyromonas and scattered other species. The enzyme
from Corynebacterium glutamicum has been crystallized
and characterized.
Length = 324
Score = 35.7 bits (82), Expect = 0.009
Identities = 15/33 (45%), Positives = 22/33 (66%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAV 33
M K++ I G+G +GR V + I Q+ D+ELV V
Sbjct: 1 MSKIRAAIVGYGNLGRSVEKAIQQQPDMELVGV 33
>gnl|CDD|130609 TIGR01546, GAPDH-II_archae, glyceraldehyde-3-phosphate
dehydrogenase, type II. This model describes the type
II glyceraldehyde-3-phosphate dehydrogenases which are
limited to archaea. These enzymes catalyze the
interconversion of 1,3-diphosphoglycerate and
glyceraldehyde-3-phosphate, a central step in
glycolysis and gluconeogenesis. In archaea, either NAD
or NADP may be utilized as the cofactor. The class I
GAPDH's from bacteria and eukaryotes are covered by
TIGR01534. All of the members of the seed are
characterized. See, for instance. This model is very
solid, there are no species falling between trusted and
noise at this time. The closest relatives scoring in
the noise are the class I GAPDH's.
Length = 333
Score = 35.2 bits (81), Expect = 0.011
Identities = 13/28 (46%), Positives = 22/28 (78%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELVAV 33
+G+NG+G IG+ VA + ++DD++LV V
Sbjct: 1 VGVNGYGTIGKRVADAVTKQDDMKLVGV 28
>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 = 35.2 bits (82), Expect = 0.012
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 5 KIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYM 46
+GI GFGRIGR V +L+ + V V DP++ +
Sbjct: 152 TVGIVGFGRIGRAVVE-LLRPFGLR-VLVYDPYLPAAEAAAL 191
>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 = 35.2 bits (82), Expect = 0.012
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTD 41
+ +GI GFG IGR VA+ L+ E V V DP++ +
Sbjct: 145 LRGKTVGIVGFGAIGRRVAKR-LKAFGAE-VLVYDPYVDPE 183
>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 = 34.8 bits (81), Expect = 0.015
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 2 GKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDY 42
GK +GI G GRIG+ VAR L ++ V DP+ ++
Sbjct: 142 GK-TLGIIGLGRIGKAVAR-RLSGFGMK-VLAYDPYPDEEF 179
>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 = 34.0 bits (79), Expect = 0.022
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 5 KIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVH 53
+GI G GRIGR VAR L+ ++++A D + + +Y S+
Sbjct: 37 TVGIIGLGRIGRAVAR-RLKAFGMKVIAY-DRYPKAEAEALGARYVSLD 83
>gnl|CDD|201778 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilise NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 32.6 bits (75), Expect = 0.040
Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 4 VKIGINGFGRIGRLVARVILQ-RDDVELVAVNDP 36
+++GI G G+IGR R + + +D ELV + DP
Sbjct: 1 LRVGIVGAGKIGRRHLRALNESQDGAELVGILDP 34
>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 = 32.9 bits (76), Expect = 0.069
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTD 41
GK +GI G G IGR VAR L+ VE++ D F +
Sbjct: 141 SGK-TVGIVGLGNIGRAVAR-RLRGFGVEVIYY-DRFRDPE 178
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 32.7 bits (76), Expect = 0.089
Identities = 15/38 (39%), Positives = 24/38 (63%), Gaps = 3/38 (7%)
Query: 2 GKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFIT 39
GK +GI G GRIG VA+ + ++++A DP+I+
Sbjct: 140 GKT-LGIIGLGRIGSEVAKR-AKAFGMKVIA-YDPYIS 174
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 32.4 bits (75), Expect = 0.10
Identities = 17/38 (44%), Positives = 25/38 (65%), Gaps = 3/38 (7%)
Query: 2 GKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFIT 39
GK +GI G GRIGR VAR + ++++A DP+I+
Sbjct: 138 GKT-LGIVGLGRIGREVAR-RARAFGMKVLA-YDPYIS 172
>gnl|CDD|169409 PRK08374, PRK08374, homoserine dehydrogenase; Provisional.
Length = 336
Score = 32.1 bits (73), Expect = 0.14
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 3 KVKIGINGFGRIGRLVARVILQRDDV 28
+VK+ I GFG +GR VA V+ ++ V
Sbjct: 2 EVKVSIFGFGNVGRAVAEVLAEKSRV 27
>gnl|CDD|237845 PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 334
Score = 32.1 bits (74), Expect = 0.14
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 129 DAPMFVVGVNENEYK--PELNIVSNASCTTNCLAPLAKVIHDKFGI 172
D P+ V VN + I++N +C+T + K +HD GI
Sbjct: 102 DVPLVVPEVNPEALAEHRKKGIIANPNCSTIQMVVALKPLHDAAGI 147
>gnl|CDD|240624 cd05299, CtBP_dh, C-terminal binding protein (CtBP),
D-isomer-specific 2-hydroxyacid dehydrogenases related
repressor. The transcriptional corepressor CtBP is a
dehydrogenase with sequence and structural similarity to
the d2-hydroxyacid dehydrogenase family. CtBP was
initially identified as a protein that bound the PXDLS
sequence at the adenovirus E1A C terminus, causing the
loss of CR-1-mediated transactivation. CtBP binds NAD(H)
within a deep cleft, undergoes a conformational change
upon NAD binding, and has NAD-dependent dehydrogenase
activity.
Length = 312
Score = 32.1 bits (74), Expect = 0.14
Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 18/50 (36%)
Query: 6 IGINGFGRIGRLVA--------RVILQRDDVELVAVNDPFITTDYMTYMF 47
+G+ GFGRIGR VA RVI DP++
Sbjct: 145 LGLVGFGRIGRAVAKRAKAFGFRVI----------AYDPYVPDGVAALGG 184
>gnl|CDD|240633 cd12156, HPPR, Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific
2-hydroxyacid-related dehydrogenase.
Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the
NADP-dependent reduction of hydroxyphenylpyruvates,
hydroxypyruvate, or pyruvate to its respective lactate.
HPPR acts as a dimer and is related to D-isomer-specific
2-hydroxyacid dehydrogenases, a superfamily that
includes 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 = 301
Score = 31.7 bits (73), Expect = 0.20
Identities = 12/19 (63%), Positives = 15/19 (78%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK ++GI G GRIGR +AR
Sbjct: 141 GK-RVGIVGLGRIGRAIAR 158
>gnl|CDD|223189 COG0111, SerA, Phosphoglycerate dehydrogenase and related
dehydrogenases [Amino acid transport and metabolism].
Length = 324
Score = 31.5 bits (72), Expect = 0.22
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFI 38
GK +GI G GRIGR VA+ L+ ++++ DP+
Sbjct: 141 AGK-TVGIIGLGRIGRAVAKR-LKAFGMKVIGY-DPYS 175
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. 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 = 309
Score = 30.8 bits (71), Expect = 0.29
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK +GI G GRIG+ VAR
Sbjct: 144 GK-TLGIVGMGRIGQAVAR 161
>gnl|CDD|129147 TIGR00036, dapB, dihydrodipicolinate reductase. [Amino acid
biosynthesis, Aspartate family].
Length = 266
Score = 30.8 bits (70), Expect = 0.30
Identities = 39/144 (27%), Positives = 63/144 (43%), Gaps = 22/144 (15%)
Query: 4 VKIGING-FGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
+K+ + G GR+GR + + L + ++LVA + ++ T + + +
Sbjct: 2 IKVAVAGAAGRMGRELIKAALAAEGLQLVAAFERHGSSLQGTDAGELAGI----GKVGVP 57
Query: 63 VKDDKTLLFGEKPVTV-F----GVRNPEEIPWAETGAEYVVESTGVFTDKDK---AAAHL 114
V DD + + V + F GV N + E G VV +TG F+++DK A
Sbjct: 58 VTDDLEAVETDPDVLIDFTTPEGVLNHLKFA-LEHGVRLVVGTTG-FSEEDKQELADLAE 115
Query: 115 KGGAKKVIISAPSKDAPMFVVGVN 138
K G VI AP F +GVN
Sbjct: 116 KAGIAAVI-------APNFSIGVN 132
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 30.6 bits (70), Expect = 0.47
Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 9/44 (20%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRD---------DVELVAVND 35
M VK+G+ G G +G V ++ ++ ++ +VAV D
Sbjct: 1 MKTVKVGLLGLGTVGSGVLEILAEKQEELRKRAGIEIRVVAVAD 44
>gnl|CDD|211797 TIGR03212, uraD_N-term-dom, putative urate catabolism protein.
This model represents a protein that is predominantly
found just upstream of the UraD protein (OHCU
decarboxylase) and in a number of instances as a
N-terminal fusion with it. UraD itself catalyzes the
last step in the catabolism of urate to allantoate. The
function of this protein is presently unknown. It shows
homology with the pfam01522 polysaccharide deacetylase
domain family.
Length = 297
Score = 30.1 bits (68), Expect = 0.57
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 16/52 (30%)
Query: 43 MTYMFKYDSVHGQWKHHELKVKDDKTLLFGEK--PVTVFGV-----RNPEEI 87
M +++Y S G W+ L F E+ P+TVFGV RNPE +
Sbjct: 67 MESLYEYGSRAGFWRLLRL---------FTERGLPLTVFGVAMALARNPEAV 109
>gnl|CDD|233220 TIGR00978, asd_EA, aspartate-semialdehyde dehydrogenase
(non-peptidoglycan organisms). Two closely related
families of aspartate-semialdehyde dehydrogenase are
found. They differ by a deep split in phylogenetic and
percent identity trees and in gap patterns. Separate
models are built for the two types in order to exclude
the USG-1 protein, found in several species, which is
specifically related to the Bacillus subtilis type of
aspartate-semialdehyde dehydrogenase. Members of this
type are found primarily in organisms that lack
peptidoglycan [Amino acid biosynthesis, Aspartate
family].
Length = 341
Score = 30.1 bits (68), Expect = 0.67
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 148 IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSITG 185
IV+N +CTT L K + D FGI + +TT+ +++G
Sbjct: 140 IVTNPNCTTAGLTLALKPLIDAFGIKKVHVTTMQAVSG 177
>gnl|CDD|240646 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases.
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 = 308
Score = 29.4 bits (67), Expect = 0.92
Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 2 GKVKIGINGFGRIGRLVARV 21
GK +GI G GRIG VAR+
Sbjct: 142 GK-TLGIVGLGRIGARVARI 160
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 29.7 bits (67), Expect = 0.93
Identities = 44/170 (25%), Positives = 69/170 (40%), Gaps = 40/170 (23%)
Query: 5 KIGINGFGRIGRLVARVILQRD--DVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELK 62
KI + G G+IG VA +ILQ++ DV L YD + G + L
Sbjct: 7 KISMIGAGQIGSTVALLILQKNLGDVVL------------------YDVIKGVPQGKALD 48
Query: 63 VKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVI 122
+K TL+ + + G N E+I ++ VV + GV ++ L K++
Sbjct: 49 LKHFSTLV--GSNINILGTNNYEDI----KDSDVVVITAGVQRKEEMTREDLLTINGKIM 102
Query: 123 ISAPSKDAPMFVVGVNENEYKPELNIVSNASCTTNCLAPLAKVIHDKFGI 172
S V + +Y P ++ C TN L + KV +K GI
Sbjct: 103 KS----------VAESVKKYCPNAFVI----CVTNPLDCMVKVFQEKSGI 138
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 29.3 bits (66), Expect = 1.0
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSV 52
+ +K+ + G GRIG VA++ + ++VA DPF TY+ D++
Sbjct: 144 IKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAY-DPFPNAKAATYVDYKDTI 194
>gnl|CDD|223980 COG1052, LdhA, Lactate dehydrogenase and related dehydrogenases
[Energy production and conversion / Coenzyme metabolism
/ General function prediction only].
Length = 324
Score = 29.5 bits (67), Expect = 1.1
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK +GI G GRIG+ VAR
Sbjct: 146 GK-TLGIIGLGRIGQAVAR 163
>gnl|CDD|181041 PRK07574, PRK07574, formate dehydrogenase; Provisional.
Length = 385
Score = 29.3 bits (66), Expect = 1.1
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 5 KIGINGFGRIGRLVAR 20
+GI G GRIG V R
Sbjct: 194 TVGIVGAGRIGLAVLR 209
>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 = 29.5 bits (67), Expect = 1.1
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDDVELVAVNDPFITTD 41
GK +G+ G G IGRLVA ++++ DP+++ +
Sbjct: 134 RGK-TLGVIGLGNIGRLVAN-AALALGMKVIGY-DPYLSVE 171
>gnl|CDD|235763 PRK06270, PRK06270, homoserine dehydrogenase; Provisional.
Length = 341
Score = 29.4 bits (67), Expect = 1.1
Identities = 12/42 (28%), Positives = 25/42 (59%), Gaps = 9/42 (21%)
Query: 3 KVKIGINGFGRIGRLVARVILQRD---------DVELVAVND 35
++KI + GFG +G+ VA ++ ++ D+++VA+ D
Sbjct: 2 EMKIALIGFGGVGQGVAELLAEKREYLKKRYGLDLKVVAIAD 43
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, 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 = 317
Score = 29.1 bits (66), Expect = 1.2
Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 2 GKVKIGINGFGRIGRLVAR 20
GK +GI G GRIG+ VAR
Sbjct: 144 GKT-LGIIGMGRIGQAVAR 161
>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 = 29.0 bits (66), Expect = 1.2
Identities = 13/20 (65%), Positives = 16/20 (80%), Gaps = 1/20 (5%)
Query: 2 GKVKIGINGFGRIGRLVARV 21
GK +GI GFGRIGR VA++
Sbjct: 139 GKT-LGIIGFGRIGREVAKI 157
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms
this enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 29.2 bits (66), Expect = 1.3
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELVAV 33
+ I G G +G+ VA ++ + D+E+
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVA 28
>gnl|CDD|99958 cd05529, Bromo_WDR9_I_like, Bromodomain; WDR9 repeat I_like
subfamily. WDR9 is a human gene located in the Down
Syndrome critical region-2 of chromosome 21. It encodes
for a nuclear protein containing WD40 repeats and two
bromodomains, which may function as a transcriptional
regulator involved in chromatin remodeling and play a
role in embryonic development. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can interact
specifically with acetylated lysine.
Length = 128
Score = 28.1 bits (63), Expect = 1.5
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 5/63 (7%)
Query: 83 NPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGGAKKVIISAPSKDAPMFVVGVNENEY 142
NP W E +D+ L G K+++S + A F V+ +
Sbjct: 3 NPLSSEW-----ELFDPGWEQPHIRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRAW 57
Query: 143 KPE 145
P+
Sbjct: 58 YPD 60
>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 = 28.7 bits (65), Expect = 1.6
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 5 KIGINGFGRIGRLVAR 20
+GI G GRIG+ VA+
Sbjct: 142 TVGIVGLGRIGQRVAK 157
>gnl|CDD|235287 PRK04342, PRK04342, DNA topoisomerase VI subunit A; Provisional.
Length = 367
Score = 28.7 bits (65), Expect = 1.7
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 11/45 (24%)
Query: 83 NPEEIPWAETGAEYV--VESTGV--------FTDKDKAA-AHLKG 116
N + I + + A++V VE G+ F K A HLKG
Sbjct: 179 NVDNIEFVDVDADFVLAVEKGGMFQRLVEEGFWKKYNAILVHLKG 223
>gnl|CDD|215144 PLN02256, PLN02256, arogenate dehydrogenase.
Length = 304
Score = 28.5 bits (64), Expect = 1.8
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQR 25
K+KIGI GFG G+ +A+ +++
Sbjct: 34 SRKLKIGIVGFGNFGQFLAKTFVKQ 58
>gnl|CDD|224626 COG1712, COG1712, Predicted dinucleotide-utilizing enzyme
[General function prediction only].
Length = 255
Score = 28.5 bits (64), Expect = 1.9
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 5 KIGINGFGRIGRLVARVILQ-RDDVELVAVND 35
K+GI G G IG+ + ++ R D ELVAV D
Sbjct: 2 KVGIVGCGAIGKFLLELVRDGRVDFELVAVYD 33
>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 = 28.6 bits (65), Expect = 1.9
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 5 KIGINGFGRIGRLVARVILQRDDVELVAVNDPF 37
+GI G G +G +AR L+ + V + DP
Sbjct: 117 TVGIVGVGNVGSRLARR-LEALGMN-VLLCDPP 147
>gnl|CDD|240645 cd12168, Mand_dh_like, D-Mandelate Dehydrogenase-like
dehydrogenases. D-Mandelate dehydrogenase (D-ManDH),
identified as an enzyme that interconverts
benzoylformate and D-mandelate, is a D-2-hydroxyacid
dehydrogenase family member that catalyzes the
conversion of c3-branched 2-ketoacids. D-ManDH exhibits
broad substrate specificities for 2-ketoacids with large
hydrophobic side chains, particularly those with
C3-branched side chains. 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. Glycerate dehydrogenase catalyzes the
reaction (R)-glycerate + NAD+ to hydroxypyruvate + NADH
+ H+. 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 = 321
Score = 28.7 bits (65), Expect = 1.9
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 1 MGKVKIGINGFGRIGRLVAR 20
GK +GI G G IG+ +AR
Sbjct: 153 RGKT-LGILGLGGIGKAIAR 171
>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 = 28.4 bits (64), Expect = 2.0
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 1 MGKVKIGINGFGRIGRLVARV 21
GK +G+ G GRIGR VAR+
Sbjct: 138 AGKT-LGVVGTGRIGRRVARI 157
>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 = 28.4 bits (64), Expect = 2.2
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDS 51
+G+ G G+IGR VA+ + ++++A DPF + KY S
Sbjct: 146 VGVVGTGKIGRAVAQ-RAKGFGMKVIAY-DPFRNPELEDKGVKYVS 189
>gnl|CDD|235783 PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
Length = 426
Score = 28.5 bits (65), Expect = 2.2
Identities = 10/42 (23%), Positives = 20/42 (47%), Gaps = 9/42 (21%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDD---------VELVAV 33
M +K+G+ G G +G V R++ + + +E+ V
Sbjct: 1 MKPLKVGLLGLGTVGSGVVRILEENAEEIAARAGRPIEIKKV 42
>gnl|CDD|185742 cd09001, GH43_XYL_2, Glycosyl hydrolase family 43,
beta-D-xylosidase. This glycosyl hydrolase family 43
(GH43) includes mostly enzymes that have been
characterized to have beta-1,4-xylosidase
(beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC
3.2.1.37) activity. They are part of an array of
hemicellulases that are involved in the final breakdown
of plant cell-wall whereby they degrade xylan. They
hydrolyze beta-1,4 glycosidic bonds between two xylose
units in short xylooligosaccharides. These are inverting
enzymes (i.e. they invert the stereochemistry of the
anomeric carbon atom of the substrate) that have an
aspartate as the catalytic general base, a glutamate as
the catalytic general acid and another aspartate that is
responsible for pKa modulation and orienting the
catalytic acid. A common structural feature of GH43
enzymes is a 5-bladed beta-propeller domain that
contains the catalytic acid and catalytic base. A long
V-shaped groove, partially enclosed at one end, forms a
single extended substrate-binding surface across the
face of the propeller.
Length = 269
Score = 28.3 bits (64), Expect = 2.3
Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 37 FITTDYMTYMFKYDSVHGQWKHHEL-KVKDDKTLLF 71
F T TY++ D G W L D +LLF
Sbjct: 92 FCTNTGGTYIYTADDPEGPWTKTALDGGYHDPSLLF 127
>gnl|CDD|183914 PRK13243, PRK13243, glyoxylate reductase; Reviewed.
Length = 333
Score = 28.2 bits (63), Expect = 2.4
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 6 IGINGFGRIGRLVAR 20
IGI GFGRIG+ VAR
Sbjct: 153 IGIIGFGRIGQAVAR 167
>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 = 3.1
Identities = 11/20 (55%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 2 GKVKIGINGFGRIGRLVARV 21
GK +GI G+G IG+ VAR+
Sbjct: 147 GK-TLGIIGYGNIGQAVARI 165
>gnl|CDD|149729 pfam08759, DUF1792, Domain of unknown function (DUF1792). This
putative domain is probably missannotated as a glycosyl
transferase 8 family member. This domain is found at the
C-terminus of proteins that also contain the glycosyl
transferase domain at the N-terminus.
Length = 225
Score = 27.6 bits (62), Expect = 3.3
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 37 FITTDYMTYMFKYDSVHGQWKHHELKVKDDKTLLFGEKPVTVFGVRN 83
FI+ Y+ Y K S + H ++ ++ +L E + GV N
Sbjct: 88 FISRPYIDYKDKSKSAR--YFHKLKQIWQNRDILIVEGEKSRSGVGN 132
>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 = 27.7 bits (62), Expect = 3.4
Identities = 11/38 (28%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYM 43
+GI G+G IG VA ++ + + +++A DP+++ + +
Sbjct: 150 VGIIGYGNIGSRVAEILKEGFNAKVLAY-DPYVSEEVI 186
>gnl|CDD|240640 cd12163, 2-Hacid_dh_5, 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 = 334
Score = 28.0 bits (63), Expect = 3.4
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 5 KIGINGFGRIGRLVARV 21
++GI G+G IGR AR+
Sbjct: 135 RVGILGYGSIGRQTARL 151
>gnl|CDD|240662 cd12186, LDH, D-Lactate dehydrogenase and D-2-Hydroxyisocaproic
acid dehydrogenase (D-HicDH), NAD-binding and catalytic
domains. D-Lactate dehydrogenase (LDH) catalyzes the
interconversion of pyruvate and lactate, and is a member
of the 2-hydroxyacid dehydrogenases family. LDH is
homologous to D-2-hydroxyisocaproic acid
dehydrogenase(D-HicDH) and shares the 2 domain structure
of formate dehydrogenase. D-HicDH is a NAD-dependent
member of the hydroxycarboxylate dehydrogenase family,
and shares the Rossmann fold typical of many NAD binding
proteins. HicDH from Lactobacillus casei forms a monomer
and catalyzes the reaction R-CO-COO(-) + NADH + H+ to
R-COH-COO(-) + NAD+. D-HicDH, like the structurally
distinct L-HicDH, exhibits low side-chain R specificity,
accepting a wide range of 2-oxocarboxylic acid side
chains. Formate/glycerate and related dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-Adenosylhomocysteine Hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 329
Score = 27.5 bits (62), Expect = 3.8
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 1 MGKVKIGINGFGRIGRLVAR 20
+ + +GI G GRIG A+
Sbjct: 143 IRDLTVGIIGTGRIGSAAAK 162
>gnl|CDD|223745 COG0673, MviM, Predicted dehydrogenases and related proteins
[General function prediction only].
Length = 342
Score = 27.5 bits (61), Expect = 3.9
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 1 MGKVKIGINGFGRIGRL-VARVILQRDD-VELVAVNDP 36
M +++GI G G I + +ELVAV D
Sbjct: 1 MKMIRVGIIGAGGIAGKAHLPALAALGGGLELVAVVDR 38
>gnl|CDD|177941 PLN02306, PLN02306, hydroxypyruvate reductase.
Length = 386
Score = 27.5 bits (61), Expect = 4.4
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 16/82 (19%)
Query: 6 IGINGFGRIGRLVARVILQRDDVELVAVNDPFITTDYMTYMFKYDSVHGQWKHHELKVKD 65
+G+ G GRIG AR++++ + L+ D + +T + K+ + +GQ+
Sbjct: 168 VGVIGAGRIGSAYARMMVEGFKMNLIYY-DLYQSTR----LEKFVTAYGQFLKAN----- 217
Query: 66 DKTLLFGEKPVTVFGVRNPEEI 87
GE+PVT + EE+
Sbjct: 218 ------GEQPVTWKRASSMEEV 233
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 27.3 bits (61), Expect = 5.0
Identities = 10/43 (23%), Positives = 21/43 (48%)
Query: 93 GAEYVVESTGVFTDKDKAAAHLKGGAKKVIISAPSKDAPMFVV 135
GA+ V+++ G +A L+ G + V++ S P+ +
Sbjct: 201 GADVVIDAVGGPETLAQALRLLRPGGRIVVVGGTSGGPPLDDL 243
>gnl|CDD|224459 COG1542, COG1542, Uncharacterized conserved protein [Function
unknown].
Length = 593
Score = 27.5 bits (61), Expect = 5.4
Identities = 25/100 (25%), Positives = 34/100 (34%), Gaps = 31/100 (31%)
Query: 62 KVKDDKTLLFGEKPVTVFGVR-----------NPEEIPWAETGAEYVVESTGVFTDKDKA 110
KV +D EK VT GV+ N E W E E + S G T+K +
Sbjct: 358 KVLED-----LEKSVTADGVKAITYTEEFDAPNAE---WYEQAKEEGLVSRGAITEKGRL 409
Query: 111 AA----------HLKGGAKKVIISAPSK--DAPMFVVGVN 138
A +L KV+I P K + +
Sbjct: 410 YAKLSKTIKRKPYLTKYEIKVLIKIPRKYIKRGELIEDIQ 449
>gnl|CDD|215812 pfam00239, Resolvase, Resolvase, N terminal domain. The N-terminal
domain of the resolvase family (this family) contains
the active site and the dimer interface. The extended
arm at the C-terminus of this domain connects to the
C-terminal helix-turn-helix domain of resolvase - see
pfam02796.
Length = 139
Score = 26.8 bits (60), Expect = 5.4
Identities = 8/40 (20%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 13 RIGRLVARVI-----LQRDDVELVAVNDPFITTDYMTYMF 47
R+GR + ++ L+ V LV++++ T+ +
Sbjct: 68 RLGRSLRDLLELVEELREKGVRLVSLDEGIDTSTPAGRLL 107
>gnl|CDD|237341 PRK13302, PRK13302, putative L-aspartate dehydrogenase;
Provisional.
Length = 271
Score = 27.1 bits (60), Expect = 5.7
Identities = 12/46 (26%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 1 MGKVKIGINGFGRIGRLVARVILQRDD---VELVAVNDPFITTDYM 43
++++ I G G IG+ +A+ + + + VAV DP D++
Sbjct: 4 RPELRVAIAGLGAIGKAIAQALDRGLPGLTLSAVAVRDPQRHADFI 49
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 27.3 bits (60), Expect = 6.3
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 3 KVKIGINGFGRIGRLVARVILQR 25
K+KI I GFG G+ +A+ ++++
Sbjct: 369 KLKIAIVGFGNFGQFLAKTMVKQ 391
>gnl|CDD|180598 PRK06512, PRK06512, thiamine-phosphate pyrophosphorylase;
Provisional.
Length = 221
Score = 26.6 bits (59), Expect = 7.0
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 6/44 (13%)
Query: 90 AETGAEYVVESTGVFTDKDKAAAHLKGGAKKVIISAPSKDAPMF 133
AETGAE+V VF D A + A + AP F
Sbjct: 182 AETGAEFVALERAVFDAHDPPLAVAQANALL------DEKAPRF 219
>gnl|CDD|130271 TIGR01204, bioW, 6-carboxyhexanoate--CoA ligase. Alternate name:
pimeloyl-CoA synthase [Biosynthesis of cofactors,
prosthetic groups, and carriers, Biotin].
Length = 232
Score = 26.8 bits (59), Expect = 7.4
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 62 KVKDDKTLLFGEKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHL 114
KVKD + + F ++ + +PEE A A + GV + K A +
Sbjct: 47 KVKDFEIVKFNPLKISTYSFSSPEE---ARKFARKKLTQEGVSEEVAKKAVEI 96
>gnl|CDD|176257 cd08297, CAD3, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 26.7 bits (60), Expect = 7.8
Identities = 11/40 (27%), Positives = 17/40 (42%)
Query: 91 ETGAEYVVESTGVFTDKDKAAAHLKGGAKKVIISAPSKDA 130
E GA+ V+ + GGA V+++A S A
Sbjct: 208 ELGADAFVDFKKSDDVEAVKELTGGGGAHAVVVTAVSAAA 247
>gnl|CDD|212101 cd10789, GH38N_AMII_ER_cytosolic, N-terminal catalytic domain of
endoplasmic reticulum(ER)/cytosolic class II
alpha-mannosidases; glycoside hydrolase family 38
(GH38). The subfamily is represented by Saccharomyces
cerevisiae vacuolar alpha-mannosidase Ams1, rat
ER/cytosolic alpha-mannosidase Man2C1, and similar
proteins. Members in this family share high sequence
similarity. None of them have any classical signal
sequence or membrane spanning domains, which are typical
of sorting or targeting signals. Ams1 functions as a
second resident vacuolar hydrolase in S. cerevisiae. It
aids in recycling macromolecular components of the cell
through hydrolysis of terminal, non-reducing
alpha-d-mannose residues. Ams1 utilizes both the
cytoplasm to vacuole targeting (Cvt, nutrient-rich
conditions) and autophagic (starvation conditions)
pathways for biosynthetic delivery to the vacuole.
Man2C1is involved in oligosaccharide catabolism in both
the ER and cytosol. It can catalyze the cobalt-dependent
cleavage of alpha 1,2-, alpha 1,3-, and alpha 1,6-linked
mannose residues. Members in this family are retaining
glycosyl hydrolases of family GH38 that employs a
two-step mechanism involving the formation of a covalent
glycosyl-enzyme complex. Two carboxylic acids positioned
within the active site act in concert: one as a
catalytic nucleophile and the other as a general
acid/base catalyst.
Length = 252
Score = 26.7 bits (60), Expect = 8.2
Identities = 9/35 (25%), Positives = 14/35 (40%)
Query: 37 FITTDYMTYMFKYDSVHGQWKHHELKVKDDKTLLF 71
FI T Y + + W++ K D+ LL
Sbjct: 173 FIPTGYYNGDLTPEEILEAWRNFRDKDVSDELLLL 207
>gnl|CDD|226961 COG4598, HisP, ABC-type histidine transport system, ATPase
component [Amino acid transport and metabolism].
Length = 256
Score = 26.6 bits (59), Expect = 8.2
Identities = 17/45 (37%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 73 EKPVTVFGVRNPEEIPWAETGAEYVVESTGVFTDKDKAAAHLKGG 117
E PV V GV E A AE + G+ D AHL GG
Sbjct: 116 EAPVHVLGVSKAE----AIERAEKYLAKVGIAEKADAYPAHLSGG 156
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 26.2 bits (58), Expect = 8.3
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 88 PWA--ETGAEYVVESTGVFTDKDKAAAHLKGGAKKVIISAP 126
W E G ++E G T + A A L G V + P
Sbjct: 87 DWVSVEPGRRLIIEGVGSLTAANVALASLLGEVLTVWLDGP 127
>gnl|CDD|237343 PRK13304, PRK13304, L-aspartate dehydrogenase; Reviewed.
Length = 265
Score = 26.5 bits (59), Expect = 8.6
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 4 VKIGINGFGRIGRLVARVILQ-RDDVELVAVND 35
+KIGI G G I L+ + IL R + EL A D
Sbjct: 2 LKIGIVGCGAIASLITKAILSGRINAELYAFYD 34
>gnl|CDD|215528 PLN02977, PLN02977, glutathione synthetase.
Length = 478
Score = 26.6 bits (59), Expect = 9.0
Identities = 21/72 (29%), Positives = 29/72 (40%), Gaps = 14/72 (19%)
Query: 58 HHELKVKDDKTLLFGEKPVTVFGVRN-------PEEIPWAETGAEYVVE-STGVFTDKDK 109
E + +D TL +PV V R P E W A ++E S+ V K
Sbjct: 247 AAEGSLDEDGTLTVDGQPVAVVYFRAGYAPTDYPSEAEWR---ARLLLERSSAV---KCP 300
Query: 110 AAAHLKGGAKKV 121
+ A+ G KKV
Sbjct: 301 SIAYHLAGTKKV 312
>gnl|CDD|235131 PRK03562, PRK03562, glutathione-regulated potassium-efflux system
protein KefC; Provisional.
Length = 621
Score = 26.5 bits (59), Expect = 9.1
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 8 INGFGRIGRLVARVIL 23
I GFGR G++V R++L
Sbjct: 405 IAGFGRFGQIVGRLLL 420
>gnl|CDD|240657 cd12180, 2-Hacid_dh_15, 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 = 308
Score = 26.5 bits (59), Expect = 9.6
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 6 IGINGFGRIGRLVAR 20
+GI GFG IG+ +AR
Sbjct: 138 LGIVGFGAIGQALAR 152
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.137 0.404
Gapped
Lambda K H
0.267 0.0856 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,666,817
Number of extensions: 897222
Number of successful extensions: 984
Number of sequences better than 10.0: 1
Number of HSP's gapped: 932
Number of HSP's successfully gapped: 114
Length of query: 188
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 97
Effective length of database: 6,901,388
Effective search space: 669434636
Effective search space used: 669434636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.1 bits)