RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021899
(306 letters)
>gnl|CDD|165999 PLN02358, PLN02358, glyceraldehyde-3-phosphate dehydrogenase.
Length = 338
Score = 540 bits (1392), Expect = 0.0
Identities = 267/292 (91%), Positives = 282/292 (96%)
Query: 12 TYMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGV 71
TYMFKYDSVHGQWKH+ELKVKD+KTLLFGEKPV VFG RNPE+IPW + GA++VVESTGV
Sbjct: 46 TYMFKYDSVHGQWKHHELKVKDDKTLLFGEKPVTVFGIRNPEDIPWGEAGADFVVESTGV 105
Query: 72 FTDKDKAAAHLKGGAKKVVISAPSKDAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLA 131
FTDKDKAAAHLKGGAKKVVISAPSKDAPMFVVGVNE EYK +LDIVSNASCTTNCLAPLA
Sbjct: 106 FTDKDKAAAHLKGGAKKVVISAPSKDAPMFVVGVNEHEYKSDLDIVSNASCTTNCLAPLA 165
Query: 132 KVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVL 191
KVI+D+FGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVL
Sbjct: 166 KVINDRFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVL 225
Query: 192 PALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTEEDV 251
P+LNGKLTGMSFRVPTVDVSVVDLTVRLEK ATY+EIK AIKEESEGKLKGILGYTE+DV
Sbjct: 226 PSLNGKLTGMSFRVPTVDVSVVDLTVRLEKAATYDEIKKAIKEESEGKLKGILGYTEDDV 285
Query: 252 VSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDLIVHMAK 303
VSTDFVGD+RSSIFDAKAGIALS FVKLVSWYDNEWGYSSRV+DLIVHM+K
Sbjct: 286 VSTDFVGDNRSSIFDAKAGIALSDKFVKLVSWYDNEWGYSSRVVDLIVHMSK 337
>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
Length = 421
Score = 533 bits (1374), Expect = 0.0
Identities = 225/294 (76%), Positives = 250/294 (85%), Gaps = 1/294 (0%)
Query: 13 YMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVF 72
YMFKYDS HG +K + V D+ TL K + V R+P EIPW GAEYVVES+GVF
Sbjct: 127 YMFKYDSTHGNFK-GTINVVDDSTLEINGKQIKVTSKRDPAEIPWGDFGAEYVVESSGVF 185
Query: 73 TDKDKAAAHLKGGAKKVVISAPSKDAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAK 132
T +KA+AHLKGGAKKVVISAPS DAPMFVVGVNEK YKP ++IVSNASCTTNCLAPLAK
Sbjct: 186 TTVEKASAHLKGGAKKVVISAPSADAPMFVVGVNEKTYKPNMNIVSNASCTTNCLAPLAK 245
Query: 133 VIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVLP 192
V+H++FGI+EGLMTTVH+ TATQKTVDGPSMKDWRGGR AS NIIPSSTGAAKAVGKVLP
Sbjct: 246 VVHEEFGILEGLMTTVHATTATQKTVDGPSMKDWRGGRGASQNIIPSSTGAAKAVGKVLP 305
Query: 193 ALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTEEDVV 252
LNGKLTGM+FRVPT +VSVVDLT RLEK A+YE++K AIK SEG LKGILGYT+EDVV
Sbjct: 306 ELNGKLTGMAFRVPTPNVSVVDLTCRLEKSASYEDVKAAIKYASEGPLKGILGYTDEDVV 365
Query: 253 STDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDLIVHMAKTQA 306
S DFVGDSRSSIFDAKAGI LS +F+KLVSWYDNEWGYS+RV+DLI HMA A
Sbjct: 366 SNDFVGDSRSSIFDAKAGIGLSASFMKLVSWYDNEWGYSNRVLDLIEHMALVAA 419
>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 = 442 bits (1140), Expect = e-158
Identities = 167/287 (58%), Positives = 212/287 (73%), Gaps = 5/287 (1%)
Query: 13 YMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVF 72
Y+ KYDSVHG+++ E+ ++ ++ G++ ++VF R+P ++PW G + V+E TG F
Sbjct: 42 YLLKYDSVHGRFEG-EVTADEDGLVVNGKEVISVFSERDPSDLPWKALGVDIVIECTGKF 100
Query: 73 TDKDKAAAHLKGGAKKVVISAPSK-DAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLA 131
DK+K HL+ GAKKV+ISAPSK D V GVN EY P IVSNASCTTNCLAPLA
Sbjct: 101 RDKEKLEGHLEAGAKKVLISAPSKGDVKTIVYGVNHDEYDPSERIVSNASCTTNCLAPLA 160
Query: 132 KVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVL 191
KV+ + FGIV GLMTTVHS T Q VDGP KD R RAA+ NIIP+STGAAKA+GKVL
Sbjct: 161 KVLDEAFGIVSGLMTTVHSYTNDQNLVDGP-HKDLRRARAAALNIIPTSTGAAKAIGKVL 219
Query: 192 PALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTEEDV 251
P L GKLTGM+ RVPT +VS+VDL V LEK+ T EE+ A+KE +EG+LKG+LGYTE+++
Sbjct: 220 PELAGKLTGMAIRVPTPNVSLVDLVVNLEKDVTVEEVNAALKEAAEGELKGVLGYTEDEL 279
Query: 252 VSTDFVGDSRSSIFDAKAGIA--LSKNFVKLVSWYDNEWGYSSRVID 296
VS+DF+G SSI DA A L + VK+V+WYDNEWGYS+RV+D
Sbjct: 280 VSSDFIGSPYSSIVDATATKVTGLGDSLVKVVAWYDNEWGYSNRVVD 326
>gnl|CDD|173322 PTZ00023, PTZ00023, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 337
Score = 443 bits (1141), Expect = e-158
Identities = 194/304 (63%), Positives = 231/304 (75%), Gaps = 5/304 (1%)
Query: 5 YFEINMQTYMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEY 64
+ ++ Y+ KYDSVHG E+ V D L+ G K V VF ++P IPW K G +
Sbjct: 36 FMTLDYMCYLLKYDSVHGSLPA-EVSVTDG-FLMIGSKKVHVFFEKDPAAIPWGKNGVDV 93
Query: 65 VVESTGVFTDKDKAAAHLKGGAKKVVISAPSKD-APMFVVGVNEKEYKPELDIVSNASCT 123
V ESTGVF K+KA AHLKGGAKKV++SAP KD P++V+GVN +Y IVSNASCT
Sbjct: 94 VCESTGVFLTKEKAQAHLKGGAKKVIMSAPPKDDTPIYVMGVNHTQYDKSQRIVSNASCT 153
Query: 124 TNCLAPLAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSM--KDWRGGRAASFNIIPSST 181
TNCLAPLAKV++DKFGIVEGLMTTVH+ TA Q TVDGPS KDWR GR A NIIP+ST
Sbjct: 154 TNCLAPLAKVVNDKFGIVEGLMTTVHASTANQLTVDGPSKGGKDWRAGRCAGVNIIPAST 213
Query: 182 GAAKAVGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLK 241
GAAKAVGKV+P LNGKLTGM+FRVP DVSVVDLT +L K A YEEI A+K+ +EG LK
Sbjct: 214 GAAKAVGKVIPELNGKLTGMAFRVPVPDVSVVDLTCKLAKPAKYEEIVAAVKKAAEGPLK 273
Query: 242 GILGYTEEDVVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDLIVHM 301
GILGYT+++VVS+DFV D RSSIFD KAGIAL+ FVKLVSWYDNEWGYS+R++DL ++
Sbjct: 274 GILGYTDDEVVSSDFVHDKRSSIFDVKAGIALNDTFVKLVSWYDNEWGYSNRLLDLAHYI 333
Query: 302 AKTQ 305
+
Sbjct: 334 TQKY 337
>gnl|CDD|223135 COG0057, GapA, Glyceraldehyde-3-phosphate
dehydrogenase/erythrose-4-phosphate dehydrogenase
[Carbohydrate transport and metabolism].
Length = 335
Score = 440 bits (1135), Expect = e-157
Identities = 178/293 (60%), Positives = 211/293 (72%), Gaps = 5/293 (1%)
Query: 13 YMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVF 72
++ KYDSVHG++ E++V + L+ K + V R+P +PWA G + VVE TG F
Sbjct: 43 HLLKYDSVHGRFDG-EVEV-KDDALVVNGKGIKVLAERDPANLPWADLGVDIVVECTGKF 100
Query: 73 TDKDKAAAHL-KGGAKKVVISAPSKDA-PMFVVGVNEKEYKPELDIVSNASCTTNCLAPL 130
T ++KA HL GGAKKV+ISAP KD V GVN Y IVSNASCTTNCLAP+
Sbjct: 101 TGREKAEKHLKAGGAKKVLISAPGKDDVATVVYGVNHNYYDAGHTIVSNASCTTNCLAPV 160
Query: 131 AKVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKV 190
AKV++D FGI +GLMTTVH+ T QK VDGP KD R RAA+ NIIP+STGAAKAVG V
Sbjct: 161 AKVLNDAFGIEKGLMTTVHAYTNDQKLVDGPH-KDLRRARAAALNIIPTSTGAAKAVGLV 219
Query: 191 LPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTEED 250
LP L GKLTGM+ RVPT +VSVVDLTV LEKE T EEI A+K SE LKGILGYTE+
Sbjct: 220 LPELKGKLTGMAIRVPTPNVSVVDLTVELEKEVTVEEINAALKAASEIGLKGILGYTEDP 279
Query: 251 VVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDLIVHMAK 303
+VS+DF GD SSIFDA A I L N VKLV+WYDNEWGYS+RV+DL+ +AK
Sbjct: 280 LVSSDFNGDPHSSIFDASATIVLGGNLVKLVAWYDNEWGYSNRVVDLLAMVAK 332
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 370 bits (952), Expect = e-129
Identities = 193/292 (66%), Positives = 234/292 (80%), Gaps = 4/292 (1%)
Query: 13 YMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVF 72
YM KYDS HG++ ++VKD ++ G+K + V R+P + W + G + V E+TG+F
Sbjct: 43 YMLKYDSTHGRFD-GTVEVKDGHLIVNGKK-IRVTAERDPANLKWDEVGVDVVAEATGLF 100
Query: 73 TDKDKAAAHLKGGAKKVVISAPSKD-APMFVVGVNEKEYKPELDIVSNASCTTNCLAPLA 131
+ A H+ GAKKVV++ PSKD PMFV G N +Y + DIVSNASCTTNCLAPLA
Sbjct: 101 LTDETARKHITAGAKKVVMTGPSKDNTPMFVKGANFDKYAGQ-DIVSNASCTTNCLAPLA 159
Query: 132 KVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVL 191
KVI+D FGI+EGLMTTVH+ TATQKTVDGPS KDWRGGR AS NIIPSSTGAAKAVGKVL
Sbjct: 160 KVINDNFGIIEGLMTTVHATTATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAKAVGKVL 219
Query: 192 PALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTEEDV 251
P LNGKLTGM+FRVPT +VSVVDLTVRLEK ATYE+IK A+K +EG++KG+LGYTE+DV
Sbjct: 220 PELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAAAEGEMKGVLGYTEDDV 279
Query: 252 VSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDLIVHMAK 303
VSTDF G+ +S+FDAKAGIAL+ NFVKLVSWYDNE GYS++V+DLI H++K
Sbjct: 280 VSTDFNGEVCTSVFDAKAGIALNDNFVKLVSWYDNETGYSNKVLDLIAHISK 331
>gnl|CDD|185614 PTZ00434, PTZ00434, cytosolic glyceraldehyde 3-phosphate
dehydrogenase; Provisional.
Length = 361
Score = 363 bits (933), Expect = e-126
Identities = 177/308 (57%), Positives = 222/308 (72%), Gaps = 14/308 (4%)
Query: 13 YMFKYDSVHGQWKHNELKVK-------DEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYV 65
Y KYD+VHG+ K+ K D+ ++ G + V RNP ++PW K G +YV
Sbjct: 49 YQMKYDTVHGRPKYTVETTKSSPSVKTDDVLVVNGHRIKCVKAQRNPADLPWGKLGVDYV 108
Query: 66 VESTGVFTDKDKAAAHLKGGAKKVVISAP-SKDAPMFVVGVNEKEYKP-ELDIVSNASCT 123
+ESTG+FTDK A HLKGGAKKVVISAP S A V+GVN+ EY P E +VSNASCT
Sbjct: 109 IESTGLFTDKLAAEGHLKGGAKKVVISAPASGGAKTIVMGVNQHEYSPTEHHVVSNASCT 168
Query: 124 TNCLAPLAKVI-HDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTG 182
TNCLAP+ V+ + FGI GLMTT+HS TATQKTVDG S+KDWRGGRAA+ NIIPS+TG
Sbjct: 169 TNCLAPIVHVLTKEGFGIETGLMTTIHSYTATQKTVDGVSVKDWRGGRAAAVNIIPSTTG 228
Query: 183 AAKAVGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKG 242
AAKAVG V+P+ GKLTGMSFRVPT DVSVVDLT R ++ + +EI AIK S+ +KG
Sbjct: 229 AAKAVGMVIPSTKGKLTGMSFRVPTPDVSVVDLTFRATRDTSIQEIDAAIKRASQTYMKG 288
Query: 243 ILGYTEEDVVSTDFVGDSRSSIFDAKA----GIALSKNFVKLVSWYDNEWGYSSRVIDLI 298
ILG+T++++VS DF+ D+RSSI+D+KA + + F K+VSWYDNEWGYS RV+DL+
Sbjct: 289 ILGFTDDELVSADFINDNRSSIYDSKATLQNNLPGERRFFKIVSWYDNEWGYSHRVVDLV 348
Query: 299 VHMAKTQA 306
+MA A
Sbjct: 349 RYMAAKDA 356
>gnl|CDD|236079 PRK07729, PRK07729, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 343
Score = 335 bits (862), Expect = e-115
Identities = 143/294 (48%), Positives = 201/294 (68%), Gaps = 7/294 (2%)
Query: 13 YMFKYDSVHGQWKHNELKVK-DEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGV 71
++ KYD+VHG++ + V+ E LL K + + R+P+E+PW G + V+E+TG
Sbjct: 43 HLIKYDTVHGKF---DGTVEAFEDHLLVDGKKIRLLNNRDPKELPWTDLGIDIVIEATGK 99
Query: 72 FTDKDKAAAHLKGGAKKVVISAPSKDAPM-FVVGVNEKEYKPELD-IVSNASCTTNCLAP 129
F K+KA H++ GAKKV+++AP K+ + VVGVNE + E I+SNASCTTNCLAP
Sbjct: 100 FNSKEKAILHVEAGAKKVILTAPGKNEDVTIVVGVNEDQLDIEKHTIISNASCTTNCLAP 159
Query: 130 LAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGK 189
+ KV+ ++FGI GLMTTVH+ T QK +D P KD R RA +IIP++TGAAKA+ K
Sbjct: 160 VVKVLDEQFGIENGLMTTVHAYTNDQKNIDNPH-KDLRRARACGQSIIPTTTGAAKALAK 218
Query: 190 VLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTEE 249
VLP LNGKL GM+ RVPT +VS+VDL V ++++ T EEI A K + G LKGIL ++EE
Sbjct: 219 VLPHLNGKLHGMALRVPTPNVSLVDLVVDVKRDVTVEEINEAFKTAANGALKGILEFSEE 278
Query: 250 DVVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDLIVHMAK 303
+VS DF ++ S+I D + + + VK+++WYDNEWGYS RV+DL+ +A
Sbjct: 279 PLVSIDFNTNTHSAIIDGLSTMVMGDRKVKVLAWYDNEWGYSCRVVDLVTLVAD 332
>gnl|CDD|180962 PRK07403, PRK07403, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 337
Score = 307 bits (787), Expect = e-104
Identities = 145/288 (50%), Positives = 197/288 (68%), Gaps = 6/288 (2%)
Query: 13 YMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVF 72
++ KYDS+ G K N DE ++ K + RNP +PW + G + ++ESTGVF
Sbjct: 44 HLLKYDSMLG--KLNADISADENSITVNGKTIKCVSDRNPLNLPWKEWGIDLIIESTGVF 101
Query: 73 TDKDKAAAHLKGGAKKVVISAPSK--DAPMFVVGVNEKEYKPEL-DIVSNASCTTNCLAP 129
K+ A+ H++ GAKKV+I+AP K D +VVGVN EY E +I+SNASCTTNCLAP
Sbjct: 102 VTKEGASKHIQAGAKKVLITAPGKGEDIGTYVVGVNHHEYDHEDHNIISNASCTTNCLAP 161
Query: 130 LAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGK 189
+AKV+HD FGI++G MTT HS T Q+ +D S +D R RAA+ NI+P+STGAAKAV
Sbjct: 162 IAKVLHDNFGIIKGTMTTTHSYTGDQRILDA-SHRDLRRARAAAVNIVPTSTGAAKAVAL 220
Query: 190 VLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTEE 249
V+P L GKL G++ RVPT +VSVVDL V++EK E++ +K+ SEG LKGIL Y++
Sbjct: 221 VIPELKGKLNGIALRVPTPNVSVVDLVVQVEKRTITEQVNEVLKDASEGPLKGILEYSDL 280
Query: 250 DVVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDL 297
+VS+D+ G SSI DA + + + VK+++WYDNEWGYS RV+DL
Sbjct: 281 PLVSSDYRGTDASSIVDASLTMVMGGDMVKVIAWYDNEWGYSQRVVDL 328
>gnl|CDD|215572 PLN03096, PLN03096, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 395
Score = 304 bits (781), Expect = e-102
Identities = 140/287 (48%), Positives = 191/287 (66%), Gaps = 3/287 (1%)
Query: 12 TYMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGV 71
+++ KYDS G + ++K + + K + V RNP +PW + G + V+E TGV
Sbjct: 102 SHLLKYDSTLGTFD-ADVKPVGDDAISVDGKVIKVVSDRNPLNLPWGELGIDLVIEGTGV 160
Query: 72 FTDKDKAAAHLKGGAKKVVISAPSK-DAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPL 130
F D++ A H++ GAKKV+I+AP K D P +VVGVN +YK I+SNASCTTNCLAP
Sbjct: 161 FVDREGAGKHIQAGAKKVLITAPGKGDIPTYVVGVNADDYKHSDPIISNASCTTNCLAPF 220
Query: 131 AKVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKV 190
KV+ KFGI++G MTT HS T Q+ +D S +D R RAA+ NI+P+STGAAKAV V
Sbjct: 221 VKVLDQKFGIIKGTMTTTHSYTGDQRLLDA-SHRDLRRARAAALNIVPTSTGAAKAVALV 279
Query: 191 LPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTEED 250
LP L GKL G++ RVPT +VSVVDL V++EK+ EE+ A ++ +E +LKGIL +E
Sbjct: 280 LPNLKGKLNGIALRVPTPNVSVVDLVVQVEKKTFAEEVNAAFRDAAEKELKGILAVCDEP 339
Query: 251 VVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDL 297
+VS DF SS D+ + + + VK+V+WYDNEWGYS RV+DL
Sbjct: 340 LVSVDFRCSDVSSTIDSSLTMVMGDDMVKVVAWYDNEWGYSQRVVDL 386
>gnl|CDD|215131 PLN02237, PLN02237, glyceraldehyde-3-phosphate dehydrogenase B.
Length = 442
Score = 306 bits (785), Expect = e-102
Identities = 146/290 (50%), Positives = 202/290 (69%), Gaps = 6/290 (2%)
Query: 12 TYMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGV 71
+++ KYDS+ G +K ++K+ D++T+ KP+ V R+P ++PWA+ G + V+E TGV
Sbjct: 117 SHLLKYDSMLGTFK-ADVKIVDDETISVDGKPIKVVSNRDPLKLPWAELGIDIVIEGTGV 175
Query: 72 FTDKDKAAAHLKGGAKKVVISAPSK--DAPMFVVGVNEKEYKPEL-DIVSNASCTTNCLA 128
F D A H++ GAKKV+I+AP+K D P +VVGVNE +Y E+ +IVSNASCTTNCLA
Sbjct: 176 FVDGPGAGKHIQAGAKKVIITAPAKGADIPTYVVGVNEDDYDHEVANIVSNASCTTNCLA 235
Query: 129 PLAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVG 188
P KV+ ++FGIV+G MTT HS T Q+ +D S +D R RAA+ NI+P+STGAAKAV
Sbjct: 236 PFVKVLDEEFGIVKGTMTTTHSYTGDQRLLDA-SHRDLRRARAAALNIVPTSTGAAKAVS 294
Query: 189 KVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEA-TYEEIKNAIKEESEGKLKGILGYT 247
VLP L GKL G++ RVPT +VSVVDL V +EK+ T E++ A ++ ++G LKGIL
Sbjct: 295 LVLPQLKGKLNGIALRVPTPNVSVVDLVVNVEKKGITAEDVNAAFRKAADGPLKGILAVC 354
Query: 248 EEDVVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDL 297
+ +VS DF SS DA + + + VK+V+WYDNEWGYS RV+DL
Sbjct: 355 DVPLVSVDFRCSDVSSTIDASLTMVMGDDMVKVVAWYDNEWGYSQRVVDL 404
>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 = 279 bits (715), Expect = 1e-95
Identities = 114/158 (72%), Positives = 130/158 (82%), Gaps = 1/158 (0%)
Query: 127 LAPLAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKA 186
LAPLAKV++D FGI +GLMTTVH+ TA QK VD PS KD R GRAA+ NIIP+STGAAKA
Sbjct: 1 LAPLAKVLNDNFGIEKGLMTTVHAYTADQKLVD-PSHKDLRRGRAAAPNIIPTSTGAAKA 59
Query: 187 VGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGY 246
VG VLP L GKLTGM+FRVPT +VSVVDLTV LEK T EE+ A+KE +EG LKGILGY
Sbjct: 60 VGLVLPELKGKLTGMAFRVPTPNVSVVDLTVELEKPVTVEEVNAALKEAAEGALKGILGY 119
Query: 247 TEEDVVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWY 284
TEE +VS+DFVGD SSIFDAKA I L+ NFVK+V+WY
Sbjct: 120 TEEPLVSSDFVGDPHSSIFDAKATIVLNGNFVKVVAWY 157
>gnl|CDD|169599 PRK08955, PRK08955, glyceraldehyde-3-phosphate dehydrogenase;
Validated.
Length = 334
Score = 257 bits (658), Expect = 1e-84
Identities = 119/289 (41%), Positives = 179/289 (61%), Gaps = 8/289 (2%)
Query: 13 YMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVF 72
++ ++DSVHG+W H + ++ K + + + W +G + V+E++GV
Sbjct: 44 HLLEFDSVHGRWHHE--VTAEGDAIVINGKRIRTTQNKAIADTDW--SGCDVVIEASGVM 99
Query: 73 TDKDKAAAHLKGGAKKVVISAPSKDAPMF--VVGVNEKEYKPELD-IVSNASCTTNCLAP 129
K A+L G K+VV++AP K+ + V+GVN+ + P + IV+ ASCTTNCLAP
Sbjct: 100 KTKALLQAYLDQGVKRVVVTAPVKEEGVLNIVMGVNDHLFDPAIHPIVTAASCTTNCLAP 159
Query: 130 LAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGK 189
+ KVIH+K GI G MTT+H +T TQ +D P KD R RA ++IP++TG+A A+ +
Sbjct: 160 VVKVIHEKLGIKHGSMTTIHDLTNTQTILDAPH-KDLRRARACGMSLIPTTTGSATAITE 218
Query: 190 VLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTEE 249
+ P L GKL G + RVP + S+ D +E++ T EE+ +KE +EG+LKGILGY E
Sbjct: 219 IFPELKGKLNGHAVRVPLANASLTDCVFEVERDTTVEEVNALLKEAAEGELKGILGYEER 278
Query: 250 DVVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDLI 298
+VS D+ D RSSI DA + + ++ VKL +WYDNEWGY++R +L
Sbjct: 279 PLVSIDYKTDPRSSIVDALSTMVVNGTQVKLYAWYDNEWGYANRTAELA 327
>gnl|CDD|236219 PRK08289, PRK08289, glyceraldehyde-3-phosphate dehydrogenase;
Reviewed.
Length = 477
Score = 256 bits (656), Expect = 2e-82
Identities = 116/294 (39%), Positives = 170/294 (57%), Gaps = 8/294 (2%)
Query: 16 KYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAE--YVVESTGVFT 73
+ DSVHG + ++ ++ + V +PEE+ + G VV++TG +
Sbjct: 179 RRDSVHGPFNGTITVDEENNAIIANGNYIQVIYANSPEEVDYTAYGINNALVVDNTGKWR 238
Query: 74 DKDKAAAHLKG-GAKKVVISAPSK-DAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLA 131
D++ + HLK G KV+++AP K D V GVN + E IVS ASCTTN + P+
Sbjct: 239 DEEGLSQHLKSKGVAKVLLTAPGKGDIKNIVHGVNHSDITDEDKIVSAASCTTNAITPVL 298
Query: 132 KVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVL 191
K ++DK+GIV G + TVHS T Q +D D R GR+A N++ + TGAAKAV K L
Sbjct: 299 KAVNDKYGIVNGHVETVHSYTNDQNLIDNYHKGD-RRGRSAPLNMVITETGAAKAVAKAL 357
Query: 192 PALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEES-EGKLKGILGYTEE- 249
P L GKLTG + RVPT +VS+ L + LEKE + EE+ +++ S L+ + YT+
Sbjct: 358 PELAGKLTGNAIRVPTPNVSMAILNLNLEKETSREELNEYLRQMSLHSPLQNQIDYTDST 417
Query: 250 DVVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDLIVHMAK 303
+VVS+DFVG + + D++A I V L WYDNE+GYS +V+ ++ MA
Sbjct: 418 EVVSSDFVGSRHAGVVDSQATIVNGNRAV-LYVWYDNEFGYSCQVVRVMEQMAG 470
>gnl|CDD|184122 PRK13535, PRK13535, erythrose 4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 243 bits (621), Expect = 6e-79
Identities = 107/297 (36%), Positives = 170/297 (57%), Gaps = 9/297 (3%)
Query: 13 YMFKYDSVHGQWKHNELKVKDEKTLLF-GEKPVAVFGFRNPEEIPWAKTGAEYVVESTGV 71
++ KYD+ HG++ V+ E+ LF G+ + + R+ +PW + G + V++ TGV
Sbjct: 45 HLLKYDTSHGRFAW---DVRQERDQLFVGDDAIRLLHERDIASLPWRELGVDVVLDCTGV 101
Query: 72 FTDKDKAAAHLKGGAKKVVISAPSK---DAPMFVVGVNEKEYKPELDIVSNASCTTNCLA 128
+ ++ AH+ GAKKV+ S P DA + V GVN + + E IVSNASCTTNC+
Sbjct: 102 YGSREDGEAHIAAGAKKVLFSHPGSNDLDATV-VYGVNHDQLRAEHRIVSNASCTTNCII 160
Query: 129 PLAKVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVG 188
P+ K++ D FGI G +TT+HS Q+ +D D R RAAS +IIP T A +
Sbjct: 161 PVIKLLDDAFGIESGTVTTIHSAMNDQQVIDA-YHPDLRRTRAASQSIIPVDTKLAAGIT 219
Query: 189 KVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTE 248
++ P N + +S RVPT++V+ +DL+V ++K E+ +++ ++G GI+ YTE
Sbjct: 220 RIFPQFNDRFEAISVRVPTINVTAIDLSVTVKKPVKVNEVNQLLQKAAQGAFHGIVDYTE 279
Query: 249 EDVVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDLIVHMAKTQ 305
+VS DF D S+I D + +K + W DNEWG+++R++D + MA
Sbjct: 280 LPLVSIDFNHDPHSAIVDGTQTRVSGAHLIKTLVWCDNEWGFANRMLDTTLAMAAAG 336
>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 = 226 bits (577), Expect = 1e-72
Identities = 105/286 (36%), Positives = 169/286 (59%), Gaps = 5/286 (1%)
Query: 13 YMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVF 72
++ KYD+ HG++ E++ D L G+ + V R+ + +PW + G + V++ TGV+
Sbjct: 43 HLLKYDTSHGRFA-WEVRQ-DRDQLFVGDDAIRVLHERSLQSLPWRELGVDLVLDCTGVY 100
Query: 73 TDKDKAAAHLKGGAKKVVISAP-SKDAPMFVV-GVNEKEYKPELDIVSNASCTTNCLAPL 130
++ AH+ GAKKV+ S P + D +V GVN+ + + E IVSNASCTTNC+ P+
Sbjct: 101 GSREHGEAHIAAGAKKVLFSHPGASDLDATIVYGVNQDQLRAEHRIVSNASCTTNCIVPV 160
Query: 131 AKVIHDKFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKV 190
K++ D +GI G +TT+HS Q+ +D D R RAAS +IIP T A + +
Sbjct: 161 IKLLDDAYGIESGTITTIHSAMNDQQVIDA-YHPDLRRTRAASQSIIPVDTKLAAGIERF 219
Query: 191 LPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYTEED 250
P N + ++ RVPTV+V+ +DL+V ++K E+ +++ ++G L+GI+ YTE
Sbjct: 220 FPQFNDRFEAIAVRVPTVNVTAIDLSVTVKKPVKANEVNLLLQKAAQGALRGIVDYTELP 279
Query: 251 VVSTDFVGDSRSSIFDAKAGIALSKNFVKLVSWYDNEWGYSSRVID 296
+VS DF D S+I D + VK + W DNEWG+++R++D
Sbjct: 280 LVSVDFNHDPHSAIVDGTQTRVSGAHLVKTLVWCDNEWGFANRMLD 325
>gnl|CDD|173546 PTZ00353, PTZ00353, glycosomal glyceraldehyde-3-phosphate
dehydrogenase; Provisional.
Length = 342
Score = 165 bits (418), Expect = 1e-48
Identities = 80/296 (27%), Positives = 152/296 (51%), Gaps = 3/296 (1%)
Query: 8 INMQTYMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVE 67
I Y+ + +S ++V E+ +L G + + V + EI W G +YVVE
Sbjct: 39 IAYIAYVLEQESPLSAPDGASIRVVGEQIVLNGTQKIRVSAKHDLVEIAWRDYGVQYVVE 98
Query: 68 STGVFTDKDKAAAHLKGGAKKVVISAPSKDAPMFVVGVNEKEYKPELDIVSNASCTTNCL 127
TG+++ + + H+ GGAK V ++ S DAP + G N++ L + + L
Sbjct: 99 CTGLYSTRSRCWGHVTGGAKGVFVAGQSADAPTVMAGSNDERLSASLPVCCAGAPIAVAL 158
Query: 128 APLAKVIHDKFGIVEGLMTTVHSITATQKT-VDGPSMKDWRGGRAASFNIIPSSTGAAKA 186
AP+ + +H+ +G+ E T +H + + + +DWR R A I P A+
Sbjct: 159 APVIRALHEVYGVEECSYTAIHGMQPQEPIAARSKNSQDWRQTRVAIDAIAPYRDNGAET 218
Query: 187 VGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGY 246
V K+LP L G+++G +F+VP +D+ VR ++ + E + +A+ E + +L G+L
Sbjct: 219 VCKLLPHLVGRISGSAFQVPVKKGCAIDMLVRTKQPVSKEVVDSALAEAASDRLNGVLCI 278
Query: 247 TEEDVVSTDFVGDSRSSIFDAKAGIALSKNFV-KLVSWYDNEWGYSSRVIDLIVHM 301
++ D++S D + + + +DA + + + V K+V W+D E Y++R++ L+ +
Sbjct: 279 SKRDMISVDCIPNGK-LCYDATSSSSSREGEVHKMVLWFDVECYYAARLLSLVKQL 333
>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 = 156 bits (397), Expect = 9e-48
Identities = 62/110 (56%), Positives = 80/110 (72%), Gaps = 3/110 (2%)
Query: 13 YMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVF 72
Y+ KYDSVHG++ E++V ++ L+ K + VF R+P E+PW + G + VVESTGVF
Sbjct: 41 YLLKYDSVHGRFDG-EVEVDEDG-LIVNGKKIKVFAERDPAELPWGELGVDIVVESTGVF 98
Query: 73 TDKDKAAAHLKGGAKKVVISAPSKD-APMFVVGVNEKEYKPELDIVSNAS 121
T +KA AHLK GAKKV+ISAP+KD P FV GVN ++Y PE DIVSNAS
Sbjct: 99 TTAEKAEAHLKAGAKKVIISAPAKDDDPTFVYGVNHEDYDPEDDIVSNAS 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 = 151 bits (383), Expect = 1e-45
Identities = 59/111 (53%), Positives = 77/111 (69%), Gaps = 3/111 (2%)
Query: 13 YMFKYDSVHGQWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVF 72
Y+ KYDSVHG++ ++V+ + L+ K + VF R+P +PW + G + VVE TG F
Sbjct: 41 YLLKYDSVHGRFPG-TVEVEGD-GLVVNGKAIKVFAERDPANLPWGELGVDIVVECTGGF 98
Query: 73 TDKDKAAAHLKGGAKKVVISAPSKDA-PMFVVGVNEKEYKPELDIVSNASC 122
T ++KA+AHLK GAKKV+ISAPSKDA P FV GVN EY E I+SNASC
Sbjct: 99 TTREKASAHLKAGAKKVIISAPSKDADPTFVYGVNHDEYDGEDHIISNASC 149
>gnl|CDD|223214 COG0136, Asd, Aspartate-semialdehyde dehydrogenase [Amino acid
transport and metabolism].
Length = 334
Score = 55.3 bits (134), Expect = 9e-09
Identities = 53/235 (22%), Positives = 87/235 (37%), Gaps = 43/235 (18%)
Query: 39 FGEKPVAVFGFRNPEEIP--WAKTGAEYVVESTGVFTDKDKAAAHLKGGAK--KVVISAP 94
FG K + V PE+ + + + V + G + A+ VVI
Sbjct: 47 FGGKSIGV-----PEDAADEFVFSDVDIVFFAAG----GSVSKEVEPKAAEAGCVVIDNS 97
Query: 95 S-----KDAPMFVVGVNE---KEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMT 146
S D P+ V VN +Y+ I++N +C+T L K +HD FGI +++
Sbjct: 98 SAFRMDPDVPLVVPEVNPEHLIDYQKRGFIIANPNCSTIQLVLALKPLHDAFGIKRVVVS 157
Query: 147 TVHSI----------TATQKTVDGPSMKDWRGGRAASFNIIP-----SSTGAAKA----- 186
T ++ A Q + G +FN+IP G K
Sbjct: 158 TYQAVSGAGAEGGVELAGQTDALLNGIPILPIGYPLAFNVIPHIDGFLDNGYTKEEWKIE 217
Query: 187 --VGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGK 239
K+L + K++ RVP +TV +K+ EEI+ + + G
Sbjct: 218 AETRKILGDPDIKVSATCVRVPVFYGHSEAVTVEFKKDVDPEEIREELLPSAPGV 272
>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 = 45.6 bits (108), Expect = 2e-05
Identities = 55/249 (22%), Positives = 90/249 (36%), Gaps = 46/249 (18%)
Query: 68 STGVFTDKDKAAAHLKGGAKKVVISAPS-----KDAPMFVVGVNEKEYK--PELDIVSNA 120
S G K+ A K G +VI S D P+ V VN ++ K I++N
Sbjct: 68 SAGGSVSKEFAPKAAKAGV--IVIDNTSAFRMDPDVPLVVPEVNFEDLKEFNPKGIIANP 125
Query: 121 SCTTNCLAPLAKVIHDKFGIVEGLMTTVHSIT-ATQKTVDG--PSMKDWRGGRAA----- 172
+C+T + + K +HD+ I +++T +++ A V+ K G
Sbjct: 126 NCSTIQMVVVLKPLHDEAKIKRVVVSTYQAVSGAGNAGVEELYNQTKAVLEGAEQLPYIQ 185
Query: 173 ----------SFNIIP------------SSTGAAKAVGKVLPALNGKLTGMSFRVPTVDV 210
+FN IP K++ + K++ RVP
Sbjct: 186 PKANKFPYQIAFNAIPHIDSFVDDGYTKEEQKMLFETRKIMGIPDLKVSATCVRVPVFTG 245
Query: 211 SVVDLTVRLEKEATYEEIKNAIKEESEGKL----KGILGYTEEDVVSTD--FVGDSRSSI 264
+ + EKE + E+ + +K +L G L T V D FVG R +
Sbjct: 246 HSESINIEFEKEISPEDARELLKNAPGVQLIDDPSGNLYPTPLAAVGVDEVFVGRIRKDL 305
Query: 265 FDAKAGIAL 273
D G+ L
Sbjct: 306 PDGN-GLHL 313
>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 = 38.2 bits (89), Expect = 0.003
Identities = 52/194 (26%), Positives = 77/194 (39%), Gaps = 36/194 (18%)
Query: 86 AKKVVISAPSK-----DAPMFVVGVN---------EKEYKPELDIVSNASCTTNCLAPLA 131
A K V S S D P+ + VN +KE + IV+N +CTT L
Sbjct: 96 AGKPVFSNASNHRMDPDVPLIIPEVNSDHLELLKVQKERGWKGFIVTNPNCTTAGLTLAL 155
Query: 132 KVIHDKFGIVEGLMTTVHSIT-ATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKV 190
K + D FGI + +TT+ +++ A V PSM NIIP G + + +
Sbjct: 156 KPLIDAFGIKKVHVTTMQAVSGAGYPGV--PSM-------DILDNIIPHIGGEEEKIERE 206
Query: 191 LPALNGKLTG------------MSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEG 238
+ GKL + RVP +D + V +K+ EEI+ A+K
Sbjct: 207 TRKILGKLENGKIEPAPFSVSATTTRVPVLDGHTESVHVEFDKKFDIEEIREALKSFRGL 266
Query: 239 KLKGILGYTEEDVV 252
K L E +
Sbjct: 267 PQKLGLPSAPEKPI 280
>gnl|CDD|236329 PRK08664, PRK08664, aspartate-semialdehyde dehydrogenase; Reviewed.
Length = 349
Score = 36.0 bits (84), Expect = 0.021
Identities = 34/133 (25%), Positives = 58/133 (43%), Gaps = 25/133 (18%)
Query: 116 IVSNASCTTNCLAPLAKVIHDKFGIVEGLMTTVHSITATQKT-VDGPSMKDWRGGRAASF 174
IV+N +C+T L K + D FGI +TT+ +I+ V + D
Sbjct: 144 IVTNPNCSTIGLVLALKPLMD-FGIERVHVTTMQAISGAGYPGVPSMDIVD--------- 193
Query: 175 NIIPSSTG-AAKAV------------GKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEK 221
N+IP G K GK++PA + ++ RVP +D + V+ ++
Sbjct: 194 NVIPYIGGEEEKIEKETLKILGKFEGGKIVPA-DFPISATCHRVPVIDGHTEAVFVKFKE 252
Query: 222 EATYEEIKNAIKE 234
+ EEI+ A++
Sbjct: 253 DVDPEEIREALES 265
>gnl|CDD|179786 PRK04207, PRK04207, glyceraldehyde-3-phosphate dehydrogenase;
Provisional.
Length = 341
Score = 33.3 bits (77), Expect = 0.13
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 177 IPSSTGAAKAVGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEES 236
+PS G V VLP L+ +T M+ +VPT + + + V L+K T EE+ A++
Sbjct: 190 VPSHHG--PDVKTVLPDLD--ITTMAVKVPTTLMHMHSVNVELKKPVTKEEVLEALENTP 245
>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 = 31.8 bits (73), Expect = 0.35
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 1 MYIVYFEINMQ-TYMFKYDSVHGQWKHNEL 29
+ V+F N TY++ D G W L
Sbjct: 87 TFYVFFCTNTGGTYIYTADDPEGPWTKTAL 116
>gnl|CDD|136022 PRK06728, PRK06728, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 347
Score = 31.6 bits (71), Expect = 0.55
Identities = 36/170 (21%), Positives = 64/170 (37%), Gaps = 33/170 (19%)
Query: 95 SKDAPMFVVGVNEKEYKPELDIVSNASCTTNCLAPLAKVIHDKFGIVEGLMTT------- 147
+ D P+ V VN K I++ +C+ + + I FG+ +++T
Sbjct: 105 AHDVPLVVPEVNAHTLKEHKGIIAVPNCSALQMVTALQPIRKVFGLERIIVSTYQAVSGS 164
Query: 148 -VHSITATQKTVDG------------PSMKDWRGGRAASFNIIPS------------STG 182
+H+I ++ P+ KD + +FN++P
Sbjct: 165 GIHAIQELKEQAKSILAGEEVESTILPAKKD-KKHYPIAFNVLPQVDIFTDNDFTFEEVK 223
Query: 183 AAKAVGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAI 232
+ K+L N K+ RVP + + + LEKEAT EIK +
Sbjct: 224 MIQETKKILEDPNLKMAATCVRVPVISGHSESVYIELEKEATVAEIKEVL 273
>gnl|CDD|129632 TIGR00541, hisDCase_pyru, histidine decarboxylase, pyruvoyl type.
This enzyme converts histadine to histamine in a single
step by catalyzing the release of CO2. This type is
synthesized as an inactive single chain precursor, then
cleaved into two chains. The Ser at the new N-terminus
at the cleavage site is converted to a pyruvoyl group
essential for activity. This type of histidine
decarboxylase appears is known so far only in some
Gram-positive bacteria, where it may play a role in
amino acid catabolism. There is also a pyridoxal
phosphate type histidine decarboxylase, as found in
human, where histamine is a biologically active amine
[Energy metabolism, Amino acids and amines].
Length = 310
Score = 31.1 bits (70), Expect = 0.68
Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 13/101 (12%)
Query: 23 QWKHNELKVKDEKTLLFGEKPVAVFGFRNPEEIPWAKTGAEYVVESTGVFTDKDKAAAHL 82
Q+ +ELK+ D K LL + + +FG A GA + + G ++ K A L
Sbjct: 113 QFDGSELKIYDAKPLL--DAGIELFGTEKDRRFTPAP-GAFIICANKGATAERPKEDADL 169
Query: 83 KGGAKKVVISA--------PSKDAPMFV--VGVNEKEYKPE 113
K G V SA P A +F+ G+ EK +
Sbjct: 170 KEGEAYGVWSAIAISFAKDPDHCADLFIEDAGLWEKNDNED 210
>gnl|CDD|237845 PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase;
Provisional.
Length = 334
Score = 30.5 bits (70), Expect = 0.97
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 14/72 (19%)
Query: 77 KAAAHLKGGAKKVVI---SAPSKDA--PMFVVGVNE---KEYKPELDIVSNASCTTNCLA 128
KAAA GA VVI SA D P+ V VN E++ + I++N +C+T +
Sbjct: 82 KAAAA---GA--VVIDNSSAFRMDPDVPLVVPEVNPEALAEHRKK-GIIANPNCSTIQMV 135
Query: 129 PLAKVIHDKFGI 140
K +HD GI
Sbjct: 136 VALKPLHDAAGI 147
>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 = 28.8 bits (65), Expect = 1.7
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 5/63 (7%)
Query: 51 NPEEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVVISAPSKDAPMFVVGVNEKEY 110
NP W E +D+ L G K+++S + A F V+ + +
Sbjct: 3 NPLSSEW-----ELFDPGWEQPHIRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRAW 57
Query: 111 KPE 113
P+
Sbjct: 58 YPD 60
>gnl|CDD|197390 cd10155, BsYrkD-like_DUF156, Uncharacterized protein YrkD from
Bacillus subtilis and related domains; this domain
superfamily was previously known as part of DUF156.
This domain family contains an uncharacterized protein
YrkD from Bacillus subtilis and related proteins. This
family is part of a larger superfamily that contains
various transcriptional regulators that respond to
different stressors such as Cu(I), Ni(I), sulfite, and
formaldehyde, and includes CsoRs (copper-sensitive
operon repressors). CsoRs form homotetramers (dimer of
dimers). In Mycobacterium tuberculosis CsoR, within each
dimer, two Cys residues on opposite subunits, along with
a His residue, bind the Cu(I) ion (forming a triagonal
S2N coordination complex, C-H-C). These residues are
conserved in the majority of members of this
superfamily. In this family, however, not all these
residues are conserved, there is an Asn instead of the
His (C-N-C); also a conserved Tyr and a Glu residue that
facilitates allosteric regulation of DNA binding for
CsoRs are very poorly conserved.
Length = 82
Score = 27.6 bits (62), Expect = 1.9
Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 9/62 (14%)
Query: 225 YEEIKNAIKEESEGKLKGILGYTEE-----DVVSTDFVGDSRSSIFDAKAGIALSKNFVK 279
++IKN +K +EG+L+GIL EE DVV+ + RSS+ D G+ +++N +
Sbjct: 1 DKKIKNRLKR-AEGQLRGILKMMEEGKECKDVVTQ--LSAVRSSV-DRAIGLIVAENLEE 56
Query: 280 LV 281
V
Sbjct: 57 CV 58
>gnl|CDD|226612 COG4127, COG4127, Uncharacterized conserved protein [Function
unknown].
Length = 318
Score = 29.5 bits (66), Expect = 2.1
Identities = 21/117 (17%), Positives = 37/117 (31%), Gaps = 3/117 (2%)
Query: 188 GKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKEESEGKLKGILGYT 247
V L G S V + VV + + + +E IK+ K + L
Sbjct: 145 DLVPEKLPGSDVVPSVPVSGEEDEVVSNPLDVMEMIAFEIIKD-RKSRFDWDEMQNLV-A 202
Query: 248 EEDVVSTDFVGDSRSS-IFDAKAGIALSKNFVKLVSWYDNEWGYSSRVIDLIVHMAK 303
E + G R I + G+ + + + E S +++ I K
Sbjct: 203 EVLKIMGYKTGADREKDIIASPDGLGFENPRIIVEVKHRREQMSSQQILSFIGGRHK 259
>gnl|CDD|215528 PLN02977, PLN02977, glutathione synthetase.
Length = 478
Score = 29.6 bits (67), Expect = 2.3
Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 14/72 (19%)
Query: 26 HNELKVKDEKTLLFGEKPVAVFGFRN-------PEEIPWAKTGAEYVVE-STGVFTDKDK 77
E + ++ TL +PVAV FR P E W A ++E S+ V K
Sbjct: 247 AAEGSLDEDGTLTVDGQPVAVVYFRAGYAPTDYPSEAEWR---ARLLLERSSAV---KCP 300
Query: 78 AAAHLKGGAKKV 89
+ A+ G KKV
Sbjct: 301 SIAYHLAGTKKV 312
>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 = 29.1 bits (65), Expect = 3.4
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 177 IPSSTGAAKAVGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEIKNAIKE 234
+PS G V V+P LN + M+F VPT + V + V L+K T ++I + ++
Sbjct: 187 VPSHHG--PDVQTVIPNLN--IETMAFVVPTTLMHVHSIMVELKKPVTKDDIIDILEN 240
>gnl|CDD|177348 PHA02106, PHA02106, hypothetical protein.
Length = 91
Score = 27.4 bits (60), Expect = 3.4
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 277 FVKLVSWYDNEWGYSSRVI 295
F K V WY+ EW Y ++
Sbjct: 8 FDKAVKWYEQEWYYGKWIV 26
>gnl|CDD|223965 COG1034, NuoG, NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75
kD subunit (chain G) [Energy production and conversion].
Length = 693
Score = 28.9 bits (65), Expect = 4.3
Identities = 20/85 (23%), Positives = 28/85 (32%), Gaps = 5/85 (5%)
Query: 169 GRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKEATYEEI 228
GR FN G + +VL AL +L G+ +D L + I
Sbjct: 572 GRVQRFNQALRPGGDEREDWRVLHALASEL-GLKLDFDQLDAVRAAL---AAAHPGFALI 627
Query: 229 KNAIKEESEGKLKGILGYTEEDVVS 253
+A K E E G +S
Sbjct: 628 DSAAKGERE-PPAGEGILANRANIS 651
>gnl|CDD|148644 pfam07154, DUF1392, Protein of unknown function (DUF1392). This
family consists of several hypothetical cyanobacterial
proteins of around 150 residues in length which seem to
be specific to Anabaena species. The function of this
family is unknown.
Length = 150
Score = 27.8 bits (62), Expect = 4.9
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 281 VSWYDNEWGYSSRVIDLIVHMAKTQ 305
V WYD+ W YS + I++ K Q
Sbjct: 47 VEWYDDCWNYSIESDNEIIYATKHQ 71
>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 = 28.1 bits (63), Expect = 5.1
Identities = 12/51 (23%), Positives = 22/51 (43%)
Query: 53 EEIPWAKTGAEYVVESTGVFTDKDKAAAHLKGGAKKVVISAPSKDAPMFVV 103
E GA+ V+++ G +A L+ G + VV+ S P+ +
Sbjct: 193 ELRLTGGGGADVVIDAVGGPETLAQALRLLRPGGRIVVVGGTSGGPPLDDL 243
>gnl|CDD|235287 PRK04342, PRK04342, DNA topoisomerase VI subunit A; Provisional.
Length = 367
Score = 27.9 bits (63), Expect = 6.3
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 11/45 (24%)
Query: 51 NPEEIPWAKTGAEYV--VESTGV--------FTDKDKAA-AHLKG 84
N + I + A++V VE G+ F K A HLKG
Sbjct: 179 NVDNIEFVDVDADFVLAVEKGGMFQRLVEEGFWKKYNAILVHLKG 223
>gnl|CDD|153089 cd02888, RNR_II_dimer, Class II ribonucleotide reductase, dimeric
form. Ribonucleotide reductase (RNR) catalyzes the
reductive synthesis of deoxyribonucleotides from their
corresponding ribonucleotides. It provides the
precursors necessary for DNA synthesis. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs, found in
eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophage, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class II RNRs are found in bacteria that
can live under both aerobic and anaerobic conditions.
Many, but not all members of this class are found to be
homodimers. Adenosylcobalamin interacts directly with an
active site cysteine to form the reactive cysteine
radical.
Length = 464
Score = 28.0 bits (63), Expect = 8.0
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 216 TVRLEKEATYEEIKNAIKEESEGKLKGI 243
T+ L +AT E+++ + LKGI
Sbjct: 431 TINLPNDATVEDVEAVYLLAWKLGLKGI 458
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
0.315 0.132 0.381
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: 15,395,020
Number of extensions: 1469625
Number of successful extensions: 1542
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1480
Number of HSP's successfully gapped: 54
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
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 (21.6 bits)
S2: 59 (26.4 bits)