RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8193
(428 letters)
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 522 bits (1348), Expect = 0.0
Identities = 190/411 (46%), Positives = 270/411 (65%), Gaps = 1/411 (0%)
Query: 18 LGPWGVYLQQIDRVTPYLGSLSRWIEILKHPKKILIVDVPIEHDNGEVFHYEGYRVQHNI 77
+ ++++++ L +E LK P++++ V +P+ D+G V + GYRVQHN
Sbjct: 1 ENEFEQAVKELEKALEPLYLDEGVLERLKEPERVIQVRIPVRMDDGSVKVFRGYRVQHNS 60
Query: 78 LRGPGKGGVRFHPDVTLSEIIALSGWMTIKNAAVNIPYGGAKGGIRVNPKNLSNNELMRL 137
GP KGGVRFHP VTL E+ ALS WMT+KNA +PYGG KGGI V+PK LS+ EL RL
Sbjct: 61 ALGPYKGGVRFHPYVTLEEVKALSFWMTLKNALAGLPYGGGKGGIIVDPKGLSDGELERL 120
Query: 138 TRRYTNEISSIIGLNKDIPAPDVGTDMQIMSWMMDTYSTKKNYTIPGIVTGKPISIGGSF 197
+R + I +IG + DIPAPDVGT+ Q M+WMMD YS + PG+ TGKP+ +GGS
Sbjct: 121 SRAFGRAIYRLIGPDTDIPAPDVGTNPQDMAWMMDEYSKIVGNSAPGVFTGKPLELGGSL 180
Query: 198 GRQKATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDK 257
GR +ATG GVF + + ++ +++++QGFGNVG AA + GAK+VA+ D K
Sbjct: 181 GRSEATGYGVFYAIREALKALGDDLEGARVAVQGFGNVGQYAAEKLHELGAKVVAVSDSK 240
Query: 258 TTIYNPNGFNIPKLQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPAAIEDQITINN 317
IY+ +G ++ L + S+ ++ E I ++E + CDILIP A+E+ IT +N
Sbjct: 241 GGIYDEDGLDVEALLELKERRGSVAEYAGAEYI-TNEELLEVDCDILIPCALENVITEDN 299
Query: 318 ANNVTAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSNLLWT 377
A+ + AKI++EGANGPTT EAD+IL ++GI++ PD++ NAGGVIVSY EWVQN L WT
Sbjct: 300 ADQLKAKIVVEGANGPTTPEADEILLERGILVVPDILANAGGVIVSYLEWVQNAQGLYWT 359
Query: 378 EQEINLRLNNIICNAFDAIWELANTKKVSLRTAAFIIGCTRVLQAHKTRGL 428
E+E++ +L I+ NAF+A+++ A V LRTAA+I+ RV A K RG
Sbjct: 360 EEEVDEKLERIMVNAFEAVYQAAKEYGVDLRTAAYILAFERVADAMKARGW 410
>gnl|CDD|178095 PLN02477, PLN02477, glutamate dehydrogenase.
Length = 410
Score = 429 bits (1106), Expect = e-149
Identities = 182/412 (44%), Positives = 255/412 (61%), Gaps = 5/412 (1%)
Query: 16 NDLGPWGVYLQQIDRVTPYLGSLSRWIEILKHPKKILIVDVPIEHDNGEVFHYEGYRVQH 75
N L ++ R+ L + + I P + + V+ I D+G + + G+RVQH
Sbjct: 2 NALAATNRNFREAARLLGLDSKLEKSLLI---PFREIKVECTIPKDDGTLASFVGFRVQH 58
Query: 76 NILRGPGKGGVRFHPDVTLSEIIALSGWMTIKNAAVNIPYGGAKGGIRVNPKNLSNNELM 135
+ RGP KGG+R+HP+V E+ AL+ MT K A NIPYGGAKGGI +P++LS +EL
Sbjct: 59 DNARGPMKGGIRYHPEVDPDEVNALAQLMTWKTAVANIPYGGAKGGIGCDPRDLSESELE 118
Query: 136 RLTRRYTNEISSIIGLNKDIPAPDVGTDMQIMSWMMDTYSTKKNYTIPGIVTGKPISIGG 195
RLTR +T +I +IG++ D+PAPD+GT+ Q M+W++D YS ++ P +VTGKPI +GG
Sbjct: 119 RLTRVFTQKIHDLIGIHTDVPAPDMGTNAQTMAWILDEYSKFHGFS-PAVVTGKPIDLGG 177
Query: 196 SFGRQKATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQD 255
S GR+ ATGRGV + ++ +I IQGFGNVGS AA L + G KIVA+ D
Sbjct: 178 SLGREAATGRGVVFATEALLAEHGKSIAGQTFVIQGFGNVGSWAAQLIHEKGGKIVAVSD 237
Query: 256 DKTTIYNPNGFNIPKLQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPAAIEDQITI 315
+ N NG +IP L+K+V +K F G+ I D + PCD+LIPAA+ I
Sbjct: 238 ITGAVKNENGLDIPALRKHVAEGGGLKGFPGGDPI-DPDDILVEPCDVLIPAALGGVINK 296
Query: 316 NNANNVTAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSNLL 375
NA +V AK I+E AN PT EAD+ILR KG+++ PD+ N+GGV VSYFEWVQN+ +
Sbjct: 297 ENAADVKAKFIVEAANHPTDPEADEILRKKGVVVLPDIYANSGGVTVSYFEWVQNIQGFM 356
Query: 376 WTEQEINLRLNNIICNAFDAIWELANTKKVSLRTAAFIIGCTRVLQAHKTRG 427
W E+++N L+ + +AF A+ E+ T SLR AF +G RV +A RG
Sbjct: 357 WEEEKVNRELDRYMTDAFKALKEMCKTHNCSLRMGAFTLGVNRVARATVLRG 408
>gnl|CDD|133445 cd01076, NAD_bind_1_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 1. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
assimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 227
Score = 300 bits (770), Expect = e-101
Identities = 111/228 (48%), Positives = 155/228 (67%), Gaps = 1/228 (0%)
Query: 194 GGSFGRQKATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAI 253
GGS GR++ATGRGV + K+ + + ++++IQGFGNVGS AA +AGAK+VA+
Sbjct: 1 GGSLGREEATGRGVAYATREALKKLGIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVAV 60
Query: 254 QDDKTTIYNPNGFNIPKLQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPAAIEDQI 313
D TIYNP+G ++P L Y S+ F E+I + +E + CDILIPAA+E+QI
Sbjct: 61 SDSDGTIYNPDGLDVPALLAYKKEHGSVLGFPGAERITN-EELLELDCDILIPAALENQI 119
Query: 314 TINNANNVTAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSN 373
T +NA+ + AKII+E ANGPTT EAD+IL ++G+++ PD++ NAGGV VSYFEWVQNL
Sbjct: 120 TADNADRIKAKIIVEAANGPTTPEADEILHERGVLVVPDILANAGGVTVSYFEWVQNLQG 179
Query: 374 LLWTEQEINLRLNNIICNAFDAIWELANTKKVSLRTAAFIIGCTRVLQ 421
W E+E+N RL + AF+A+ E A V LRTAA+++ RV +
Sbjct: 180 FYWDEEEVNSRLETKMREAFEAVLETAEKYGVDLRTAAYVLALERVAE 227
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 283 bits (726), Expect = 2e-94
Identities = 104/237 (43%), Positives = 143/237 (60%), Gaps = 3/237 (1%)
Query: 194 GGSFGRQKATGRGVFIIGSKIASKINLNII-NSKISIQGFGNVGSVAANLFFKAGAKIVA 252
GGS GR +ATG GV + K+ + + +++QGFGNVGS AA + GAK+VA
Sbjct: 1 GGSLGRPEATGYGVVYFVEEALKKLGGDSLEGKTVAVQGFGNVGSYAAEKLLELGAKVVA 60
Query: 253 IQDDKTTIYNPNGFNIPKLQKYVTFTRS-IKDF-NEGEKINDSKEFWSIPCDILIPAAIE 310
+ D IY+PNG +I +L + + ++ G + +E W I CDIL+P A +
Sbjct: 61 VSDSSGYIYDPNGIDIEELLELKEEGGGRVVEYAGSGAEYISGEELWEIDCDILVPCATQ 120
Query: 311 DQITINNANNVTAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQN 370
++I NA + AK ++EGAN PTT EAD+IL ++GI+ APD NAGGV VSY E VQN
Sbjct: 121 NEINEENAKLIKAKAVVEGANMPTTPEADEILEERGILYAPDKAANAGGVTVSYLEMVQN 180
Query: 371 LSNLLWTEQEINLRLNNIICNAFDAIWELANTKKVSLRTAAFIIGCTRVLQAHKTRG 427
S L WTE+E++ +L I+ N F+A+ E A + LRTAA I G RV A K RG
Sbjct: 181 SSRLSWTEEEVDEKLEKIMTNIFEAVVETAKEYGIDLRTAANIAGFERVADAMKARG 237
>gnl|CDD|185433 PTZ00079, PTZ00079, NADP-specific glutamate dehydrogenase;
Provisional.
Length = 454
Score = 240 bits (613), Expect = 1e-74
Identities = 135/406 (33%), Positives = 207/406 (50%), Gaps = 17/406 (4%)
Query: 34 YLGSLSRWIEILKHPKKILIVDVPIEHDNGEVFHYEGYRVQHNILRGPGKGGVRFHPDVT 93
YLG L R +E P++++ VP D GE G+RVQ+N GP KGG+RFHP V
Sbjct: 52 YLGVLERLVE----PERVIQFRVPWVDDKGEQRVNRGFRVQYNSALGPYKGGLRFHPSVN 107
Query: 94 LSEIIALSGWMTIKNAAVNIPYGGAKGGIRVNPKNLSNNELMRLTRRYTNEISSIIGLNK 153
LS + L KN+ +P GG KGG +PK S+NE+MR + + E+ IG +
Sbjct: 108 LSILKFLGFEQIFKNSLTTLPMGGGKGGSDFDPKGKSDNEVMRFCQSFMTELYRHIGPDT 167
Query: 154 DIPAPDVGTDMQIMSWMMDTYSTKKNYTIPGIVTGKPISIGGSFGRQKATGRGVFIIGSK 213
D+PA D+G + + ++ Y +N G +TGK + GGS R +ATG G+ +
Sbjct: 168 DVPAGDIGVGGREIGYLFGQYKKLRN-NFEGTLTGKNVKWGGSNIRPEATGYGLVYFVLE 226
Query: 214 IASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKLQK 273
+ K+N ++ + + G GNV A + GAK++ + D I+ PNGF KL
Sbjct: 227 VLKKLNDSLEGKTVVVSGSGNVAQYAVEKLLQLGAKVLTMSDSDGYIHEPNGFTKEKLAY 286
Query: 274 YVTF----TRSIKDF---NEGEKINDSKEFWSIPCDILIPAAIEDQITINNANNVTA--- 323
+ +K++ + K K+ W +PCDI P A +++I + +A +
Sbjct: 287 LMDLKNVKRGRLKEYAKHSSTAKYVPGKKPWEVPCDIAFPCATQNEINLEDAKLLIKNGC 346
Query: 324 KIILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSNLLWTEQEINL 383
K++ EGAN PTT EA + + G+I P NAGGV +S E QN + L WT +E++
Sbjct: 347 KLVAEGANMPTTIEATHLFKKNGVIFCPGKAANAGGVAISGLEMSQNAARLQWTAEEVDE 406
Query: 384 RLNNIICNAFDAIWELANT--KKVSLRTAAFIIGCTRVLQAHKTRG 427
+L I+ + F+A + A K L A I G +V + +G
Sbjct: 407 KLREIMKSIFEACVKYAEKYGGKSDLVAGANIAGFLKVADSMIEQG 452
>gnl|CDD|202408 pfam02812, ELFV_dehydrog_N, Glu/Leu/Phe/Val dehydrogenase,
dimerisation domain.
Length = 131
Score = 206 bits (528), Expect = 4e-66
Identities = 69/129 (53%), Positives = 88/129 (68%)
Query: 48 PKKILIVDVPIEHDNGEVFHYEGYRVQHNILRGPGKGGVRFHPDVTLSEIIALSGWMTIK 107
P++++ V VP+ D+GEV GYRVQHN GP KGG+RFHP VTL E+ L+ MT K
Sbjct: 1 PERVIQVRVPVRMDDGEVEGLRGYRVQHNTALGPAKGGIRFHPYVTLEEVKRLAFGMTYK 60
Query: 108 NAAVNIPYGGAKGGIRVNPKNLSNNELMRLTRRYTNEISSIIGLNKDIPAPDVGTDMQIM 167
NA +P+GG KGGI +PK LS+ EL RLTR + E+ SIIG +DIPAPDVGT + M
Sbjct: 61 NALAGLPFGGGKGGIIGDPKGLSDAELERLTRAFGRELESIIGPGRDIPAPDVGTGPREM 120
Query: 168 SWMMDTYST 176
+W+ D Y
Sbjct: 121 AWIADEYRR 129
>gnl|CDD|181834 PRK09414, PRK09414, glutamate dehydrogenase; Provisional.
Length = 445
Score = 216 bits (553), Expect = 9e-66
Identities = 139/400 (34%), Positives = 209/400 (52%), Gaps = 31/400 (7%)
Query: 42 IEILKHPKKILIVDVPIEHDNGEVFHYEGYRVQHNILRGPGKGGVRFHPDVTLSEIIALS 101
+E L P++++I VP D G+V G+RVQ N GP KGG+RFHP V LS I+
Sbjct: 51 LERLVEPERVIIFRVPWVDDKGQVQVNRGFRVQFNSAIGPYKGGLRFHPSVNLS-ILKFL 109
Query: 102 GW-MTIKNAAVNIPYGGAKGGIRVNPKNLSNNELMRLTRRYTNEISSIIGLNKDIPAPDV 160
G+ KNA +P GG KGG +PK S+ E+MR + + E+ IG + D+PA D+
Sbjct: 110 GFEQIFKNALTGLPIGGGKGGSDFDPKGKSDAEIMRFCQSFMTELYRHIGPDTDVPAGDI 169
Query: 161 GTDMQIMSWMMDTYSTKK---NYTIPGIVTGKPISIGGSFGRQKATGRG-VFIIGSKIAS 216
G + + ++ Y K+ + G++TGK +S GGS R +ATG G V+ + +
Sbjct: 170 GVGGREIGYLFGQY--KRLTNRFE--GVLTGKGLSFGGSLIRTEATGYGLVYFAEEMLKA 225
Query: 217 KINLNIINSKISIQGFGNVGSVAANLFFKA---GAKIVAIQDDKTTIYNPNGFNIPKLQ- 272
+ + ++ + G GNV A KA GAK+V D +Y+ G ++ KL+
Sbjct: 226 R-GDSFEGKRVVVSGSGNVAIYAIE---KAQQLGAKVVTCSDSSGYVYDEEGIDLEKLKE 281
Query: 273 -KYVTFTRSIKDFNE--GEKINDSKEFWSIPCDILIPAAIEDQITINNA-----NNVTAK 324
K V R I ++ E G + + WS+PCDI +P A ++++ +A N V K
Sbjct: 282 IKEVRRGR-ISEYAEEFGAEYLEGGSPWSVPCDIALPCATQNELDEEDAKTLIANGV--K 338
Query: 325 IILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSNLLWTEQEINLR 384
+ EGAN P+T EA ++ + G++ AP NAGGV S E QN S L WT +E++ R
Sbjct: 339 AVAEGANMPSTPEAIEVFLEAGVLFAPGKAANAGGVATSGLEMSQNASRLSWTFEEVDAR 398
Query: 385 LNNIICNAFDAIWELANT--KKVSLRTAAFIIGCTRVLQA 422
L++I+ N A E A K + A I G +V A
Sbjct: 399 LHDIMKNIHHACVETAEEYGKPGNYVAGANIAGFVKVADA 438
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 205 bits (522), Expect = 2e-61
Identities = 120/358 (33%), Positives = 173/358 (48%), Gaps = 11/358 (3%)
Query: 42 IEILKHPKKILIVDVPIEHDNGEVFHYEGYRVQHNILRGPGKGGVRFHPDVTLSEIIALS 101
IE + P +I VP D GEV GYRVQ N GP KGG+RFHP V LS + L
Sbjct: 47 IERIVEPDRIFTFRVPWVDDKGEVQVNLGYRVQFNNAIGPYKGGIRFHPSVNLSILKFLG 106
Query: 102 GWMTIKNAAVNIPYGGAKGGIRVNPKNLSNNELMRLTRRYTNEISSIIGLNKDIPAPDVG 161
T KNA +P GG KGG +P+ S+ E+MR + + E+ IG + D+PA D+G
Sbjct: 107 FEQTFKNALTTLPMGGGKGGSDFSPRGKSDAEIMRFCQAFMLELWRHIGPDTDVPAGDIG 166
Query: 162 TDMQIMSWMMDTYSTKKNYTIPGIVTGKPISIGGSFGRQKATGRGVFIIGSKIASKINLN 221
+ + +M Y K G +TGK + GGS R +ATG G ++ ++
Sbjct: 167 VGGREVGYMFGMYK-KLTREFTGTLTGKGLEFGGSLIRPEATGFGALYFVHQMLETKGID 225
Query: 222 IINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRSI 281
I ++I GFGNV AA + GAK+V I IY+P+G + K+ + S
Sbjct: 226 IKGKTVAISGFGNVAWGAATKATELGAKVVTISGPDGYIYDPDGISGEKIDYMLELRASG 285
Query: 282 KDFNE--GEKINDSKEF-----WSIPCDILIPAAIEDQITINNANNVTA---KIILEGAN 331
D EK S F W DI +P A ++++ +A+ + + E +N
Sbjct: 286 NDIVAPYAEKFPGSTFFAGKKPWEQKVDIALPCATQNELNGEDADKLIKNGVLCVAEVSN 345
Query: 332 GPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSNLLWTEQEINLRLNNII 389
T EA D + AP NAGGV S E QN +L W+ +E++ +L+ I+
Sbjct: 346 MGCTAEAIDKFIAAKQLFAPGKAVNAGGVATSGLEMSQNAMHLSWSAEEVDEKLHQIM 403
>gnl|CDD|184464 PRK14031, PRK14031, glutamate dehydrogenase; Provisional.
Length = 444
Score = 199 bits (506), Expect = 4e-59
Identities = 120/361 (33%), Positives = 184/361 (50%), Gaps = 14/361 (3%)
Query: 42 IEILKHPKKILIVDVPIEHDNGEVFHYEGYRVQHNILRGPGKGGVRFHPDVTLSEIIALS 101
IE L P ++ V D G V GYRVQHN GP KGG+RFH V L + L+
Sbjct: 47 IERLCIPDRVYQFRVTWVDDKGNVQTNMGYRVQHNNAIGPYKGGIRFHASVNLGILKFLA 106
Query: 102 GWMTIKNAAVNIPYGGAKGGIRVNPKNLSNNELMRLTRRYTNEISSIIGLNKDIPAPDVG 161
T KN+ +P GG KGG +P+ SN E+MR + + E+ IG D+PA D+G
Sbjct: 107 FEQTFKNSLTTLPMGGGKGGSDFSPRGKSNAEVMRFCQAFMLELWRHIGPETDVPAGDIG 166
Query: 162 TDMQIMSWMMDTYSTKKNYTIPGIVTGKPISIGGSFGRQKATGRG-VFIIGSKIASKINL 220
+ + +M Y K ++ G TGK GGS R +ATG G ++ + + +K
Sbjct: 167 VGGREVGFMFGMYK-KLSHEFTGTFTGKGREFGGSLIRPEATGYGNIYFLMEMLKTK-GT 224
Query: 221 NIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRS 280
++ + G GNV A + G K+V + D IY+P+G + KL Y+ ++
Sbjct: 225 DLKGKVCLVSGSGNVAQYTAEKVLELGGKVVTMSDSDGYIYDPDGIDREKLD-YIMELKN 283
Query: 281 -----IKDFNE--GEKINDSKEFWSIPCDILIPAAIEDQITINNANNVTAKIIL---EGA 330
I+++ E G K + W DI +P+A ++++ ++A + A ++ EGA
Sbjct: 284 LYRGRIREYAEKYGCKYVEGARPWGEKGDIALPSATQNELNGDDARQLVANGVIAVSEGA 343
Query: 331 NGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSNLLWTEQEINLRLNNIIC 390
N P+T EA + +D I+ AP NAGGV VS E QN L W+ +E++ +L +I+
Sbjct: 344 NMPSTPEAIKVFQDAKILYAPGKAANAGGVSVSGLEMTQNSIKLSWSSEEVDEKLKSIMK 403
Query: 391 N 391
N
Sbjct: 404 N 404
>gnl|CDD|133450 cd05211, NAD_bind_Glu_Leu_Phe_Val, NAD(P) binding domain of
glutamate dehydrogenase, leucine dehydrogenase,
phenylalanine dehydrogenase, and valine dehydrogenase.
Amino acid dehydrogenase (DH) is a widely distributed
family of enzymes that catalyzes the oxidative
deamination of an amino acid to its keto acid and
ammonia with concomitant reduction of NAD(P)+. This
subfamily includes glutamate, leucine, phenylalanine,
and valine DHs. Glutamate DH is a multi-domain enzyme
that catalyzes the reaction from glutamate to
2-oxyoglutarate and ammonia in the presence of NAD or
NADP. It is present in all organisms. Enzymes involved
in ammonia assimilation are typically NADP+-dependent,
while those involved in glutamate catabolism are
generally NAD+-dependent. As in other NAD+-dependent
DHs, monomers in this family have 2 domains separated by
a deep cleft. Here the c-terminal domain contains a
modified NAD-binding Rossmann fold with 7 rather than
the usual 6 beta strands and one strand anti-parrallel
to the others. Amino acid DH-like NAD(P)-binding domains
are members of the Rossmann fold superfamily and include
glutamate, leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 217
Score = 178 bits (454), Expect = 4e-54
Identities = 72/218 (33%), Positives = 116/218 (53%), Gaps = 2/218 (0%)
Query: 202 ATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIY 261
ATG GV + + ++ +++QG GNVG A + G K++A+ D IY
Sbjct: 1 ATGYGVVVAMKAAMKHLGDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIY 60
Query: 262 NPNGFNIPKLQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPAAIEDQITINNANNV 321
+P + V S + + + + DI P A+ + I + NA +
Sbjct: 61 DPGITTEELINYAVALGGS--ARVKVQDYFPGEAILGLDVDIFAPCALGNVIDLENAKKL 118
Query: 322 TAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSNLLWTEQEI 381
AK++ EGAN PTT EA IL ++GI++APD++ NAGGVIVSYFEWVQNL L W +E+
Sbjct: 119 KAKVVAEGANNPTTDEALRILHERGIVVAPDIVANAGGVIVSYFEWVQNLQRLSWDAEEV 178
Query: 382 NLRLNNIICNAFDAIWELANTKKVSLRTAAFIIGCTRV 419
+L ++ + + ++ ++ V++R AA I+ R+
Sbjct: 179 RSKLEQVMTDIHNGVFAISERDGVTMRAAANILAFERI 216
>gnl|CDD|214847 smart00839, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase. Glutamate, leucine, phenylalanine and
valine dehydrogenases are structurally and functionally
related. They contain a Gly-rich region containing a
conserved Lys residue, which has been implicated in the
catalytic activity, in each case a reversible oxidative
deamination reaction.
Length = 102
Score = 136 bits (345), Expect = 2e-39
Identities = 52/103 (50%), Positives = 67/103 (65%), Gaps = 3/103 (2%)
Query: 301 CDILIPAAIEDQITINNANNVTAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGV 360
CDI IP A+++ I NAN + AKII EGAN P T EADDIL D+G++ APD NAGGV
Sbjct: 3 CDIFIPCALQNVINEANANRLGAKIIAEGANMPLTDEADDILEDRGVLYAPDFAANAGGV 62
Query: 361 IVSYFEWVQNLSNLLWTEQEINLRLNNIICNAFDAIWELANTK 403
IVS E +QNL+ T +E+ L+ I+ NA + I+E A
Sbjct: 63 IVSALEMLQNLAR---TAEEVFTDLSEIMRNALEEIFETAQKY 102
>gnl|CDD|133455 cd05313, NAD_bind_2_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 2. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
asimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 254
Score = 134 bits (340), Expect = 9e-37
Identities = 85/257 (33%), Positives = 123/257 (47%), Gaps = 20/257 (7%)
Query: 187 TGKPISIGGSFGRQKATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLFFKA 246
TGK +S GGS R +ATG G+ ++ N + +++I G GNV AA +
Sbjct: 1 TGKGLSWGGSLIRPEATGYGLVYFVEEMLKDRNETLKGKRVAISGSGNVAQYAAEKLLEL 60
Query: 247 GAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRSIK-----------DFNEGEKINDSKE 295
GAK+V + D K +Y+P+GF KL + IK K + K+
Sbjct: 61 GAKVVTLSDSKGYVYDPDGFTGEKLA----ELKEIKEVRRGRVSEYAKKYGTAKYFEGKK 116
Query: 296 FWSIPCDILIPAAIEDQITINNANNVTA---KIILEGANGPTTTEADDILRDKGIILAPD 352
W +PCDI P A ++++ +A + K + EGAN P T EA ++ R G++ AP
Sbjct: 117 PWEVPCDIAFPCATQNEVDAEDAKLLVKNGCKYVAEGANMPCTAEAIEVFRQAGVLFAPG 176
Query: 353 VITNAGGVIVSYFEWVQNLSNLLWTEQEINLRLNNIICNAFDAIWELANT--KKVSLRTA 410
NAGGV VS E QN L WT +E++ +L +I+ N DA E A L
Sbjct: 177 KAANAGGVAVSGLEMSQNSQRLSWTAEEVDAKLKDIMKNIHDACAETAKKYGDPPDLVAG 236
Query: 411 AFIIGCTRVLQAHKTRG 427
A I G +V A +G
Sbjct: 237 ANIAGFLKVADAMLAQG 253
>gnl|CDD|133444 cd01075, NAD_bind_Leu_Phe_Val_DH, NAD(P) binding domain of leucine
dehydrogenase, phenylalanine dehydrogenase, and valine
dehydrogenase. Amino acid dehydrogenase (DH) is a
widely distributed family of enzymes that catalyzes the
oxidative deamination of an amino acid to its keto acid
and ammonia with concomitant reduction of NADP+. For
example, leucine DH catalyzes the reversible oxidative
deamination of L-leucine and several other straight or
branched chain amino acids to the corresponding
2-oxoacid derivative. Amino acid DH -like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 200
Score = 75.3 bits (186), Expect = 8e-16
Identities = 41/163 (25%), Positives = 71/163 (43%), Gaps = 24/163 (14%)
Query: 203 TGRGVFIIGSKIASKINL---NIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTT 259
T GVF+ G K A++ L ++ +++QG G VG A + GAK++ ++
Sbjct: 5 TAYGVFL-GMKAAAEHLLGTDSLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEA 63
Query: 260 IYNPNGFNIPKLQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPAAIEDQITINNAN 319
+ R+ + G + +E +S+ D+ P A+ I +
Sbjct: 64 V-----------------ARAAE--LFGATVVAPEEIYSVDADVFAPCALGGVINDDTIP 104
Query: 320 NVTAKIILEGANGPTTTEA-DDILRDKGIILAPDVITNAGGVI 361
+ AK I AN +L ++GI+ APD + NAGG+I
Sbjct: 105 QLKAKAIAGAANNQLADPRHGQMLHERGILYAPDYVVNAGGLI 147
>gnl|CDD|240359 PTZ00324, PTZ00324, glutamate dehydrogenase 2; Provisional.
Length = 1002
Score = 54.0 bits (130), Expect = 1e-07
Identities = 71/311 (22%), Positives = 118/311 (37%), Gaps = 61/311 (19%)
Query: 112 NIPYGGAKGGIRVNPKNLSNNELMRLTRRYTNEISSII-----------GLNKD---IPA 157
+IP GG+KG I ++ + L+ +R + I +++ L ++
Sbjct: 536 DIPEGGSKGTILLSSRYLNKFAQVRCQHAFLQYIDALLDVMLPGEKVVDHLKQEEIIFLG 595
Query: 158 PDVGTDMQIMSWMMDTYSTKKNYTI-PGIVTGKPISIGG----SFGRQKATGRGVFIIGS 212
PD T +M W ++ K+ Y TGK S+GG ++G + R ++ G
Sbjct: 596 PDEHTTGTLMDWA-ALHAKKRGYPFWKSFTTGKSPSMGGIPHDTYGMTTRSVR-AYVTG- 652
Query: 213 KIASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKLQ 272
I K+ LN Q G G + +N + K V I D +++P G N +L+
Sbjct: 653 -ILEKLGLNE-EEVTKFQTGGPDGDLGSNELLLSKEKTVGIVDGSGVLHDPEGLNREELR 710
Query: 273 KYVTFTRSIKDFNE---------------------GEKINDSKEFWS-------IPCDIL 304
+ ++F+E G + F + D+
Sbjct: 711 RLAHHRLPAREFDESKLSPQGFLVLTDDRDVKLPDGTIVESGLRFRNEFHLLPYSDADVF 770
Query: 305 IP-AAIEDQITINNAN--------NVTAKIILEGANGPTTTEADDILRDKGIILAPDVIT 355
+P +T+ N + KII+EGAN T +A L + G+IL D
Sbjct: 771 VPCGGRPRSVTLFNVGRFFDEKNGKLRFKIIVEGANLFITQDARLALEECGVILFKDASA 830
Query: 356 NAGGVIVSYFE 366
N GGV S E
Sbjct: 831 NKGGVTSSSLE 841
>gnl|CDD|225455 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid
transport and metabolism].
Length = 1592
Score = 43.9 bits (104), Expect = 2e-04
Identities = 88/405 (21%), Positives = 139/405 (34%), Gaps = 113/405 (27%)
Query: 52 LIVDVPIEHDNGEVFHYEGYRVQHNILR-GP-GKGGVRF---HPDVTLSEIIALSGWMTI 106
LI ++P E+F Y G V+ LR GP +GG+R+ + D +E++ L +
Sbjct: 765 LIDELPYPRPYREIFVY-GPEVEGVHLRFGPVARGGLRWSDRNQDFR-TEVLGLVKAQQV 822
Query: 107 KNAAVNIPYGGAKGGIRVN--PKNLSNNELM-------RLTRRYTNEISSIIGLNKDIP- 156
KNA I GAKGG + P + + + +I+ I ++ +P
Sbjct: 823 KNAV--IVPVGAKGGFLLKRLPTGGDRDAIFAEGIACYKAFISGLLDITDNIIDDQVVPP 880
Query: 157 ---------------APDVGTDMQIMSWMMDTYSTKKN-----YTIPGIVTGKPISIGGS 196
A D GT T+S N Y G + GGS
Sbjct: 881 ADVVRLDGDDPYLVVAADKGTA---------TFSDIANSVAREYGFW---LGDAFASGGS 928
Query: 197 FG-RQKA---TGRGVFIIGSKIASKINLNIINSKISIQGFGNV-GSVAAN-LFFKAGAKI 250
G K T RG + + ++ L+ S ++ G G++ G V N + ++
Sbjct: 929 AGYDHKKMGITARGAWEAVKRHFRELGLDTQTSPFTVVGIGDMSGDVFGNGMLLSKHIRL 988
Query: 251 VAIQDDKTTIYNPN------------GFNIP----------KLQK--YVTFTRSIKDF-- 284
+A D + +PN F +P K+ K V +RS K
Sbjct: 989 IAAFDHRHIFIDPNPDLAVSFAERKRLFALPRSSWSDYDASKISKGGGV-VSRSAKAITL 1047
Query: 285 -NEGEKINDSKE-------------------FWSIPCDILIPAAIE-DQITINNANN--- 320
E + W+ + A+ E + + AN+
Sbjct: 1048 SPEVIAALGIDKTELAPNELITAILKAPVDLLWNGGIGTYVKASGETNADVGDRANDAIR 1107
Query: 321 -----VTAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGV 360
V AK+I EGAN T G + D I N+ GV
Sbjct: 1108 VNGEEVRAKVIGEGANLGVTQRGRIEFALAGGRINTDAIDNSAGV 1152
>gnl|CDD|169409 PRK08374, PRK08374, homoserine dehydrogenase; Provisional.
Length = 336
Score = 33.6 bits (77), Expect = 0.15
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 10/53 (18%)
Query: 226 KISIQGFGNVGSVAANL------FFKAGA----KIVAIQDDKTTIYNPNGFNI 268
K+SI GFGNVG A + FK K+V+I D TI+ P ++
Sbjct: 4 KVSIFGFGNVGRAVAEVLAEKSRVFKERYGVELKVVSITDTSGTIWLPEDIDL 56
>gnl|CDD|235763 PRK06270, PRK06270, homoserine dehydrogenase; Provisional.
Length = 341
Score = 33.3 bits (77), Expect = 0.22
Identities = 27/100 (27%), Positives = 42/100 (42%), Gaps = 14/100 (14%)
Query: 226 KISIQGFGNVGSVAANLF----------FKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYV 275
KI++ GFG VG A L + K+VAI D + +P+G ++ K
Sbjct: 4 KIALIGFGGVGQGVAELLAEKREYLKKRYGLDLKVVAIADSSGSAIDPDGLDLELALKVK 63
Query: 276 TFTRSIKDFNEGEKINDSKE-FWSIPCDILI---PAAIED 311
T + D+ EG E S+ D+++ P IE
Sbjct: 64 EETGKLADYPEGGGEISGLEVIRSVDADVVVEATPTNIET 103
>gnl|CDD|180840 PRK07105, PRK07105, pyridoxamine kinase; Validated.
Length = 284
Score = 31.0 bits (71), Expect = 1.1
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 9/51 (17%)
Query: 31 VTPYLGS------LSRWIEILKHPKKILIVDVPIEHDNGEVFHYEGYRVQH 75
+ YLGS +S +I+ K +++VD P+ DNG++ Y+G+ +
Sbjct: 80 YSGYLGSPRQIQIVSDFIKYFKKKDLLVVVD-PVMGDNGKL--YQGFDQEM 127
>gnl|CDD|240623 cd05199, SDH_like, Saccharopine Dehydrogenase like proteins.
Saccharopine Dehydrogenase (SDH) and related proteins,
including bifunctional lysine ketoglutarate
reductase/SDH enzymes and N(5)-(carboxyethyl)ornithine
synthases. SDH catalyzes the final step in the
reversible NAD-dependent oxidative deamination of
saccharopine to alpha-ketoglutarate and lysine, in the
alpha-aminoadipate pathway of L-lysine biosynthesis. SDH
is structurally related to formate dehydrogenase and
similar enzymes, having a 2-domain structure in which a
Rossmann-fold NAD(P)-binding domain is inserted within
the linear sequence of a catalytic domain of related
structure. Bifunctional lysine ketoglutarate
reductase/SDH protein is a pair of enzymes linked on a
single polypeptide chain that catalyze the initial,
consecutive steps of lysine degradation. These proteins
are related to the 2-domain saccharopine dehydrogenases.
Length = 319
Score = 30.7 bits (70), Expect = 1.4
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 226 KISIQGFGNVGSVAANLFFKAGAKIVAIQD 255
KI I G G VGS AA + G K V+ +D
Sbjct: 178 KIVITGSGRVGSGAAEVLKALGIKEVSPED 207
>gnl|CDD|233580 TIGR01809, Shik-DH-AROM, shikimate-5-dehydrogenase, fungal
AROM-type. This model represents a clade of
shikimate-5-dehydrogenases found in Corynebacterium,
Mycobacteria and fungi. The fungal sequences are
pentafunctional proteins known as AroM which contain the
central five seven steps in the chorismate biosynthesis
pathway. The Corynebacterium and Mycobacterial sequences
represent the sole shikimate-5-dehydrogenases in species
which otherwise have every enzyme of the chorismate
biosynthesis pathway [Amino acid biosynthesis, Aromatic
amino acid family].
Length = 282
Score = 30.3 bits (68), Expect = 1.8
Identities = 19/70 (27%), Positives = 23/70 (32%), Gaps = 4/70 (5%)
Query: 45 LKHPKKILIVDVPIEHDNGEVFHYEGYRVQHNILRGPGKGGVRFHPDVTLSEIIALSGWM 104
K PKK I+ PI H H GY IL P K + +
Sbjct: 2 NKGPKKAFIIGKPIAHSRSPHLHNAGYE----ILGLPDKTYEFETCSAEELKEVLSGFGP 57
Query: 105 TIKNAAVNIP 114
A+V IP
Sbjct: 58 QFGGASVTIP 67
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 29.7 bits (67), Expect = 3.1
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 11/63 (17%)
Query: 222 IINSKISIQGFGNVGSVAANLFFKA-GAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRS 280
I + K+++ G G +G A +F K G+ +VA Y+P F K YV + +
Sbjct: 144 IKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVA--------YDP--FPNAKAATYVDYKDT 193
Query: 281 IKD 283
I++
Sbjct: 194 IEE 196
>gnl|CDD|130522 TIGR01455, glmM, phosphoglucosamine mutase. This model describes
GlmM, phosphoglucosamine mutase, also designated in MrsA
and YhbF E. coli, UreC in Helicobacter pylori, and
femR315 or FemD in Staphlococcus aureus. It converts
glucosamine-6-phosphate to glucosamine-1-phosphate as
part of the pathway toward UDP-N-acetylglucosamine for
peptidoglycan and lipopolysaccharides [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan, Central intermediary metabolism, Amino
sugars].
Length = 443
Score = 29.6 bits (67), Expect = 3.3
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 6/32 (18%)
Query: 237 SVAANLFFKAGAKIVAIQDDKTTIYNPNGFNI 268
VA ++F + GA+++AI + P+G NI
Sbjct: 186 KVAPHVFRELGAEVIAIGVE------PDGLNI 211
>gnl|CDD|100095 cd05802, GlmM, GlmM is a bacterial phosphoglucosamine mutase (PNGM)
that belongs to the alpha-D-phosphohexomutase
superfamily. It is required for the interconversion of
glucosamine-6-phosphate and glucosamine-1-phosphate in
the biosynthetic pathway of UDP-N-acetylglucosamine, an
essential precursor to components of the cell envelope.
In order to be active, GlmM must be phosphorylated,
which can occur via autophosphorylation or by the
Ser/Thr kinase StkP. GlmM functions in a classical
ping-pong bi-bi mechanism with
glucosamine-1,6-diphosphate as an intermediate. Other
members of the alpha-D-phosphohexomutase superfamily
include phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 434
Score = 29.8 bits (68), Expect = 3.3
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 237 SVAANLFFKAGAKIVAIQDDKTTIYNPNGFNI 268
VA +F + GA+++ I + P+G NI
Sbjct: 183 KVAPEVFRELGAEVIVINNA------PDGLNI 208
>gnl|CDD|240445 cd13430, LDT_IgD_like, IgD-like repeat domain of mycobacterial
L,D-transpeptidases. Immunoglobulin-like domain found
in actinobacterial L,D-transpeptidases, including
Mycobacterium tuberculosis LdtMt2, which is a
non-classical transpeptidase that generates 3->3
transpeptide linkages. LdtMt2 is associated with
virulence and resistance to amoxicillin. This domain may
occur in a tandem-repeat arrangement and is found
N-terminal to the catalytic L,D-transpeptidase domain.
Length = 98
Score = 28.1 bits (62), Expect = 3.4
Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 1/52 (1%)
Query: 329 GANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSNLLWTEQE 380
G P D+ + D+G IT V + F W+ + + W +
Sbjct: 13 GVGAPVAIRFDENIADRGAAEKAITITTDPPVEGA-FYWLPDGRRVRWRPEH 63
>gnl|CDD|236787 PRK10887, glmM, phosphoglucosamine mutase; Provisional.
Length = 443
Score = 29.3 bits (67), Expect = 4.6
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 6/31 (19%)
Query: 238 VAANLFFKAGAKIVAIQDDKTTIYNPNGFNI 268
+A N+F + GA+++AI PNG NI
Sbjct: 186 IAPNVFRELGAEVIAIGC------EPNGLNI 210
>gnl|CDD|132727 cd06929, NR_LBD_F1, Ligand-binding domain of nuclear receptor
family 1. Ligand-binding domain (LBD) of nuclear
receptor (NR) family 1: This is one of the major
subfamily of nuclear receptors, including thyroid
receptor, retinoid acid receptor, ecdysone receptor,
farnesoid X receptor, vitamin D receptor, and other
related receptors. Nuclear receptors form a superfamily
of ligand-activated transcription regulators, which
regulate various physiological functions, from
development, reproduction, to homeostasis and metabolism
in animals (metazoans). The family contains not only
receptors for known ligands but also orphan receptors
for which ligands do not exist or have not been
identified. NRs share a common structural organization
with a central well conserved DNA binding domain (DBD),
a variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 174
Score = 28.3 bits (64), Expect = 4.8
Identities = 23/115 (20%), Positives = 40/115 (34%), Gaps = 24/115 (20%)
Query: 271 LQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPAAIEDQITINNANNVTAKIILEGA 330
+++ V F + I F E + EDQI + ++L A
Sbjct: 15 IRRVVEFAKRIPGFRE------------LSQ--------EDQIALLKGGCFEI-LLLRSA 53
Query: 331 NGPTTTEADDILRDKGIILAPDVITNAG--GVIVSYFEWVQNLSNLLWTEQEINL 383
E + + G + DV+ N G I FE+ + ++ L + E L
Sbjct: 54 TL-YDPEKNSLTFGDGKGNSRDVLLNGGFGEFIEPLFEFAEKMNKLQLDDNEYAL 107
>gnl|CDD|239933 cd04487, RecJ_OBF2_like, RecJ_OBF2_like: A subfamily of OB folds
corresponding to the second OB fold (OBF2) of
archaeal-specific proteins with similarity to
eubacterial RecJ. RecJ is an ssDNA-specific exonuclease.
Although the overall sequence similarity of these
proteins to eubacterial RecJ proteins is marginal, they
appear to carry motifs, which have been shown to be
essential for nuclease function in Escherichia coli
RecJ. In addition to this OB fold, most proteins in this
subfamily contain: i) an N-terminal OB fold belonging to
a different domain family (the ribosomal S1-like
RNA-binding family); and ii) a domain, C-terminal to
OBF2, characteristic of DHH family proteins. DHH family
proteins include E. coli RecJ, and are predicted to have
a phosphoesterase function.
Length = 73
Score = 26.9 bits (60), Expect = 5.6
Identities = 8/29 (27%), Positives = 19/29 (65%)
Query: 85 GVRFHPDVTLSEIIALSGWMTIKNAAVNI 113
GVR +P+V + +I+ ++G + ++ + I
Sbjct: 37 GVRAYPEVEVGDIVRVTGEVEPRDGQLQI 65
>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 = 28.7 bits (65), Expect = 6.6
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 10/62 (16%)
Query: 222 IINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRSI 281
I + + I G G +GS AA +F GAK++A Y+P + P+L+K++ + S+
Sbjct: 143 IRDLTVGIIGTGRIGSAAAKIFKGFGAKVIA--------YDP--YPNPELEKFLLYYDSL 192
Query: 282 KD 283
+D
Sbjct: 193 ED 194
>gnl|CDD|107337 cd06342, PBP1_ABC_LIVBP_like, Type I periplasmic ligand-binding
domain of ABC (Atpase Binding Cassette)-type active
transport systems that are involved in the transport of
all three branched chain aliphatic amino acids (leucine,
isoleucine and valine). This subgroup includes the type
I periplasmic ligand-binding domain of ABC (Atpase
Binding Cassette)-type active transport systems that are
involved in the transport of all three branched chain
aliphatic amino acids (leucine, isoleucine and valine).
This subgroup also includes a leucine-specific binding
protein (or LivK), which is very similar in sequence and
structure to leucine-isoleucine-valine binding protein
(LIVBP). ABC-type active transport systems are
transmembrane proteins that function in the transport of
diverse sets of substrates across extra- and
intracellular membranes, including carbohydrates, amino
acids, inorganic ions, dipeptides and oligopeptides,
metabolic products, lipids and sterols, and heme, to
name a few.
Length = 334
Score = 28.7 bits (65), Expect = 6.7
Identities = 26/87 (29%), Positives = 36/87 (41%), Gaps = 27/87 (31%)
Query: 200 QKATGRGV-FIIG------SKIASKI--NLNII-------NSKISIQGFGNV-------- 235
QK GV ++G + AS I + I+ N K++ +G+ NV
Sbjct: 60 QKLVDDGVVGVVGHLNSGVTIPASPIYADAGIVMISPAATNPKLTERGYKNVFRVVARDD 119
Query: 236 --GSVAANLFFK-AGAKIVAIQDDKTT 259
G AA + AK VAI DDKT
Sbjct: 120 QQGPAAAKYAVETLKAKKVAIIDDKTA 146
>gnl|CDD|237672 PRK14318, glmM, phosphoglucosamine mutase; Provisional.
Length = 448
Score = 28.7 bits (65), Expect = 6.8
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 6/31 (19%)
Query: 238 VAANLFFKAGAKIVAIQDDKTTIYNPNGFNI 268
VA + AGA ++AI D P+G NI
Sbjct: 190 VAPEAYRAAGADVIAINAD------PDGLNI 214
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 28.2 bits (64), Expect = 7.7
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 225 SKISIQGFGNVGSVAANL 242
KISI G GNVG+ A+L
Sbjct: 3 KKISIIGAGNVGATLAHL 20
>gnl|CDD|133449 cd05191, NAD_bind_amino_acid_DH, NAD(P) binding domain of amino
acid dehydrogenase-like proteins. Amino acid
dehydrogenase(DH)-like NAD(P)-binding domains are
members of the Rossmann fold superfamily and are found
in glutamate, leucine, and phenylalanine DHs (DHs),
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha-beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 86
Score = 26.6 bits (59), Expect = 8.2
Identities = 14/54 (25%), Positives = 20/54 (37%)
Query: 202 ATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQD 255
AT G + N ++ + + G G VG A L G K V + D
Sbjct: 1 ATAAGAVALLKAAGKVTNKSLKGKTVVVLGAGEVGKGIAKLLADEGGKKVVLCD 54
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 28.1 bits (63), Expect = 8.6
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 226 KISIQGFGNVGSVAANLFFKAGAKIV 251
I+I G GN+GS A KAG +++
Sbjct: 3 IIAIIGTGNIGSALALRLAKAGHEVI 28
>gnl|CDD|183656 PRK12656, PRK12656, fructose-6-phosphate aldolase; Reviewed.
Length = 222
Score = 27.8 bits (62), Expect = 9.7
Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 6/65 (9%)
Query: 212 SKIASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKL 271
++A I+ +SKI F NV V N F GA+ V D F +P +
Sbjct: 149 GQLAEAIDRENSDSKILAASFKNVAQV--NKAFALGAQAVTAGPDVFE----AAFAMPSI 202
Query: 272 QKYVT 276
QK V
Sbjct: 203 QKAVD 207
>gnl|CDD|212528 cd10004, RPD3-like, reduced potassium dependency-3 (RPD3)-like.
Proteins of the Rpd3-like family are class I
Zn-dependent Histone deacetylases that catalyze
hydrolysis of an N(6)-acetyl-lysine residue of a histone
to yield a deacetylated histone (EC 3.5.1.98). RPD3 is
the yeast homolog of class I HDACs. The main function of
RPD3-like group members is regulation of a number of
different processes through protein (mostly different
histones) modification (deacetylation). This group
includes fungal RPD3 and acts via the formation of large
multiprotein complexes. Members of this group are
involved in cell cycle regulation, DNA damage response,
embryonic development and cytokine signaling important
for immune response. Histone deacetylation by yeast RPD3
represses genes regulated by the Ash1 and Ume6
DNA-binding proteins. In mammals, they are known to be
involved in progression of various tumors. Specific
inhibitors of mammalian histone deacetylases could be a
therapeutic drug option.
Length = 375
Score = 28.2 bits (63), Expect = 9.8
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 18/79 (22%)
Query: 42 IEILKHPKKILIVDVPIEHDNG-EVFHYEGYRVQHNILRG-----PGKGGVRFHPDVTLS 95
+E+L++ +++L +D+ + H +G E Y RV PG G +R D+
Sbjct: 154 LELLRYHQRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEYFPGTGELR---DI--- 207
Query: 96 EIIALSGWMTIKNAAVNIP 114
G T KN AVN+P
Sbjct: 208 ------GIGTGKNYAVNVP 220
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 0.409
Gapped
Lambda K H
0.267 0.0831 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,186,377
Number of extensions: 2215254
Number of successful extensions: 2085
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2048
Number of HSP's successfully gapped: 67
Length of query: 428
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 328
Effective length of database: 6,502,202
Effective search space: 2132722256
Effective search space used: 2132722256
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: 60 (26.7 bits)