RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14499
(262 letters)
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 313 bits (803), Expect = e-106
Identities = 119/262 (45%), Positives = 173/262 (66%), Gaps = 1/262 (0%)
Query: 1 MSWMMDTYSTKKNYTIPGIVTGKPISIGGSFGRQKATGRGVFIIGSKIASKINLNIINSK 60
M+WMMD YS + PG+ TGKP+ +GGS GR +ATG GVF + + ++ ++
Sbjct: 150 MAWMMDEYSKIVGNSAPGVFTGKPLELGGSLGRSEATGYGVFYAIREALKALGDDLEGAR 209
Query: 61 ISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRSIKDFNE 120
+++QGFGNVG AA + GAK+VA+ D K IY+ +G ++ L + S+ ++
Sbjct: 210 VAVQGFGNVGQYAAEKLHELGAKVVAVSDSKGGIYDEDGLDVEALLELKERRGSVAEYAG 269
Query: 121 GEKINDSKEFWSIPCDILIPAAIEDQITINNANNVTAKIILEGANGPTTTEADDILRDKG 180
E I ++E + CDILIP A+E+ IT +NA+ + AKI++EGANGPTT EAD+IL ++G
Sbjct: 270 AEYI-TNEELLEVDCDILIPCALENVITEDNADQLKAKIVVEGANGPTTPEADEILLERG 328
Query: 181 IILAPDVITNAGGVIVSYFEWVQNLSNLLWTEQEINLRLNNIICNAFDAIWELANTKKVS 240
I++ PD++ NAGGVIVSY EWVQN L WTE+E++ +L I+ NAF+A+++ A V
Sbjct: 329 ILVVPDILANAGGVIVSYLEWVQNAQGLYWTEEEVDEKLERIMVNAFEAVYQAAKEYGVD 388
Query: 241 LRTAAFIIGCTRVLQAHKTRGL 262
LRTAA+I+ RV A K RG
Sbjct: 389 LRTAAYILAFERVADAMKARGW 410
>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 = 295 bits (759), Expect = e-102
Identities = 111/228 (48%), Positives = 155/228 (67%), Gaps = 1/228 (0%)
Query: 28 GGSFGRQKATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAI 87
GGS GR++ATGRGV + K+ + + ++++IQGFGNVGS AA +AGAK+VA+
Sbjct: 1 GGSLGREEATGRGVAYATREALKKLGIGLAGARVAIQGFGNVGSHAARFLHEAGAKVVAV 60
Query: 88 QDDKTTIYNPNGFNIPKLQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPAAIEDQI 147
D TIYNP+G ++P L Y S+ F E+I + +E + CDILIPAA+E+QI
Sbjct: 61 SDSDGTIYNPDGLDVPALLAYKKEHGSVLGFPGAERITN-EELLELDCDILIPAALENQI 119
Query: 148 TINNANNVTAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSN 207
T +NA+ + AKII+E ANGPTT EAD+IL ++G+++ PD++ NAGGV VSYFEWVQNL
Sbjct: 120 TADNADRIKAKIIVEAANGPTTPEADEILHERGVLVVPDILANAGGVTVSYFEWVQNLQG 179
Query: 208 LLWTEQEINLRLNNIICNAFDAIWELANTKKVSLRTAAFIIGCTRVLQ 255
W E+E+N RL + AF+A+ E A V LRTAA+++ RV +
Sbjct: 180 FYWDEEEVNSRLETKMREAFEAVLETAEKYGVDLRTAAYVLALERVAE 227
>gnl|CDD|178095 PLN02477, PLN02477, glutamate dehydrogenase.
Length = 410
Score = 288 bits (738), Expect = 2e-96
Identities = 118/261 (45%), Positives = 161/261 (61%), Gaps = 2/261 (0%)
Query: 1 MSWMMDTYSTKKNYTIPGIVTGKPISIGGSFGRQKATGRGVFIIGSKIASKINLNIINSK 60
M+W++D YS ++ P +VTGKPI +GGS GR+ ATGRGV + ++ +I
Sbjct: 150 MAWILDEYSKFHGFS-PAVVTGKPIDLGGSLGREAATGRGVVFATEALLAEHGKSIAGQT 208
Query: 61 ISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRSIKDFNE 120
IQGFGNVGS AA L + G KIVA+ D + N NG +IP L+K+V +K F
Sbjct: 209 FVIQGFGNVGSWAAQLIHEKGGKIVAVSDITGAVKNENGLDIPALRKHVAEGGGLKGFPG 268
Query: 121 GEKINDSKEFWSIPCDILIPAAIEDQITINNANNVTAKIILEGANGPTTTEADDILRDKG 180
G+ I D + PCD+LIPAA+ I NA +V AK I+E AN PT EAD+ILR KG
Sbjct: 269 GDPI-DPDDILVEPCDVLIPAALGGVINKENAADVKAKFIVEAANHPTDPEADEILRKKG 327
Query: 181 IILAPDVITNAGGVIVSYFEWVQNLSNLLWTEQEINLRLNNIICNAFDAIWELANTKKVS 240
+++ PD+ N+GGV VSYFEWVQN+ +W E+++N L+ + +AF A+ E+ T S
Sbjct: 328 VVVLPDIYANSGGVTVSYFEWVQNIQGFMWEEEKVNRELDRYMTDAFKALKEMCKTHNCS 387
Query: 241 LRTAAFIIGCTRVLQAHKTRG 261
LR AF +G RV +A RG
Sbjct: 388 LRMGAFTLGVNRVARATVLRG 408
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 278 bits (714), Expect = 4e-95
Identities = 104/237 (43%), Positives = 143/237 (60%), Gaps = 3/237 (1%)
Query: 28 GGSFGRQKATGRGVFIIGSKIASKINLNII-NSKISIQGFGNVGSVAANLFFKAGAKIVA 86
GGS GR +ATG GV + K+ + + +++QGFGNVGS AA + GAK+VA
Sbjct: 1 GGSLGRPEATGYGVVYFVEEALKKLGGDSLEGKTVAVQGFGNVGSYAAEKLLELGAKVVA 60
Query: 87 IQDDKTTIYNPNGFNIPKLQKYVTFTRS-IKDF-NEGEKINDSKEFWSIPCDILIPAAIE 144
+ D IY+PNG +I +L + + ++ G + +E W I CDIL+P A +
Sbjct: 61 VSDSSGYIYDPNGIDIEELLELKEEGGGRVVEYAGSGAEYISGEELWEIDCDILVPCATQ 120
Query: 145 DQITINNANNVTAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQN 204
++I NA + AK ++EGAN PTT EAD+IL ++GI+ APD NAGGV VSY E VQN
Sbjct: 121 NEINEENAKLIKAKAVVEGANMPTTPEADEILEERGILYAPDKAANAGGVTVSYLEMVQN 180
Query: 205 LSNLLWTEQEINLRLNNIICNAFDAIWELANTKKVSLRTAAFIIGCTRVLQAHKTRG 261
S L WTE+E++ +L I+ N F+A+ E A + LRTAA I G RV A K RG
Sbjct: 181 SSRLSWTEEEVDEKLEKIMTNIFEAVVETAKEYGIDLRTAANIAGFERVADAMKARG 237
>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 = 176 bits (448), Expect = 4e-55
Identities = 72/218 (33%), Positives = 116/218 (53%), Gaps = 2/218 (0%)
Query: 36 ATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIY 95
ATG GV + + ++ +++QG GNVG A + G K++A+ D IY
Sbjct: 1 ATGYGVVVAMKAAMKHLGDSLEGLTVAVQGLGNVGWGLAKKLAEEGGKVLAVSDPDGYIY 60
Query: 96 NPNGFNIPKLQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPAAIEDQITINNANNV 155
+P + V S + + + + DI P A+ + I + NA +
Sbjct: 61 DPGITTEELINYAVALGGS--ARVKVQDYFPGEAILGLDVDIFAPCALGNVIDLENAKKL 118
Query: 156 TAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSNLLWTEQEI 215
AK++ EGAN PTT EA IL ++GI++APD++ NAGGVIVSYFEWVQNL L W +E+
Sbjct: 119 KAKVVAEGANNPTTDEALRILHERGIVVAPDIVANAGGVIVSYFEWVQNLQRLSWDAEEV 178
Query: 216 NLRLNNIICNAFDAIWELANTKKVSLRTAAFIIGCTRV 253
+L ++ + + ++ ++ V++R AA I+ R+
Sbjct: 179 RSKLEQVMTDIHNGVFAISERDGVTMRAAANILAFERI 216
>gnl|CDD|185433 PTZ00079, PTZ00079, NADP-specific glutamate dehydrogenase;
Provisional.
Length = 454
Score = 145 bits (368), Expect = 8e-41
Identities = 80/256 (31%), Positives = 127/256 (49%), Gaps = 12/256 (4%)
Query: 18 GIVTGKPISIGGSFGRQKATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLF 77
G +TGK + GGS R +ATG G+ ++ K+N ++ + + G GNV A
Sbjct: 197 GTLTGKNVKWGGSNIRPEATGYGLVYFVLEVLKKLNDSLEGKTVVVSGSGNVAQYAVEKL 256
Query: 78 FKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYVTF----TRSIKDF---NEGEKINDSKEF 130
+ GAK++ + D I+ PNGF KL + +K++ + K K+
Sbjct: 257 LQLGAKVLTMSDSDGYIHEPNGFTKEKLAYLMDLKNVKRGRLKEYAKHSSTAKYVPGKKP 316
Query: 131 WSIPCDILIPAAIEDQITINNANNVTA---KIILEGANGPTTTEADDILRDKGIILAPDV 187
W +PCDI P A +++I + +A + K++ EGAN PTT EA + + G+I P
Sbjct: 317 WEVPCDIAFPCATQNEINLEDAKLLIKNGCKLVAEGANMPTTIEATHLFKKNGVIFCPGK 376
Query: 188 ITNAGGVIVSYFEWVQNLSNLLWTEQEINLRLNNIICNAFDAIWELANT--KKVSLRTAA 245
NAGGV +S E QN + L WT +E++ +L I+ + F+A + A K L A
Sbjct: 377 AANAGGVAISGLEMSQNAARLQWTAEEVDEKLREIMKSIFEACVKYAEKYGGKSDLVAGA 436
Query: 246 FIIGCTRVLQAHKTRG 261
I G +V + +G
Sbjct: 437 NIAGFLKVADSMIEQG 452
>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 = 132 bits (335), Expect = 1e-39
Identities = 52/103 (50%), Positives = 67/103 (65%), Gaps = 3/103 (2%)
Query: 135 CDILIPAAIEDQITINNANNVTAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGV 194
CDI IP A+++ I NAN + AKII EGAN P T EADDIL D+G++ APD NAGGV
Sbjct: 3 CDIFIPCALQNVINEANANRLGAKIIAEGANMPLTDEADDILEDRGVLYAPDFAANAGGV 62
Query: 195 IVSYFEWVQNLSNLLWTEQEINLRLNNIICNAFDAIWELANTK 237
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 = 132 bits (334), Expect = 1e-37
Identities = 85/257 (33%), Positives = 123/257 (47%), Gaps = 20/257 (7%)
Query: 21 TGKPISIGGSFGRQKATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLFFKA 80
TGK +S GGS R +ATG G+ ++ N + +++I G GNV AA +
Sbjct: 1 TGKGLSWGGSLIRPEATGYGLVYFVEEMLKDRNETLKGKRVAISGSGNVAQYAAEKLLEL 60
Query: 81 GAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRSIK-----------DFNEGEKINDSKE 129
GAK+V + D K +Y+P+GF KL + IK K + K+
Sbjct: 61 GAKVVTLSDSKGYVYDPDGFTGEKLA----ELKEIKEVRRGRVSEYAKKYGTAKYFEGKK 116
Query: 130 FWSIPCDILIPAAIEDQITINNANNVTA---KIILEGANGPTTTEADDILRDKGIILAPD 186
W +PCDI P A ++++ +A + K + EGAN P T EA ++ R G++ AP
Sbjct: 117 PWEVPCDIAFPCATQNEVDAEDAKLLVKNGCKYVAEGANMPCTAEAIEVFRQAGVLFAPG 176
Query: 187 VITNAGGVIVSYFEWVQNLSNLLWTEQEINLRLNNIICNAFDAIWELANT--KKVSLRTA 244
NAGGV VS E QN L WT +E++ +L +I+ N DA E A L
Sbjct: 177 KAANAGGVAVSGLEMSQNSQRLSWTAEEVDAKLKDIMKNIHDACAETAKKYGDPPDLVAG 236
Query: 245 AFIIGCTRVLQAHKTRG 261
A I G +V A +G
Sbjct: 237 ANIAGFLKVADAMLAQG 253
>gnl|CDD|181834 PRK09414, PRK09414, glutamate dehydrogenase; Provisional.
Length = 445
Score = 134 bits (339), Expect = 1e-36
Identities = 86/254 (33%), Positives = 130/254 (51%), Gaps = 22/254 (8%)
Query: 18 GIVTGKPISIGGSFGRQKATGRG-VFIIGSKIASKINLNIINSKISIQGFGNVGSVAANL 76
G++TGK +S GGS R +ATG G V+ + ++ + ++ + G GNV A
Sbjct: 192 GVLTGKGLSFGGSLIRTEATGYGLVYFAEEMLKAR-GDSFEGKRVVVSGSGNVAIYAIE- 249
Query: 77 FFKA---GAKIVAIQDDKTTIYNPNGFNIPKLQ--KYVTFTRSIKDFNE--GEKINDSKE 129
KA GAK+V D +Y+ G ++ KL+ K V R I ++ E G + +
Sbjct: 250 --KAQQLGAKVVTCSDSSGYVYDEEGIDLEKLKEIKEVRRGR-ISEYAEEFGAEYLEGGS 306
Query: 130 FWSIPCDILIPAAIEDQITINNA-----NNVTAKIILEGANGPTTTEADDILRDKGIILA 184
WS+PCDI +P A ++++ +A N V K + EGAN P+T EA ++ + G++ A
Sbjct: 307 PWSVPCDIALPCATQNELDEEDAKTLIANGV--KAVAEGANMPSTPEAIEVFLEAGVLFA 364
Query: 185 PDVITNAGGVIVSYFEWVQNLSNLLWTEQEINLRLNNIICNAFDAIWELANT--KKVSLR 242
P NAGGV S E QN S L WT +E++ RL++I+ N A E A K +
Sbjct: 365 PGKAANAGGVATSGLEMSQNASRLSWTFEEVDARLHDIMKNIHHACVETAEEYGKPGNYV 424
Query: 243 TAAFIIGCTRVLQA 256
A I G +V A
Sbjct: 425 AGANIAGFVKVADA 438
>gnl|CDD|184464 PRK14031, PRK14031, glutamate dehydrogenase; Provisional.
Length = 444
Score = 113 bits (284), Expect = 6e-29
Identities = 68/219 (31%), Positives = 112/219 (51%), Gaps = 13/219 (5%)
Query: 18 GIVTGKPISIGGSFGRQKATGRG-VFIIGSKIASKINLNIINSKISIQGFGNVGSVAANL 76
G TGK GGS R +ATG G ++ + + +K ++ + G GNV A
Sbjct: 188 GTFTGKGREFGGSLIRPEATGYGNIYFLMEMLKTK-GTDLKGKVCLVSGSGNVAQYTAEK 246
Query: 77 FFKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRS-----IKDFNE--GEKINDSKE 129
+ G K+V + D IY+P+G + KL Y+ ++ I+++ E G K +
Sbjct: 247 VLELGGKVVTMSDSDGYIYDPDGIDREKLD-YIMELKNLYRGRIREYAEKYGCKYVEGAR 305
Query: 130 FWSIPCDILIPAAIEDQITINNANNVTAKIIL---EGANGPTTTEADDILRDKGIILAPD 186
W DI +P+A ++++ ++A + A ++ EGAN P+T EA + +D I+ AP
Sbjct: 306 PWGEKGDIALPSATQNELNGDDARQLVANGVIAVSEGANMPSTPEAIKVFQDAKILYAPG 365
Query: 187 VITNAGGVIVSYFEWVQNLSNLLWTEQEINLRLNNIICN 225
NAGGV VS E QN L W+ +E++ +L +I+ N
Sbjct: 366 KAANAGGVSVSGLEMTQNSIKLSWSSEEVDEKLKSIMKN 404
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 107 bits (268), Expect = 1e-26
Identities = 65/216 (30%), Positives = 100/216 (46%), Gaps = 10/216 (4%)
Query: 18 GIVTGKPISIGGSFGRQKATGRGVFIIGSKIASKINLNIINSKISIQGFGNVGSVAANLF 77
G +TGK + GGS R +ATG G ++ ++I ++I GFGNV AA
Sbjct: 188 GTLTGKGLEFGGSLIRPEATGFGALYFVHQMLETKGIDIKGKTVAISGFGNVAWGAATKA 247
Query: 78 FKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRSIKDFNE--GEKINDSKEF----- 130
+ GAK+V I IY+P+G + K+ + S D EK S F
Sbjct: 248 TELGAKVVTISGPDGYIYDPDGISGEKIDYMLELRASGNDIVAPYAEKFPGSTFFAGKKP 307
Query: 131 WSIPCDILIPAAIEDQITINNANNVTA---KIILEGANGPTTTEADDILRDKGIILAPDV 187
W DI +P A ++++ +A+ + + E +N T EA D + AP
Sbjct: 308 WEQKVDIALPCATQNELNGEDADKLIKNGVLCVAEVSNMGCTAEAIDKFIAAKQLFAPGK 367
Query: 188 ITNAGGVIVSYFEWVQNLSNLLWTEQEINLRLNNII 223
NAGGV S E QN +L W+ +E++ +L+ I+
Sbjct: 368 AVNAGGVATSGLEMSQNAMHLSWSAEEVDEKLHQIM 403
>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 = 73.8 bits (182), Expect = 6e-16
Identities = 41/163 (25%), Positives = 71/163 (43%), Gaps = 24/163 (14%)
Query: 37 TGRGVFIIGSKIASKINL---NIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTT 93
T GVF+ G K A++ L ++ +++QG G VG A + GAK++ ++
Sbjct: 5 TAYGVFL-GMKAAAEHLLGTDSLEGKTVAVQGLGKVGYKLAEHLLEEGAKLIVADINEEA 63
Query: 94 IYNPNGFNIPKLQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPAAIEDQITINNAN 153
+ R+ + G + +E +S+ D+ P A+ I +
Sbjct: 64 V-----------------ARAAE--LFGATVVAPEEIYSVDADVFAPCALGGVINDDTIP 104
Query: 154 NVTAKIILEGANGPTTTEA-DDILRDKGIILAPDVITNAGGVI 195
+ AK I AN +L ++GI+ APD + NAGG+I
Sbjct: 105 QLKAKAIAGAANNQLADPRHGQMLHERGILYAPDYVVNAGGLI 147
>gnl|CDD|240359 PTZ00324, PTZ00324, glutamate dehydrogenase 2; Provisional.
Length = 1002
Score = 48.6 bits (116), Expect = 1e-06
Identities = 57/242 (23%), Positives = 90/242 (37%), Gaps = 47/242 (19%)
Query: 1 MSWMMDTYSTKKNYTI-PGIVTGKPISIGG----SFGRQKATGRGVFIIGSKIASKINLN 55
M W ++ K+ Y TGK S+GG ++G + R ++ G I K+ LN
Sbjct: 605 MDWA-ALHAKKRGYPFWKSFTTGKSPSMGGIPHDTYGMTTRSVR-AYVTG--ILEKLGLN 660
Query: 56 IINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRSI 115
Q G G + +N + K V I D +++P G N +L++
Sbjct: 661 E-EEVTKFQTGGPDGDLGSNELLLSKEKTVGIVDGSGVLHDPEGLNREELRRLAHHRLPA 719
Query: 116 KDFNE---------------------GEKINDSKEFWS-------IPCDILIP-AAIEDQ 146
++F+E G + F + D+ +P
Sbjct: 720 REFDESKLSPQGFLVLTDDRDVKLPDGTIVESGLRFRNEFHLLPYSDADVFVPCGGRPRS 779
Query: 147 ITINNAN--------NVTAKIILEGANGPTTTEADDILRDKGIILAPDVITNAGGVIVSY 198
+T+ N + KII+EGAN T +A L + G+IL D N GGV S
Sbjct: 780 VTLFNVGRFFDEKNGKLRFKIIVEGANLFITQDARLALEECGVILFKDASANKGGVTSSS 839
Query: 199 FE 200
E
Sbjct: 840 LE 841
>gnl|CDD|225455 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid
transport and metabolism].
Length = 1592
Score = 40.8 bits (96), Expect = 5e-04
Identities = 27/131 (20%), Positives = 45/131 (34%), Gaps = 24/131 (18%)
Query: 87 IQD-DKTTIYNPNGFNIPKLQKYVTFTRSIKDFNEGEKINDSKE-------------FWS 132
D D + I + G + + K +T + + +K + W+
Sbjct: 1023 WSDYDASKI-SKGGGVVSRSAKAITLSPEVIAALGIDKTELAPNELITAILKAPVDLLWN 1081
Query: 133 IPCDILIPAAIE-DQITINNANN--------VTAKIILEGANGPTTTEADDILRDKGIIL 183
+ A+ E + + AN+ V AK+I EGAN T G +
Sbjct: 1082 GGIGTYVKASGETNADVGDRANDAIRVNGEEVRAKVIGEGANLGVTQRGRIEFALAGGRI 1141
Query: 184 APDVITNAGGV 194
D I N+ GV
Sbjct: 1142 NTDAIDNSAGV 1152
>gnl|CDD|169409 PRK08374, PRK08374, homoserine dehydrogenase; Provisional.
Length = 336
Score = 33.2 bits (76), Expect = 0.10
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 10/53 (18%)
Query: 60 KISIQGFGNVGSVAANL------FFKAGA----KIVAIQDDKTTIYNPNGFNI 102
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 = 32.5 bits (75), Expect = 0.16
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 10/72 (13%)
Query: 60 KISIQGFGNVGSVAANLF----------FKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYV 109
KI++ GFG VG A L + K+VAI D + +P+G ++ K
Sbjct: 4 KIALIGFGGVGQGVAELLAEKREYLKKRYGLDLKVVAIADSSGSAIDPDGLDLELALKVK 63
Query: 110 TFTRSIKDFNEG 121
T + D+ EG
Sbjct: 64 EETGKLADYPEG 75
>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 = 0.73
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 60 KISIQGFGNVGSVAANLFFKAGAKIVAIQD 89
KI I G G VGS AA + G K V+ +D
Sbjct: 178 KIVITGSGRVGSGAAEVLKALGIKEVSPED 207
>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 = 30.0 bits (68), Expect = 1.5
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 6/32 (18%)
Query: 71 SVAANLFFKAGAKIVAIQDDKTTIYNPNGFNI 102
VA ++F + GA+++AI + P+G NI
Sbjct: 186 KVAPHVFRELGAEVIAIGVE------PDGLNI 211
>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 = 1.7
Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 1/52 (1%)
Query: 163 GANGPTTTEADDILRDKGIILAPDVITNAGGVIVSYFEWVQNLSNLLWTEQE 214
G P D+ + D+G IT V + F W+ + + W +
Sbjct: 13 GVGAPVAIRFDENIADRGAAEKAITITTDPPVEGA-FYWLPDGRRVRWRPEH 63
>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 = 29.4 bits (67), Expect = 1.9
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 71 SVAANLFFKAGAKIVAIQDDKTTIYNPNGFNI 102
VA +F + GA+++ I + P+G NI
Sbjct: 183 KVAPEVFRELGAEVIVINNA------PDGLNI 208
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 29.3 bits (66), Expect = 2.1
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 11/63 (17%)
Query: 56 IINSKISIQGFGNVGSVAANLFFKA-GAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRS 114
I + K+++ G G +G A +F K G+ +VA Y+P F K YV + +
Sbjct: 144 IKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVA--------YDP--FPNAKAATYVDYKDT 193
Query: 115 IKD 117
I++
Sbjct: 194 IEE 196
>gnl|CDD|236787 PRK10887, glmM, phosphoglucosamine mutase; Provisional.
Length = 443
Score = 29.3 bits (67), Expect = 2.3
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 6/31 (19%)
Query: 72 VAANLFFKAGAKIVAIQDDKTTIYNPNGFNI 102
+A N+F + GA+++AI PNG NI
Sbjct: 186 IAPNVFRELGAEVIAIGC------EPNGLNI 210
>gnl|CDD|237672 PRK14318, glmM, phosphoglucosamine mutase; Provisional.
Length = 448
Score = 28.7 bits (65), Expect = 3.1
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 6/31 (19%)
Query: 72 VAANLFFKAGAKIVAIQDDKTTIYNPNGFNI 102
VA + AGA ++AI D P+G NI
Sbjct: 190 VAPEAYRAAGADVIAINAD------PDGLNI 214
>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 = 3.2
Identities = 23/115 (20%), Positives = 40/115 (34%), Gaps = 24/115 (20%)
Query: 105 LQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPAAIEDQITINNANNVTAKIILEGA 164
+++ V F + I F E + EDQI + ++L A
Sbjct: 15 IRRVVEFAKRIPGFRE------------LSQ--------EDQIALLKGGCFEI-LLLRSA 53
Query: 165 NGPTTTEADDILRDKGIILAPDVITNAG--GVIVSYFEWVQNLSNLLWTEQEINL 217
E + + G + DV+ N G I FE+ + ++ L + E L
Sbjct: 54 TL-YDPEKNSLTFGDGKGNSRDVLLNGGFGEFIEPLFEFAEKMNKLQLDDNEYAL 107
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 28.2 bits (64), Expect = 4.4
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 59 SKISIQGFGNVGSVAANL 76
KISI G GNVG+ A+L
Sbjct: 3 KKISIIGAGNVGATLAHL 20
>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 = 28.3 bits (64), Expect = 4.5
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 10/62 (16%)
Query: 56 IINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRSI 115
I + + I G G +GS AA +F GAK++A Y+P + P+L+K++ + S+
Sbjct: 143 IRDLTVGIIGTGRIGSAAAKIFKGFGAKVIA--------YDP--YPNPELEKFLLYYDSL 192
Query: 116 KD 117
+D
Sbjct: 193 ED 194
>gnl|CDD|131338 TIGR02285, TIGR02285, conserved hypothetical protein. Members of
this family are found in several Proteobacteria,
including Pseudomonas putida KT2440, Bdellovibrio
bacteriovorus HD100 (three members), Aeromonas
hydrophila, and Chromobacterium violaceum ATCC 12472.
The function is unknown [Hypothetical proteins,
Conserved].
Length = 268
Score = 27.8 bits (62), Expect = 5.5
Identities = 20/118 (16%), Positives = 40/118 (33%), Gaps = 22/118 (18%)
Query: 82 AKIVAIQDDKTTIYNPNGFNIPKLQKYVTFTRSIKDFNEGEKINDSKEFWSIPCDILIPA 141
A+ + K + N P+ +K++ F+ ++P +++
Sbjct: 67 ARSLKELQGKGGVCTVNLLRTPEREKFLIFSD--------------PTLRALPVGLVLRK 112
Query: 142 AIEDQITINNANNVTAKIILE--------GANGPTTTEADDILRDKGIILAPDVITNA 191
+ + +V K +L A+ + DDIL D G +I NA
Sbjct: 113 ELTAGVRDEQDGDVDLKKLLASKKKRLGVIASRSYGQQIDDILSDSGYQHNTRIIGNA 170
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 28.0 bits (62), Expect = 6.3
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 60 KISIQGFGNVGSVAANLFFKAGAKIVA 86
KI+I GFGN G A K G ++A
Sbjct: 371 KIAIVGFGNFGQFLAKTMVKQGHTVLA 397
>gnl|CDD|224996 COG2085, COG2085, Predicted dinucleotide-binding enzymes [General
function prediction only].
Length = 211
Score = 27.3 bits (61), Expect = 6.5
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 60 KISIQGFGNVGSVAANLFFKAGAKIV 85
I+I G GN+GS A KAG +++
Sbjct: 3 IIAIIGTGNIGSALALRLAKAGHEVI 28
>gnl|CDD|240660 cd12184, HGDH_like, (R)-2-Hydroxyglutarate Dehydrogenase and
related dehydrogenases, NAD-binding and catalytic
domains. (R)-2-hydroxyglutarate dehydrogenase (HGDH)
catalyzes the NAD-dependent reduction of 2-oxoglutarate
to (R)-2-hydroxyglutarate. HGDH is a member of the
D-2-hydroxyacid NAD(+)-dependent dehydrogenase family;
these proteins typically have a characteristic
arrangement of 2 similar subdomains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD+ binding domain
is inserted within the linear sequence of the mostly
N-terminal catalytic domain, which has a similar domain
structure to the internal NAD binding domain.
Structurally, these domains are connected by extended
alpha helices and create a cleft in which NAD is bound,
primarily to the C-terminal portion of the 2nd
(internal) domain.
Length = 330
Score = 27.6 bits (62), Expect = 7.5
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 56 IINSKISIQGFGNVGSVAANLFFKAGAKIVA 86
I NS + I G G +G AA LF GAK++
Sbjct: 143 IRNSTVGIIGTGRIGLTAAKLFKGLGAKVIG 173
>gnl|CDD|162820 TIGR02356, adenyl_thiF, thiazole biosynthesis adenylyltransferase
ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF
family of proteins (pfam00899) include a number of
members encoded in the midst of thiamine biosynthetic
operons. This mix of known and putative ThiF proteins
shows a deep split in phylogenetic trees, with the
Escherichia. coli ThiF and the E. coli MoeB proteins
seemingly more closely related than E. coli ThiF and
Campylobacter (for example) ThiF. This model represents
the more widely distributed clade of ThiF proteins such
found in E. coli [Biosynthesis of cofactors, prosthetic
groups, and carriers, Thiamine].
Length = 202
Score = 27.3 bits (61), Expect = 7.9
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 56 IINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDD 90
++NS + I G G +GS AA AG + I DD
Sbjct: 19 LLNSHVLIIGAGGLGSPAALYLAGAGVGTIVIVDD 53
>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral
inhibitor of apoptosis (IAP)-associated factor (VIAF)
subfamily; VIAF is a Phd-like protein that functions in
caspase activation during apoptosis. It was identified
as an IAP binding protein through a screen of a human
B-cell library using a prototype IAP. VIAF lacks a
consensus IAP binding motif and while it does not
function as an IAP antagonist, it still plays a
regulatory role in the complete activation of caspases.
VIAF itself is a substrate for IAP-mediated
ubiquitination, suggesting that it may be a target of
IAPs in the prevention of cell death. The similarity of
VIAF to Phd points to a potential role distinct from
apoptosis regulation. Phd functions as a cytosolic
regulator of G protein by specifically binding to G
protein betagamma (Gbg)-subunits. The C-terminal domain
of Phd adopts a thioredoxin fold, but it does not
contain a CXXC motif. Phd interacts with G protein beta
mostly through the N-terminal helical domain.
Length = 192
Score = 26.8 bits (60), Expect = 8.4
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 170 TEADDILRDKGII 182
TE +DILR KGI+
Sbjct: 1 TEWNDILRKKGIL 13
>gnl|CDD|239134 cd02669, Peptidase_C19M, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 440
Score = 27.3 bits (61), Expect = 9.0
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 3/60 (5%)
Query: 114 SIKDFNEG--EKINDSKEFWSIPCDILIPAAIEDQITINNANNVTAKIILEGANGPTTTE 171
K F + +K + S F + D+ P +D N V K +L+ +G T TE
Sbjct: 261 KDKFFKDSRVKKTSVSP-FLLLTLDLPPPPLFKDGNEENIIPQVPLKQLLKKYDGKTETE 319
>gnl|CDD|223477 COG0400, COG0400, Predicted esterase [General function prediction
only].
Length = 207
Score = 26.9 bits (60), Expect = 9.1
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 53 NLNIINSKISIQGFGNVGSVAANLFFKAGA 82
I +S+I + GF ++A +L
Sbjct: 93 EYGIDSSRIILIGFSQGANIALSLGLTLPG 122
>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 = 27.1 bits (61), Expect = 9.4
Identities = 26/87 (29%), Positives = 36/87 (41%), Gaps = 27/87 (31%)
Query: 34 QKATGRGV-FIIG------SKIASKI--NLNII-------NSKISIQGFGNV-------- 69
QK GV ++G + AS I + I+ N K++ +G+ NV
Sbjct: 60 QKLVDDGVVGVVGHLNSGVTIPASPIYADAGIVMISPAATNPKLTERGYKNVFRVVARDD 119
Query: 70 --GSVAANLFFK-AGAKIVAIQDDKTT 93
G AA + AK VAI DDKT
Sbjct: 120 QQGPAAAKYAVETLKAKKVAIIDDKTA 146
>gnl|CDD|183656 PRK12656, PRK12656, fructose-6-phosphate aldolase; Reviewed.
Length = 222
Score = 27.0 bits (60), Expect = 9.4
Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 6/65 (9%)
Query: 46 SKIASKINLNIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDDKTTIYNPNGFNIPKL 105
++A I+ +SKI F NV V N F GA+ V D F +P +
Sbjct: 149 GQLAEAIDRENSDSKILAASFKNVAQV--NKAFALGAQAVTAGPDVFE----AAFAMPSI 202
Query: 106 QKYVT 110
QK V
Sbjct: 203 QKAVD 207
>gnl|CDD|224562 COG1648, CysG, Siroheme synthase (precorrin-2
oxidase/ferrochelatase domain) [Coenzyme metabolism].
Length = 210
Score = 26.9 bits (60), Expect = 9.5
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 54 LNIINSKISIQGFGNVGSVAANLFFKAGAKIVAIQDD 90
L++ K+ + G G+V A L KAGA + + +
Sbjct: 8 LDLEGKKVLVVGGGSVALRKARLLLKAGADVTVVSPE 44
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
0.319 0.136 0.399
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: 13,310,458
Number of extensions: 1278274
Number of successful extensions: 1289
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1262
Number of HSP's successfully gapped: 65
Length of query: 262
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 167
Effective length of database: 6,723,972
Effective search space: 1122903324
Effective search space used: 1122903324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (25.9 bits)