RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022023
(304 letters)
>gnl|CDD|215131 PLN02237, PLN02237, glyceraldehyde-3-phosphate dehydrogenase B.
Length = 442
Score = 474 bits (1220), Expect = e-168
Identities = 229/273 (83%), Positives = 246/273 (90%), Gaps = 9/273 (3%)
Query: 3 SHSALAPSRIPAITRIPSKTTHSFPTQCSTKRLDVAEFAGLRANAGATYATGARDASFFD 62
+H+ALA SRIPA TR+PSK +H KRL+VAEF+GLRA++ T+A AR+ASFFD
Sbjct: 1 THAALASSRIPATTRLPSKASH--------KRLEVAEFSGLRASSCVTFAKNAREASFFD 52
Query: 63 AVTAQLTPKVAAGSVPVKKETVAKLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSG 122
V +QL PK AGS PV+ ETVAKLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSG
Sbjct: 53 VVASQLAPK-VAGSTPVRGETVAKLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSG 111
Query: 123 GVKNASHLLKYDSLLGTFKADVKIVDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIE 182
GVKNASHLLKYDS+LGTFKADVKIVD+ETISVDGK IKVVSNRDPL+LPWAELGIDIVIE
Sbjct: 112 GVKNASHLLKYDSMLGTFKADVKIVDDETISVDGKPIKVVSNRDPLKLPWAELGIDIVIE 171
Query: 183 GTGVFVDGPGAGKHIQAGAKKVIITAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTT 242
GTGVFVDGPGAGKHIQAGAKKVIITAPAKGADIPTYVVGVNE DYDHEVANIVSNASCTT
Sbjct: 172 GTGVFVDGPGAGKHIQAGAKKVIITAPAKGADIPTYVVGVNEDDYDHEVANIVSNASCTT 231
Query: 243 NCLAPFVKVMDEELGIVKGAMTTTHSYTGDQVI 275
NCLAPFVKV+DEE GIVKG MTTTHSYTGDQ +
Sbjct: 232 NCLAPFVKVLDEEFGIVKGTMTTTHSYTGDQRL 264
>gnl|CDD|215572 PLN03096, PLN03096, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 395
Score = 364 bits (935), Expect = e-126
Identities = 160/237 (67%), Positives = 186/237 (78%), Gaps = 6/237 (2%)
Query: 37 VAEFAGLRANAGATYATGARDASFFDAVTAQLTPKVAAGSVPVKKETVAKLKVAINGFGR 96
+EF+GL++++ T+ + T V++ + T AK+KVAINGFGR
Sbjct: 15 FSEFSGLKSSSAVTFGKRSDS----LDFVVFATSAVSSSGGARRAVTEAKIKVAINGFGR 70
Query: 97 IGRNFLRCWHGRKDSPLDVVVVNDSGGVKNASHLLKYDSLLGTFKADVKIVDNETISVDG 156
IGRNFLRCWHGRKDSPLDVV +ND+GGVK ASHLLKYDS LGTF ADVK V ++ ISVDG
Sbjct: 71 IGRNFLRCWHGRKDSPLDVVAINDTGGVKQASHLLKYDSTLGTFDADVKPVGDDAISVDG 130
Query: 157 KLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVIITAPAKGADIP 216
K+IKVVS+R+PL LPW ELGID+VIEGTGVFVD GAGKHIQAGAKKV+ITAP KG DIP
Sbjct: 131 KVIKVVSDRNPLNLPWGELGIDLVIEGTGVFVDREGAGKHIQAGAKKVLITAPGKG-DIP 189
Query: 217 TYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAMTTTHSYTGDQ 273
TYVVGVN DY H I+SNASCTTNCLAPFVKV+D++ GI+KG MTTTHSYTGDQ
Sbjct: 190 TYVVGVNADDYKHS-DPIISNASCTTNCLAPFVKVLDQKFGIIKGTMTTTHSYTGDQ 245
>gnl|CDD|180962 PRK07403, PRK07403, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 337
Score = 284 bits (729), Expect = 2e-95
Identities = 124/189 (65%), Positives = 150/189 (79%), Gaps = 1/189 (0%)
Query: 87 LKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKNASHLLKYDSLLGTFKADVKI 146
++VAINGFGRIGRNFLRCW GR++S L++V +ND+ + +HLLKYDS+LG AD+
Sbjct: 2 IRVAINGFGRIGRNFLRCWLGRENSQLELVAINDTSDPRTNAHLLKYDSMLGKLNADISA 61
Query: 147 VDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVII 206
+N +I+V+GK IK VS+R+PL LPW E GID++IE TGVFV GA KHIQAGAKKV+I
Sbjct: 62 DEN-SITVNGKTIKCVSDRNPLNLPWKEWGIDLIIESTGVFVTKEGASKHIQAGAKKVLI 120
Query: 207 TAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAMTTT 266
TAP KG DI TYVVGVN +YDHE NI+SNASCTTNCLAP KV+ + GI+KG MTTT
Sbjct: 121 TAPGKGEDIGTYVVGVNHHEYDHEDHNIISNASCTTNCLAPIAKVLHDNFGIIKGTMTTT 180
Query: 267 HSYTGDQVI 275
HSYTGDQ I
Sbjct: 181 HSYTGDQRI 189
>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 = 253 bits (648), Expect = 4e-83
Identities = 99/189 (52%), Positives = 126/189 (66%), Gaps = 4/189 (2%)
Query: 88 KVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKNASHLLKYDSLLGTFKADVKIV 147
KV INGFGRIGR LR + + L+VV +ND ++ ++LLKYDS+ G F+ +V
Sbjct: 1 KVGINGFGRIGRLVLRAILEKPGNDLEVVAINDLTDLEYLAYLLKYDSVHGRFEGEVTAD 60
Query: 148 DNETISVDGKLIKVVSN-RDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVII 206
++ + V+GK + V + RDP LPW LG+DIVIE TG F D H++AGAKKV+I
Sbjct: 61 ED-GLVVNGKEVISVFSERDPSDLPWKALGVDIVIECTGKFRDKEKLEGHLEAGAKKVLI 119
Query: 207 TAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAMTTT 266
+AP+KG D+ T V GVN +YD IVSNASCTTNCLAP KV+DE GIV G MTT
Sbjct: 120 SAPSKG-DVKTIVYGVNHDEYDPSER-IVSNASCTTNCLAPLAKVLDEAFGIVSGLMTTV 177
Query: 267 HSYTGDQVI 275
HSYT DQ +
Sbjct: 178 HSYTNDQNL 186
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 240 bits (614), Expect = 6e-78
Identities = 100/189 (52%), Positives = 126/189 (66%), Gaps = 5/189 (2%)
Query: 86 KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKNASHLLKYDSLLGTFKADVK 145
+KVAINGFGRIGR R R ++VV +ND +HLLKYDS+ G F +V+
Sbjct: 1 MIKVAINGFGRIGRLVARAALERDGD-IEVVAINDLTDPDYLAHLLKYDSVHGRFDGEVE 59
Query: 146 IVDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQA-GAKKV 204
V ++ + V+GK IKV++ RDP LPWA+LG+DIV+E TG F A KH++A GAKKV
Sbjct: 60 -VKDDALVVNGKGIKVLAERDPANLPWADLGVDIVVECTGKFTGREKAEKHLKAGGAKKV 118
Query: 205 IITAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAMT 264
+I+AP K D+ T V GVN YD IVSNASCTTNCLAP KV+++ GI KG MT
Sbjct: 119 LISAPGKD-DVATVVYGVNHNYYDAG-HTIVSNASCTTNCLAPVAKVLNDAFGIEKGLMT 176
Query: 265 TTHSYTGDQ 273
T H+YT DQ
Sbjct: 177 TVHAYTNDQ 185
>gnl|CDD|236079 PRK07729, PRK07729, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 343
Score = 238 bits (608), Expect = 5e-77
Identities = 102/188 (54%), Positives = 129/188 (68%), Gaps = 4/188 (2%)
Query: 86 KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKNASHLLKYDSLLGTFKADVK 145
K KVAINGFGRIGR R K+S ++V +N S + +HL+KYD++ G F V+
Sbjct: 2 KTKVAINGFGRIGRMVFR--KAIKESAFEIVAINASYPSETLAHLIKYDTVHGKFDGTVE 59
Query: 146 IVDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVI 205
+ + + VDGK I++++NRDP +LPW +LGIDIVIE TG F A H++AGAKKVI
Sbjct: 60 AFE-DHLLVDGKKIRLLNNRDPKELPWTDLGIDIVIEATGKFNSKEKAILHVEAGAKKVI 118
Query: 206 ITAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAMTT 265
+TAP K D+ T VVGVNE D E I+SNASCTTNCLAP VKV+DE+ GI G MTT
Sbjct: 119 LTAPGKNEDV-TIVVGVNEDQLDIEKHTIISNASCTTNCLAPVVKVLDEQFGIENGLMTT 177
Query: 266 THSYTGDQ 273
H+YT DQ
Sbjct: 178 VHAYTNDQ 185
>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 = 210 bits (536), Expect = 1e-68
Identities = 84/153 (54%), Positives = 107/153 (69%), Gaps = 5/153 (3%)
Query: 87 LKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKNASHLLKYDSLLGTFKADVKI 146
+KV INGFGRIGR LR + D L+VV +ND + ++LLKYDS+ G F +V+
Sbjct: 1 IKVGINGFGRIGRLVLRAALAQDD--LEVVAINDLTDPETLAYLLKYDSVHGRFDGEVE- 57
Query: 147 VDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVII 206
VD + + V+GK IKV + RDP +LPW ELG+DIV+E TGVF A H++AGAKKVII
Sbjct: 58 VDEDGLIVNGKKIKVFAERDPAELPWGELGVDIVVESTGVFTTAEKAEAHLKAGAKKVII 117
Query: 207 TAPAKGADIPTYVVGVNEKDYDHEVANIVSNAS 239
+APAK D PT+V GVN +DYD E +IVSNAS
Sbjct: 118 SAPAKD-DDPTFVYGVNHEDYDPE-DDIVSNAS 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 = 200 bits (512), Expect = 4e-65
Identities = 81/154 (52%), Positives = 105/154 (68%), Gaps = 5/154 (3%)
Query: 87 LKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKNASHLLKYDSLLGTFKADVKI 146
+KV INGFGRIGR LR R D ++VV +ND + ++LLKYDS+ G F V+
Sbjct: 1 IKVGINGFGRIGRLVLRAALERPD--VEVVAINDLTDPEYLAYLLKYDSVHGRFPGTVE- 57
Query: 147 VDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVII 206
V+ + + V+GK IKV + RDP LPW ELG+DIV+E TG F A H++AGAKKVII
Sbjct: 58 VEGDGLVVNGKAIKVFAERDPANLPWGELGVDIVVECTGGFTTREKASAHLKAGAKKVII 117
Query: 207 TAPAKGADIPTYVVGVNEKDYDHEVANIVSNASC 240
+AP+K AD PT+V GVN +YD E +I+SNASC
Sbjct: 118 SAPSKDAD-PTFVYGVNHDEYDGE-DHIISNASC 149
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 206 bits (526), Expect = 7e-64
Identities = 107/270 (39%), Positives = 149/270 (55%), Gaps = 12/270 (4%)
Query: 5 SALAPSRIPAITRIPSKTTHSFPTQCSTKRLDVAEFAGLRANAGATYATGARDASFFDAV 64
+A AP+ + S ++ ++ + + + AR A
Sbjct: 10 AATAPAAAARGSDFSSSSSDPSKVSSVGFSSSLSFSGSSSGASSSLQSCSARSVQPIKAT 69
Query: 65 TAQLTPKVAAGSVPVKKETVAKLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSG-G 123
+ P V +K + K K+ INGFGRIGR LR R D ++VV VND
Sbjct: 70 ATEAPPAV------LKSSSSGKTKIGINGFGRIGRLVLRIATSRDD--IEVVAVNDPFID 121
Query: 124 VKNASHLLKYDSLLGTFKADVKIVDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEG 183
K +++ KYDS G FK + +VD+ T+ ++GK IKV S RDP ++PW + G + V+E
Sbjct: 122 AKYMAYMFKYDSTHGNFKGTINVVDDSTLEINGKQIKVTSKRDPAEIPWGDFGAEYVVES 181
Query: 184 TGVFVDGPGAGKHIQAGAKKVIITAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTN 243
+GVF A H++ GAKKV+I+AP+ AD P +VVGVNEK Y + NIVSNASCTTN
Sbjct: 182 SGVFTTVEKASAHLKGGAKKVVISAPS--ADAPMFVVGVNEKTYKPNM-NIVSNASCTTN 238
Query: 244 CLAPFVKVMDEELGIVKGAMTTTHSYTGDQ 273
CLAP KV+ EE GI++G MTT H+ T Q
Sbjct: 239 CLAPLAKVVHEEFGILEGLMTTVHATTATQ 268
>gnl|CDD|173322 PTZ00023, PTZ00023, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 337
Score = 175 bits (446), Expect = 7e-53
Identities = 87/189 (46%), Positives = 120/189 (63%), Gaps = 6/189 (3%)
Query: 88 KVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDS-GGVKNASHLLKYDSLLGTFKADVKI 146
K+ INGFGRIGR R R+D ++VV +ND + +LLKYDS+ G+ A+V +
Sbjct: 4 KLGINGFGRIGRLVFRAALERED--VEVVAINDPFMTLDYMCYLLKYDSVHGSLPAEVSV 61
Query: 147 VDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVII 206
D + + K + V +DP +PW + G+D+V E TGVF+ A H++ GAKKVI+
Sbjct: 62 TD-GFLMIGSKKVHVFFEKDPAAIPWGKNGVDVVCESTGVFLTKEKAQAHLKGGAKKVIM 120
Query: 207 TAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAMTTT 266
+AP K D P YV+GVN YD IVSNASCTTNCLAP KV++++ GIV+G MTT
Sbjct: 121 SAPPKD-DTPIYVMGVNHTQYDKSQR-IVSNASCTTNCLAPLAKVVNDKFGIVEGLMTTV 178
Query: 267 HSYTGDQVI 275
H+ T +Q+
Sbjct: 179 HASTANQLT 187
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 173 bits (440), Expect = 5e-52
Identities = 85/193 (44%), Positives = 116/193 (60%), Gaps = 8/193 (4%)
Query: 87 LKVAINGFGRIGRNFLRCWH--GRKDSPLDVVVVNDSGGVKNASHLLKYDSLLGTFKADV 144
++VAINGFGRIGRN LR + GR+ + VV +N+ + +HLLKYD+ G F DV
Sbjct: 2 IRVAINGFGRIGRNVLRALYESGRRAE-ITVVAINELADAEGMAHLLKYDTSHGRFAWDV 60
Query: 145 KIVDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKV 204
+ + + + V I+++ RD LPW ELG+D+V++ TGV+ HI AGAKKV
Sbjct: 61 R-QERDQLFVGDDAIRLLHERDIASLPWRELGVDVVLDCTGVYGSREDGEAHIAAGAKKV 119
Query: 205 IITAPAKGADI-PTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAM 263
+ + P D+ T V GVN E IVSNASCTTNC+ P +K++D+ GI G +
Sbjct: 120 LFSHPG-SNDLDATVVYGVNHDQLRAE-HRIVSNASCTTNCIIPVIKLLDDAFGIESGTV 177
Query: 264 TTTHSYTGDQ-VI 275
TT HS DQ VI
Sbjct: 178 TTIHSAMNDQQVI 190
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 160 bits (405), Expect = 8e-47
Identities = 89/190 (46%), Positives = 125/190 (65%), Gaps = 7/190 (3%)
Query: 86 KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSG-GVKNASHLLKYDSLLGTFK-AD 143
K+++ INGFGRIGR R R D +++V VND + +++ KYDS+ G +K +
Sbjct: 5 KIRIGINGFGRIGRLVARVVLQRDD--VELVAVNDPFITTEYMTYMFKYDSVHGQWKHHE 62
Query: 144 VKIVDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKK 203
+K+ D++T+ K + V R+P +PW E G D V+E TGVF D A H++ GAKK
Sbjct: 63 LKVKDDKTLLFGEKPVTVFGIRNPEDIPWGEAGADFVVESTGVFTDKDKAAAHLKGGAKK 122
Query: 204 VIITAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAM 263
V+I+AP+K D P +VVGVNE +Y ++ +IVSNASCTTNCLAP KV+++ GIV+G M
Sbjct: 123 VVISAPSK--DAPMFVVGVNEHEYKSDL-DIVSNASCTTNCLAPLAKVINDRFGIVEGLM 179
Query: 264 TTTHSYTGDQ 273
TT HS T Q
Sbjct: 180 TTVHSITATQ 189
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 159 bits (403), Expect = 1e-46
Identities = 88/187 (47%), Positives = 119/187 (63%), Gaps = 6/187 (3%)
Query: 87 LKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGGVKNASHLLKYDSLLGTFKADVKI 146
+KV INGFGRIGR R R D +++V +ND +++LKYDS G F V++
Sbjct: 3 IKVGINGFGRIGRIVFRAAQKRSD--IEIVAINDLLDADYMAYMLKYDSTHGRFDGTVEV 60
Query: 147 VDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVII 206
D I V+GK I+V + RDP L W E+G+D+V E TG+F+ A KHI AGAKKV++
Sbjct: 61 KDGHLI-VNGKKIRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVM 119
Query: 207 TAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAMTTT 266
T P+K + P +V G N Y + +IVSNASCTTNCLAP KV+++ GI++G MTT
Sbjct: 120 TGPSKD-NTPMFVKGANFDKYAGQ--DIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTV 176
Query: 267 HSYTGDQ 273
H+ T Q
Sbjct: 177 HATTATQ 183
>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 = 155 bits (394), Expect = 2e-45
Identities = 80/187 (42%), Positives = 109/187 (58%), Gaps = 3/187 (1%)
Query: 88 KVAINGFGRIGRNFLRCWHGR-KDSPLDVVVVNDSGGVKNASHLLKYDSLLGTFKADVKI 146
+VAINGFGRIGRN LR + + + + VV +N+ +HLLKYD+ G F +V+
Sbjct: 1 RVAINGFGRIGRNVLRALYESGRRAEITVVAINELADAAGMAHLLKYDTSHGRFAWEVR- 59
Query: 147 VDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVII 206
D + + V I+V+ R LPW ELG+D+V++ TGV+ HI AGAKKV+
Sbjct: 60 QDRDQLFVGDDAIRVLHERSLQSLPWRELGVDLVLDCTGVYGSREHGEAHIAAGAKKVLF 119
Query: 207 TAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAMTTT 266
+ P T V GVN+ E IVSNASCTTNC+ P +K++D+ GI G +TT
Sbjct: 120 SHPGASDLDATIVYGVNQDQLRAE-HRIVSNASCTTNCIVPVIKLLDDAYGIESGTITTI 178
Query: 267 HSYTGDQ 273
HS DQ
Sbjct: 179 HSAMNDQ 185
>gnl|CDD|185614 PTZ00434, PTZ00434, cytosolic glyceraldehyde 3-phosphate
dehydrogenase; Provisional.
Length = 361
Score = 155 bits (392), Expect = 1e-44
Identities = 91/201 (45%), Positives = 123/201 (61%), Gaps = 13/201 (6%)
Query: 85 AKLKVAINGFGRIGRNFLR--CWHGRKDSPLDVVVVND-SGGVKNASHLLKYDSLLGTFK 141
A +KV INGFGRIGR + C G + +DVV V D S + ++ +KYD++ G K
Sbjct: 2 APIKVGINGFGRIGRMVFQAICDQGLIGTEIDVVAVVDMSTNAEYFAYQMKYDTVHGRPK 61
Query: 142 ADVK-------IVDNETISVDGKLIKVV-SNRDPLQLPWAELGIDIVIEGTGVFVDGPGA 193
V+ + ++ + V+G IK V + R+P LPW +LG+D VIE TG+F D A
Sbjct: 62 YTVETTKSSPSVKTDDVLVVNGHRIKCVKAQRNPADLPWGKLGVDYVIESTGLFTDKLAA 121
Query: 194 GKHIQAGAKKVIITAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMD 253
H++ GAKKV+I+APA G T V+GVN+ +Y ++VSNASCTTNCLAP V V+
Sbjct: 122 EGHLKGGAKKVVISAPASGG-AKTIVMGVNQHEYSPTEHHVVSNASCTTNCLAPIVHVLT 180
Query: 254 EE-LGIVKGAMTTTHSYTGDQ 273
+E GI G MTT HSYT Q
Sbjct: 181 KEGFGIETGLMTTIHSYTATQ 201
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 151 bits (383), Expect = 2e-43
Identities = 77/191 (40%), Positives = 110/191 (57%), Gaps = 6/191 (3%)
Query: 86 KLKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSGG-VKNASHLLKYDSLLGTFKADV 144
+KV INGFGRIGR LR + L+ V +ND G +HLL++DS+ G + +V
Sbjct: 2 TIKVGINGFGRIGRLALRAAWDWPE--LEFVQINDPAGDAATLAHLLEFDSVHGRWHHEV 59
Query: 145 KIVDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKV 204
+ + I ++GK I+ N+ W+ G D+VIE +GV ++ G K+V
Sbjct: 60 -TAEGDAIVINGKRIRTTQNKAIADTDWS--GCDVVIEASGVMKTKALLQAYLDQGVKRV 116
Query: 205 IITAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAMT 264
++TAP K + V+GVN+ +D + IV+ ASCTTNCLAP VKV+ E+LGI G+MT
Sbjct: 117 VVTAPVKEEGVLNIVMGVNDHLFDPAIHPIVTAASCTTNCLAPVVKVIHEKLGIKHGSMT 176
Query: 265 TTHSYTGDQVI 275
T H T Q I
Sbjct: 177 TIHDLTNTQTI 187
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 150 bits (380), Expect = 8e-42
Identities = 75/205 (36%), Positives = 106/205 (51%), Gaps = 32/205 (15%)
Query: 89 VAINGFGRIGR-------------NFLRCWHGRKDSPLDVVVVNDSGG---VKNASHLLK 132
V + GFGRIGR N LR L +VV K AS LL+
Sbjct: 130 VVLYGFGRIGRLLARLLIEKTGGGNGLR---------LRAIVVRKGSEGDLEKRAS-LLR 179
Query: 133 YDSLLGTFKADVKI-VDNETISVDGKLIKVVSNRDPLQLPWAELGID--IVIEGTGVFVD 189
DS+ G F + + +N I +G I+V+ P ++ + GI+ +V++ TG + D
Sbjct: 180 RDSVHGPFNGTITVDEENNAIIANGNYIQVIYANSPEEVDYTAYGINNALVVDNTGKWRD 239
Query: 190 GPGAGKHIQA-GAKKVIITAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPF 248
G +H+++ G KV++TAP KG DI V GVN D E IVS ASCTTN + P
Sbjct: 240 EEGLSQHLKSKGVAKVLLTAPGKG-DIKNIVHGVNHSDITDED-KIVSAASCTTNAITPV 297
Query: 249 VKVMDEELGIVKGAMTTTHSYTGDQ 273
+K ++++ GIV G + T HSYT DQ
Sbjct: 298 LKAVNDKYGIVNGHVETVHSYTNDQ 322
>gnl|CDD|173546 PTZ00353, PTZ00353, glycosomal glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 342
Score = 65.3 bits (159), Expect = 4e-12
Identities = 47/181 (25%), Positives = 87/181 (48%), Gaps = 7/181 (3%)
Query: 89 VAINGFGRIGRNFLRCWHGRKDSPLDVVVVND-SGGVKNASHLLKYDS-LLGTFKADVKI 146
V INGFG +G+ L + D + VV VND S + +++L+ +S L A +++
Sbjct: 5 VGINGFGPVGKAVL--FASLTDPLVTVVAVNDASVSIAYIAYVLEQESPLSAPDGASIRV 62
Query: 147 VDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVII 206
V + + + I+V + D +++ W + G+ V+E TG++ H+ GAK V +
Sbjct: 63 VGEQIVLNGTQKIRVSAKHDLVEIAWRDYGVQYVVECTGLYSTRSRCWGHVTGGAKGVFV 122
Query: 207 TAPAKGADIPTYVVGVNEKDYDHEVANIVSNASCTTNCLAPFVKVMDEELGIVKGAMTTT 266
+ AD PT + G N++ + + LAP ++ + E G+ + + T
Sbjct: 123 A--GQSADAPTVMAGSNDERLS-ASLPVCCAGAPIAVALAPVIRALHEVYGVEECSYTAI 179
Query: 267 H 267
H
Sbjct: 180 H 180
>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 = 52.5 bits (127), Expect = 1e-08
Identities = 17/31 (54%), Positives = 22/31 (70%)
Query: 245 LAPFVKVMDEELGIVKGAMTTTHSYTGDQVI 275
LAP KV+++ GI KG MTT H+YT DQ +
Sbjct: 1 LAPLAKVLNDNFGIEKGLMTTVHAYTADQKL 31
>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 = 37.5 bits (87), Expect = 0.006
Identities = 27/100 (27%), Positives = 48/100 (48%), Gaps = 6/100 (6%)
Query: 176 GIDIVIEGTGVFVDGPGAGKHIQAGAKKVII---TAPAKGADIPTYVVGVNEKD-YDHEV 231
GIDI + G V A K +AG ++I +A D+P V VN +D +
Sbjct: 61 GIDIALFSAGGSVSKEFAPKAAKAGV--IVIDNTSAFRMDPDVPLVVPEVNFEDLKEFNP 118
Query: 232 ANIVSNASCTTNCLAPFVKVMDEELGIVKGAMTTTHSYTG 271
I++N +C+T + +K + +E I + ++T + +G
Sbjct: 119 KGIIANPNCSTIQMVVVLKPLHDEAKIKRVVVSTYQAVSG 158
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 32.2 bits (74), Expect = 0.31
Identities = 24/130 (18%), Positives = 45/130 (34%), Gaps = 27/130 (20%)
Query: 86 KLKVAINGFGRIGRNFLRCWHGRKDS-----PLDVVVVNDSGGVKNASHLLKYDSLLGTF 140
+KV + G G +G L +++ +++ VV V + L
Sbjct: 3 TVKVGLLGLGTVGSGVLEILAEKQEELRKRAGIEIRVV----AVADRDGSLVR------- 51
Query: 141 KADVKIVDNETISVDGKLIKVVSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQA- 199
D+ +++ E + DG L + ID+V+E G V+
Sbjct: 52 --DLDLLNAEVWTTDGALSLGDEVLL-------DEDIDVVVELVGGDVEPAEPADLYLKA 102
Query: 200 -GAKKVIITA 208
K ++TA
Sbjct: 103 LENGKHVVTA 112
>gnl|CDD|236551 PRK09533, PRK09533, bifunctional transaldolase/phosoglucose
isomerase; Validated.
Length = 948
Score = 30.7 bits (70), Expect = 0.97
Identities = 26/67 (38%), Positives = 34/67 (50%), Gaps = 11/67 (16%)
Query: 36 DVAE--FAGL--RANAGATYATGARDASFF-----DAVTAQLTPKVAAGSVPVKKETVAK 86
+VAE +GL RA G + A ASFF AV +L K+AA + P +K +
Sbjct: 174 EVAEAYISGLEARAAKGGDPSHVASVASFFVSRIDSAVDKRLDEKIAAANDPAEKAALEA 233
Query: 87 L--KVAI 91
L KVAI
Sbjct: 234 LKGKVAI 240
>gnl|CDD|223214 COG0136, Asd, Aspartate-semialdehyde dehydrogenase [Amino acid
transport and metabolism].
Length = 334
Score = 29.5 bits (67), Expect = 2.1
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 214 DIPTYVVGVNEKDYDHEVAN--IVSNASCTTNCLAPFVKVMDEELGIVKGAMTT 265
D+P V VN + I++N +C+T L +K + + GI + ++T
Sbjct: 105 DVPLVVPEVNPEHLIDYQKRGFIIANPNCSTIQLVLALKPLHDAFGIKRVVVST 158
>gnl|CDD|236903 PRK11380, PRK11380, hypothetical protein; Provisional.
Length = 353
Score = 29.5 bits (66), Expect = 2.1
Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 12/80 (15%)
Query: 117 VVNDSGGVKNASHLLKYDSLLGTFKADVKIVDNETISVDGKLIKV-----------VSNR 165
+ + G HLL D TFKA+++ + I++ KL S +
Sbjct: 178 IEDSEGYCALMEHLLSGDHGANTFKANMEEAPEQMIALLAKLAVFPSDYISDCANHSSGK 237
Query: 166 DPLQLPWA-ELGIDIVIEGT 184
P +L WA +L I + T
Sbjct: 238 SPAKLIWAADLSWMISLSRT 257
>gnl|CDD|237845 PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 334
Score = 29.4 bits (67), Expect = 2.6
Identities = 32/116 (27%), Positives = 51/116 (43%), Gaps = 15/116 (12%)
Query: 151 TISVDGKLIKV--VSNRDPLQLPWAELGIDIVIEGTGVFVDGPGAGKHIQAGAKKVII-- 206
+S GK +KV ++ D G+DI + G V A K AGA V+I
Sbjct: 43 ELSFKGKELKVEDLTTFDFS-------GVDIALFSAGGSVSKKYAPKAAAAGA--VVIDN 93
Query: 207 -TAPAKGADIPTYVVGVNEKDYD-HEVANIVSNASCTTNCLAPFVKVMDEELGIVK 260
+A D+P V VN + H I++N +C+T + +K + + GI +
Sbjct: 94 SSAFRMDPDVPLVVPEVNPEALAEHRKKGIIANPNCSTIQMVVALKPLHDAAGIKR 149
>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 = 28.6 bits (65), Expect = 3.7
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 274 VIR-HTKMSTSLLERAPKIKLLLT 296
++R T +LLER P +KLL+T
Sbjct: 52 LMRERTPFPAALLERLPNLKLLVT 75
>gnl|CDD|233700 TIGR02053, MerA, mercuric reductase. This model represents the
mercuric reductase found in the mer operon for the
detoxification of mercury compounds. MerA is a
FAD-containing flavoprotein which reduces Hg(II) to
Hg(0) utilizing NADPH [Cellular processes,
Detoxification].
Length = 463
Score = 28.2 bits (63), Expect = 6.5
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 12/61 (19%)
Query: 173 AELGIDIVIEGTGVFVDGP----GAGKHIQAGAKKVIITAPAKGA--DIPTYVVGVNEKD 226
+ G+D + G F D G+ ++ GAK+ +I A+ A IP G+ E
Sbjct: 99 SSYGVDY-LRGRARFKDPKTVKVDLGREVR-GAKRFLIATGARPAIPPIP----GLKEAG 152
Query: 227 Y 227
Y
Sbjct: 153 Y 153
>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 = 26.8 bits (60), Expect = 7.9
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 87 LKVAINGFGRIGRNFLRCWHGRKDSPLDVVVVNDSG 122
L+V I G G+IGR LR + ++V + D
Sbjct: 1 LRVGIVGAGKIGRRHLRALN-ESQDGAELVGILDPD 35
>gnl|CDD|179786 PRK04207, PRK04207, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 341
Score = 27.5 bits (62), Expect = 8.7
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 86 KLKVAINGFGRIGR 99
+KV +NG+G IG+
Sbjct: 1 MIKVGVNGYGTIGK 14
>gnl|CDD|235701 PRK06116, PRK06116, glutathione reductase; Validated.
Length = 450
Score = 27.8 bits (63), Expect = 8.9
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 12/58 (20%)
Query: 133 YDSLLGTFKADV-----KIVDNETISVDGK-------LIKVVSNRDPLQLPWAELGID 178
Y + L D+ + VD T+ V+G+ LI +P AE GI
Sbjct: 99 YRNGLENNGVDLIEGFARFVDAHTVEVNGERYTADHILIATGGRPSIPDIPGAEYGIT 156
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
0.317 0.132 0.383
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,165,225
Number of extensions: 1467209
Number of successful extensions: 1432
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1372
Number of HSP's successfully gapped: 49
Length of query: 304
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 208
Effective length of database: 6,679,618
Effective search space: 1389360544
Effective search space used: 1389360544
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: 59 (26.4 bits)