RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2302
(292 letters)
>gnl|CDD|238386 cd00757, ThiF_MoeB_HesA_family, ThiF_MoeB_HesA. Family of E1-like
enzymes involved in molybdopterin and thiamine
biosynthesis family. The common reaction mechanism
catalyzed by MoeB and ThiF, like other E1 enzymes,
begins with a nucleophilic attack of the C-terminal
carboxylate of MoaD and ThiS, respectively, on the
alpha-phosphate of an ATP molecule bound at the active
site of the activating enzymes, leading to the formation
of a high-energy acyladenylate intermediate and
subsequently to the formation of a thiocarboxylate at
the C termini of MoaD and ThiS. MoeB, as the MPT
synthase (MoaE/MoaD complex) sulfurase, is involved in
the biosynthesis of the molybdenum cofactor, a
derivative of the tricyclic pterin, molybdopterin (MPT).
ThiF catalyzes the adenylation of ThiS, as part of the
biosynthesis pathway of thiamin pyrophosphate (vitamin
B1). .
Length = 228
Score = 228 bits (583), Expect = 8e-75
Identities = 82/242 (33%), Positives = 108/242 (44%), Gaps = 24/242 (9%)
Query: 1 MALKRMGIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR- 59
+ L +G E E ++ V+VVG GG+GS AE L G+GKL L D D VEL+N+ R
Sbjct: 6 ILLPEIGE-EGQEKLKNARVLVVGAGGLGSPAAEYLAAAGVGKLGLVDDDVVELSNLQRQ 64
Query: 60 LFFQPDQCGLSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTE--GPVDL 117
+ G K EAA L+ INPDV IE +N + + E DL
Sbjct: 65 ILHTEADVGQPKAEAAAERLRAINPDVEIEAYNERLD----------AENAEELIAGYDL 114
Query: 118 VLSCVDNFEARMTINMACNQLGQTWFESGVSENAVSGHIQLIIPGESACFACAPPLIVAS 177
VL C DNF R IN AC +LG+ V G + + IPGE C+ C P
Sbjct: 115 VLDCTDNFATRYLINDACVKLGKPLVSGAVLG--FEGQVTVFIPGEGPCYRCLFPEPPPP 172
Query: 178 SIDEKTLKKDGVCAASLPTTMGIVAGFLVQNALKKLLKFGEVSW--YLGYSALTDFFPKM 235
+ A L +G++ ALK LL GE L + AL+ F +
Sbjct: 173 GVP------SCAEAGVLGPLVGVIGSLQALEALKILLGIGEPLAGRLLLFDALSMSFRTL 226
Query: 236 KL 237
KL
Sbjct: 227 KL 228
>gnl|CDD|216180 pfam00899, ThiF, ThiF family. This family contains a repeated
domain in ubiquitin activating enzyme E1 and members of
the bacterial ThiF/MoeB/HesA family.
Length = 134
Score = 126 bits (320), Expect = 1e-36
Identities = 54/135 (40%), Positives = 72/135 (53%), Gaps = 13/135 (9%)
Query: 18 LTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR-LFFQPDQCGLSKVEAAR 76
V+VVG GG+GS AE L R G+GKL L D+D VEL+N+NR + F G K E A+
Sbjct: 2 SRVLVVGAGGLGSPAAEYLARAGVGKLTLVDFDTVELSNLNRQILFTESDIGKPKAEVAK 61
Query: 77 ITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTE--GPVDLVLSCVDNFEARMTINMA 134
L+ INPDV +E + +T +L E VDLV+ +DNF AR +N A
Sbjct: 62 ERLRAINPDVEVEAYPERLT----------PENLEELLKGVDLVVDALDNFAARYLLNDA 111
Query: 135 CNQLGQTWFESGVSE 149
C + G +G
Sbjct: 112 CVKRGIPLISAGALG 126
>gnl|CDD|223552 COG0476, ThiF, Dinucleotide-utilizing enzymes involved in
molybdopterin and thiamine biosynthesis family 2
[Coenzyme metabolism].
Length = 254
Score = 120 bits (304), Expect = 7e-33
Identities = 71/231 (30%), Positives = 101/231 (43%), Gaps = 22/231 (9%)
Query: 19 TVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR-LFFQPDQCGLSKVEAARI 77
V+VVG GG+GS A+ L G+GKL + D+D VEL+N+ R F G K E A
Sbjct: 32 RVLVVGAGGLGSPAAKYLALAGVGKLTIVDFDTVELSNLQRQFLFTEADVGKPKAEVAAK 91
Query: 78 TLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQ 137
L+ +NP V + + + +A D+VL C DNFE R IN AC +
Sbjct: 92 ALRKLNPLVEVVAYLERLDEENAEELIA--------QFDVVLDCTDNFETRYLINDACVK 143
Query: 138 LGQTWFESGVSENAVSGHIQLIIPGE-SACFACAPPLIVASSIDEKTLKKDGVCAASLPT 196
LG G G + +IIPG+ + C+ C P + + + GV L
Sbjct: 144 LGIPLVHGGA--IGFEGQVTVIIPGDKTPCYRCLFPEKPPPGLVPTSCDEAGV----LGP 197
Query: 197 TMGIVAGFLVQNALKKLLKFGEVSWYLGYSALTDF-----FPKMKLKPNPS 242
+G+V A+K L G +G L D F +KL+ P
Sbjct: 198 LVGVVGSLQALEAIKLLTGIGLEPL-IGRLLLYDALDMERFRTLKLRRRPI 247
>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 = 106 bits (267), Expect = 4e-28
Identities = 64/217 (29%), Positives = 98/217 (45%), Gaps = 24/217 (11%)
Query: 1 MALKRMGIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR- 59
+ L +G E + + V+++G GG+GS A L G+G +++ D D V+L+N+ R
Sbjct: 6 LLLPDIG-EEGQQRLLNSHVLIIGAGGLGSPAALYLAGAGVGTIVIVDDDHVDLSNLQRQ 64
Query: 60 LFFQPDQCGLSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVL 119
+ F + G KVE A L+ +N D+ + L +V A ++ + VDLVL
Sbjct: 65 ILFTEEDVGRPKVEVAAQRLRELNSDIQVT------ALKERVTAENLELLIN--NVDLVL 116
Query: 120 SCVDNFEARMTINMACNQLGQTWFESGVSENAV--SGHIQLIIPG-ESACFACAPPLIVA 176
C DNF R IN AC LG +S V G + + PG E C C P I
Sbjct: 117 DCTDNFATRYLINDACVALGTPL----ISAAVVGFGGQLMVFDPGGEGPCLRCLFPDIAD 172
Query: 177 SSIDEKTLKKDGVCAASLPTTMGIVAGFLVQNALKKL 213
+ + GV + +G++ ALK L
Sbjct: 173 T---GPSCATAGV----IGPVVGVIGSLQALEALKLL 202
>gnl|CDD|236320 PRK08644, PRK08644, thiamine biosynthesis protein ThiF;
Provisional.
Length = 212
Score = 99 bits (250), Expect = 2e-25
Identities = 43/124 (34%), Positives = 62/124 (50%), Gaps = 12/124 (9%)
Query: 10 ENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLFFQPDQCGL 69
+ E ++ V + G GG+GS A L R G+G L L D+D VE +N+NR + Q G+
Sbjct: 21 KLLEKLKKAKVGIAGAGGLGSNIAVALARSGVGNLKLVDFDVVEPSNLNRQQYFISQIGM 80
Query: 70 SKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTE--GPVDLVLSCVDNFEA 127
KVEA + L INP V IE HN I + ++ E D+V+ DN E
Sbjct: 81 PKVEALKENLLEINPFVEIEAHNEKID----------EDNIEELFKDCDIVVEAFDNAET 130
Query: 128 RMTI 131
+ +
Sbjct: 131 KAML 134
>gnl|CDD|238760 cd01483, E1_enzyme_family, Superfamily of activating enzymes (E1)
of the ubiquitin-like proteins. This family includes
classical ubiquitin-activating enzymes E1,
ubiquitin-like (ubl) activating enzymes and other
mechanistic homologes, like MoeB, Thif1 and others. The
common reaction mechanism catalyzed by MoeB, ThiF and
the E1 enzymes begins with a nucleophilic attack of the
C-terminal carboxylate of MoaD, ThiS and ubiquitin,
respectively, on the alpha-phosphate of an ATP molecule
bound at the active site of the activating enzymes,
leading to the formation of a high-energy acyladenylate
intermediate and subsequently to the formation of a
thiocarboxylate at the C termini of MoaD and ThiS.
Length = 143
Score = 97.7 bits (244), Expect = 3e-25
Identities = 50/149 (33%), Positives = 72/149 (48%), Gaps = 11/149 (7%)
Query: 19 TVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR-LFFQPDQCGLSKVEAARI 77
V++VG+GG+GS A L R G+GK+ L D+D VEL+N+NR + G K E A
Sbjct: 1 RVLLVGLGGLGSEIALNLARSGVGKITLIDFDTVELSNLNRQFLARQADIGKPKAEVAAR 60
Query: 78 TLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQ 137
L +NP V + I+ L VDLV+ +DN R +N AC +
Sbjct: 61 RLNELNPGVNVTAVPEGISEDNLDDFL--------DGVDLVIDAIDNIAVRRALNRACKE 112
Query: 138 LGQTWFESGVSENAVSGHIQLIIPGESAC 166
LG ++G + G IQ+I G +
Sbjct: 113 LGIPVIDAGGL--GLGGDIQVIDIGSLSA 139
>gnl|CDD|238384 cd00755, YgdL_like, Family of activating enzymes (E1) of
ubiquitin-like proteins related to the E.coli
hypothetical protein ygdL. The common reaction mechanism
catalyzed by E1-like enzymes begins with a nucleophilic
attack of the C-terminal carboxylate of the
ubiquitin-like substrate, on the alpha-phosphate of an
ATP molecule bound at the active site of the activating
enzymes, leading to the formation of a high-energy
acyladenylate intermediate and subsequently to the
formation of a thiocarboxylate at the C termini of the
substrate. The exact function of this family is unknown.
Length = 231
Score = 95.7 bits (239), Expect = 1e-23
Identities = 41/119 (34%), Positives = 59/119 (49%), Gaps = 8/119 (6%)
Query: 10 ENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR-LFFQPDQCG 68
E E +R V VVG+GGVGS AE L R G+GKL L D+D V ++N+NR + G
Sbjct: 4 EGLEKLRNAHVAVVGLGGVGSWAAEALARSGVGKLTLIDFDVVCVSNLNRQIHALLSTVG 63
Query: 69 LSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEA 127
KVE +++INP+ ++ +T L G D V+ +D+ A
Sbjct: 64 KPKVEVMAERIRDINPECEVDAVEEFLT-------PDNSEDLLGGDPDFVVDAIDSIRA 115
>gnl|CDD|181084 PRK07688, PRK07688, thiamine/molybdopterin biosynthesis
ThiF/MoeB-like protein; Validated.
Length = 339
Score = 97.0 bits (242), Expect = 3e-23
Identities = 55/162 (33%), Positives = 83/162 (51%), Gaps = 17/162 (10%)
Query: 13 EHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR--LFFQPD-QCGL 69
+ +R V+++G G +G+ AEML R G+GK+ + D D VE +N+ R L+ + D + L
Sbjct: 20 QKLREKHVLIIGAGALGTANAEMLVRAGVGKVTIVDRDYVEWSNLQRQQLYTESDVKNNL 79
Query: 70 SKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARM 129
K AA+ L+ IN DV +E ++T ++ L V G VDL++ DNFE R
Sbjct: 80 PKAVAAKKRLEEINSDVRVEAIVQDVT-AEELEEL-VTG------VDLIIDATDNFETRF 131
Query: 130 TINMACNQLGQTWFESGVSENAVS--GHIQLIIPGESACFAC 169
+N A + G W V G IIPG++ C C
Sbjct: 132 IVNDAAQKYGIPWIYGA----CVGSYGLSYTIIPGKTPCLRC 169
>gnl|CDD|236337 PRK08762, PRK08762, molybdopterin biosynthesis protein MoeB;
Validated.
Length = 376
Score = 97.4 bits (243), Expect = 3e-23
Identities = 73/238 (30%), Positives = 111/238 (46%), Gaps = 36/238 (15%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR-LFFQPDQCGLSKVEAARIT 78
V+++G GG+GS A L G+G L + D+D V+ +N+ R + D+ G KV++A
Sbjct: 138 VLLIGAGGLGSPAALYLAAAGVGTLGIVDHDVVDRSNLQRQILHTEDRVGQPKVDSAAQR 197
Query: 79 LQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQL 138
L +NPDV +E +T V AL +Q VD+V+ DNF R +N AC +L
Sbjct: 198 LAALNPDVQVEAVQERVT-SDNVEAL-LQD------VDVVVDGADNFPTRYLLNDACVKL 249
Query: 139 GQTWFESGVSENAV---SGHIQLIIPGESA----CFAC----APPLIVASSIDEKTLKKD 187
G+ + AV G + + G C+ C PP +A S E
Sbjct: 250 GKP-----LVYGAVFRFEGQVSVFDAGRQRGQAPCYRCLFPEPPPPELAPSCAEA----- 299
Query: 188 GVCAASLPTTMGIVAGFLVQNALKKLLKFGE--VSWYLGYSALTDFFPKMKLKPNPSC 243
GV LP +G++ A+K LL G+ L + AL F +++L P+P C
Sbjct: 300 GVLGV-LPGVIGLLQA---TEAIKLLLGIGDPLTGRLLTFDALAMRFRELRLPPDPHC 353
>gnl|CDD|180204 PRK05690, PRK05690, molybdopterin biosynthesis protein MoeB;
Provisional.
Length = 245
Score = 92.2 bits (230), Expect = 3e-22
Identities = 72/233 (30%), Positives = 104/233 (44%), Gaps = 31/233 (13%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR-LFFQPDQCGLSKVEAARIT 78
V+VVG+GG+G ++ L G+G L L D+D V L+N+ R + G KVE+AR
Sbjct: 35 VLVVGLGGLGCAASQYLAAAGVGTLTLVDFDTVSLSNLQRQVLHDDATIGQPKVESARAA 94
Query: 79 LQNINPDVTIEVHNFNI---TLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMAC 135
L INP + IE N + L + DLVL C DN R +N AC
Sbjct: 95 LARINPHIAIETINARLDDDELAALIAG-----------HDLVLDCTDNVATRNQLNRAC 143
Query: 136 NQLGQTWFESGVSENAV--SGHIQLIIPGESA-CFACAPPLIVASSIDEKTLKKDGVCAA 192
+ VS A+ G + + + C+ C L +++ T + GV A
Sbjct: 144 FAAKKPL----VSGAAIRMEGQVTVFTYQDDEPCYRCLSRLFGENAL---TCVEAGVMAP 196
Query: 193 SLPTTMGIVAGFLVQNALKKLLKFGE--VSWYLGYSALTDFFPKMKLKPNPSC 243
L G++ A+K L +GE L Y A+T F +MKLK +P C
Sbjct: 197 -LV---GVIGSLQAMEAIKLLTGYGEPLSGRLLLYDAMTMQFREMKLKRDPGC 245
>gnl|CDD|224100 COG1179, COG1179, Dinucleotide-utilizing enzymes involved in
molybdopterin and thiamine biosynthesis family 1
[Coenzyme metabolism].
Length = 263
Score = 87.0 bits (216), Expect = 5e-20
Identities = 38/120 (31%), Positives = 55/120 (45%), Gaps = 8/120 (6%)
Query: 10 ENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR-LFFQPDQCG 68
+ E ++ V VVG+GGVGS E L R GIG++ L D D V + N NR + G
Sbjct: 23 DGLEKLKQAHVCVVGIGGVGSWAVEALARSGIGRITLIDMDDVCVTNTNRQIHALLGDIG 82
Query: 69 LSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEAR 128
KVE + ++ INP+ + N IT L D V+ +D+ A+
Sbjct: 83 KPKVEVMKERIKQINPECEVTAINDFIT-------EENLEDLLSKGFDYVIDAIDSVRAK 135
>gnl|CDD|183547 PRK12475, PRK12475, thiamine/molybdopterin biosynthesis MoeB-like
protein; Provisional.
Length = 338
Score = 85.6 bits (212), Expect = 4e-19
Identities = 64/206 (31%), Positives = 94/206 (45%), Gaps = 24/206 (11%)
Query: 13 EHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR--LFFQPD--QCG 68
IR V++VG G +G+ AE L R GIGKL + D D VE +N+ R L+ + D Q
Sbjct: 20 RKIREKHVLIVGAGALGAANAEALVRAGIGKLTIADRDYVEWSNLQRQQLYTEEDAKQK- 78
Query: 69 LSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEAR 128
K AA+ L+ IN +V I ++T + L + VDL++ DNF+ R
Sbjct: 79 KPKAIAAKEHLRKINSEVEIVPVVTDVT-------VEELEELVKE-VDLIIDATDNFDTR 130
Query: 129 MTINMACNQLGQTWFESG-VSENAVSGHIQLIIPGESACFACAPPLIVASSIDEKTLKKD 187
+ IN + W G V V+ IIPG++ C C L+ + T
Sbjct: 131 LLINDLSQKYNIPWIYGGCVGSYGVT---YTIIPGKTPCLRC---LMEHVPVGGATCDTA 184
Query: 188 GVCAASLPTTMGIVAGFLVQNALKKL 213
G+ + + IV + V ALK L
Sbjct: 185 GI----IQPAVQIVVAYQVTEALKIL 206
>gnl|CDD|238766 cd01489, Uba2_SUMO, Ubiquitin activating enzyme (E1) subunit UBA2.
UBA2 is part of the heterodimeric activating enzyme
(E1), specific for the SUMO family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and Ubls C-terminus. The E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Post-translational
modification by SUMO family of ubiquitin-like proteins
(Ublps) is involved in cell division, nuclear transport,
the stress response and signal transduction. UBA2
contains both the nucleotide-binding motif involved in
adenylation and the catalytic cysteine involved in the
thioester intermediate and Ublp transfer to E2.
Length = 312
Score = 83.6 bits (207), Expect = 1e-18
Identities = 47/160 (29%), Positives = 77/160 (48%), Gaps = 24/160 (15%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARIT 78
V+VVG GG+G + L G G++ + D D ++L+N+NR F F+ G SK + A+
Sbjct: 2 VLVVGAGGIGCELLKNLVLTGFGEIHIIDLDTIDLSNLNRQFLFRKKHVGKSKAQVAKEA 61
Query: 79 LQNINPDVTIEVHN-------FNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTI 131
+ + NP+V I ++ FN+ ++ DLV + +DN AR +
Sbjct: 62 VLSFNPNVKIVAYHANIKDPDFNVEFFKQ--------------FDLVFNALDNLAARRHV 107
Query: 132 NMACNQLGQTWFESGVSENAVSGHIQLIIPGESACFACAP 171
N C ESG + G +Q+I G++ C+ C P
Sbjct: 108 NKMCLAADVPLIESGTT--GFLGQVQVIKKGKTECYECQP 145
>gnl|CDD|131408 TIGR02355, moeB, molybdopterin synthase sulfurylase MoeB. This
model describes the molybdopterin biosynthesis protein
MoeB in E. coli and related species. The enzyme
covalently modifies the molybdopterin synthase MoaD by
sulfurylation. This enzyme is closely related to ThiF, a
thiamine biosynthesis enzyme that modifies ThiS by an
analogous adenylation. Both MoeB and ThiF belong to the
HesA/MoeB/ThiF family (pfam00899) [Biosynthesis of
cofactors, prosthetic groups, and carriers,
Molybdopterin].
Length = 240
Score = 81.8 bits (202), Expect = 2e-18
Identities = 68/237 (28%), Positives = 102/237 (43%), Gaps = 25/237 (10%)
Query: 13 EHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLFFQPD-QCGLSK 71
E ++ V++VG+GG+G ++ L G+G L L D+D V L+N+ R D G K
Sbjct: 20 EALKASRVLIVGLGGLGCAASQYLAAAGVGNLTLLDFDTVSLSNLQRQVLHSDANIGQPK 79
Query: 72 VEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTI 131
VE+A+ L INP + I N + ++ AL + D+V+ C DN E R +
Sbjct: 80 VESAKDALTQINPHIAINPINAKLDD-AELAALIAE-------HDIVVDCTDNVEVRNQL 131
Query: 132 NMACNQLGQTWFESGVSENAVSGHIQLII---PGESACFACAPPLIVASSIDEKTLKKDG 188
N C VS A+ Q+ + C+ C L E L
Sbjct: 132 NRQCFAAKVPL----VSGAAIRMEGQVSVFTYQDGEPCYRCLSRLF-----GENALS--C 180
Query: 189 VCAASLPTTMGIVAGFLVQNALKKLLKFGE--VSWYLGYSALTDFFPKMKLKPNPSC 243
V A + +G+V A+K L G+ L A+T F +MKL NP+C
Sbjct: 181 VEAGVMAPVVGVVGSLQAMEAIKVLAGIGKPLSGKILMIDAMTMSFREMKLPKNPTC 237
>gnl|CDD|238764 cd01487, E1_ThiF_like, E1_ThiF_like. Member of superfamily of
activating enzymes (E1) of the ubiquitin-like proteins.
The common reaction mechanism catalyzed by E1-like
enzymes begins with a nucleophilic attack of the
C-terminal carboxylate of the ubiquitin-like substrate,
on the alpha-phosphate of an ATP molecule bound at the
active site of the activating enzymes, leading to the
formation of a high-energy acyladenylate intermediate
and subsequently to the formation of a thiocarboxylate
at the C termini of the substrate. The exact function
of this family is unknown.
Length = 174
Score = 77.4 bits (191), Expect = 2e-17
Identities = 35/78 (44%), Positives = 45/78 (57%)
Query: 19 TVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLFFQPDQCGLSKVEAARIT 78
V + G GG+GS A +L R G+G L L D+D VE +N+NR + Q G KVEA +
Sbjct: 1 KVGIAGAGGLGSNIAVLLARSGVGNLKLVDFDVVEPSNLNRQQYFLSQIGEPKVEALKEN 60
Query: 79 LQNINPDVTIEVHNFNIT 96
L+ INP V IE N I
Sbjct: 61 LREINPFVKIEAINIKID 78
>gnl|CDD|169382 PRK08328, PRK08328, hypothetical protein; Provisional.
Length = 231
Score = 76.4 bits (188), Expect = 2e-16
Identities = 50/160 (31%), Positives = 81/160 (50%), Gaps = 16/160 (10%)
Query: 9 VENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR--LFFQPDQ 66
VE E ++ V VVGVGG+GS A L G+G+++L D EL+N+NR L ++ D
Sbjct: 19 VEGQEKLKKAKVAVVGVGGLGSPVAYYLAAAGVGRILLIDEQTPELSNLNRQILHWEEDL 78
Query: 67 CGLSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQG--SLTEGPVDLVLSCVDN 124
K +A+ L+ N D+ IE VG L+ + + +G VD+++ C+DN
Sbjct: 79 GKNPKPLSAKWKLERFNSDIKIETF---------VGRLSEENIDEVLKG-VDVIVDCLDN 128
Query: 125 FEARMTINMACNQLGQTWFESGVSENAVSGHIQLIIPGES 164
FE R ++ ++ G V G + I+PG++
Sbjct: 129 FETRYLLDDYAHKKGIPLVHGAVE--GTYGQVTTIVPGKT 166
>gnl|CDD|162819 TIGR02354, thiF_fam2, thiamine biosynthesis protein ThiF, family 2.
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 one the E. 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 divergent clade of putative ThiF
proteins such found in Campylobacter [Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine].
Length = 200
Score = 74.1 bits (182), Expect = 7e-16
Identities = 36/85 (42%), Positives = 50/85 (58%)
Query: 12 YEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLFFQPDQCGLSK 71
+ + TV + G+GG+GS A L R GIGKLIL D+D VE +N+NR ++ Q G K
Sbjct: 16 VQKLEQATVAICGLGGLGSNVAINLARAGIGKLILVDFDVVEPSNLNRQQYKASQVGEPK 75
Query: 72 VEAARITLQNINPDVTIEVHNFNIT 96
EA + + INP IE ++ IT
Sbjct: 76 TEALKENISEINPYTEIEAYDEKIT 100
>gnl|CDD|238761 cd01484, E1-2_like, Ubiquitin activating enzyme (E1), repeat
2-like. E1, a highly conserved small protein present
universally in eukaryotic cells, is part of cascade to
attach ubiquitin (Ub) covalently to substrate proteins.
This cascade consists of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes and then targets them
for degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. A set of novel molecules
with a structural similarity to Ub, called Ub-like
proteins (Ubls), have similar conjugation cascades. In
contrast to ubiquitin-E1, which is a single-chain
protein with a weakly conserved two-fold repeat, many of
the Ubls-E1are a heterodimer where each subunit
corresponds to one half of a single-chain E1. This CD
represents the family homologous to the second repeat of
Ub-E1.
Length = 234
Score = 73.4 bits (180), Expect = 2e-15
Identities = 44/156 (28%), Positives = 72/156 (46%), Gaps = 11/156 (7%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARIT 78
V++VG GG+G + L G G++ + D D ++++N+NR F F+P G K E A
Sbjct: 2 VLLVGAGGIGCELLKNLALMGFGQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKSEVAAEA 61
Query: 79 LQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQL 138
+ + NP+ + + KVG ++++ +DN AR +N L
Sbjct: 62 VNDRNPNCKVVPYQ------NKVGPEQDFNDTFFEQFHIIVNALDNIIARRYVNGMLIFL 115
Query: 139 GQTWFESGVSENAVSGHIQLIIPGESACFACA--PP 172
ESG G+ Q+I+PG + C C PP
Sbjct: 116 IVPLIESGTE--GFKGNAQVILPGMTECIECTLYPP 149
>gnl|CDD|181156 PRK07878, PRK07878, molybdopterin biosynthesis-like protein MoeZ;
Validated.
Length = 392
Score = 74.4 bits (183), Expect = 5e-15
Identities = 68/243 (27%), Positives = 105/243 (43%), Gaps = 46/243 (18%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR--LFFQPDQCGLSKVEAARI 77
V+V+G GG+GS T L G+G L + ++D V+ +N+ R + Q D G SK ++AR
Sbjct: 45 VLVIGAGGLGSPTLLYLAAAGVGTLGIVEFDVVDESNLQRQVIHGQSD-VGRSKAQSARD 103
Query: 78 TLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQ 137
++ INP V + +H F L A+ + DL+L DNF R +N A
Sbjct: 104 SIVEINPLVNVRLHEFR---LDPSNAVELFSQY-----DLILDGTDNFATRYLVNDAAVL 155
Query: 138 LGQ--TW-----FESGVS---ENAVSGHIQLIIPGESACFAC-----APPLIVASSIDEK 182
G+ W FE S E+A G + PP +V S +
Sbjct: 156 AGKPYVWGSIYRFEGQASVFWEDAPDGL--------GLNYRDLYPEPPPPGMVPSCAEGG 207
Query: 183 TLKKDGVCAASLPTTMGIVAGFLVQNALKKLLKFGE--VSWYLGYSALTDFFPKMKLKPN 240
L GV AS+ + M A+K + GE + + Y AL + +K++ +
Sbjct: 208 VL---GVLCASIGSIM-------GTEAIKLITGIGEPLLGRLMVYDALEMTYRTIKIRKD 257
Query: 241 PSC 243
PS
Sbjct: 258 PST 260
>gnl|CDD|235528 PRK05600, PRK05600, thiamine biosynthesis protein ThiF; Validated.
Length = 370
Score = 68.0 bits (166), Expect = 6e-13
Identities = 73/301 (24%), Positives = 109/301 (36%), Gaps = 47/301 (15%)
Query: 1 MALKRMGIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR- 59
+AL GI E E + V+V+G GG+G + L G+G + L D D V+++N++R
Sbjct: 26 LALPGFGI-EQQERLHNARVLVIGAGGLGCPAMQSLASAGVGTITLIDDDTVDVSNIHRQ 84
Query: 60 LFFQPDQCGLSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVL 119
+ F G KVE A L+ I PD+ + +T V L VDLVL
Sbjct: 85 ILFGASDVGRPKVEVAAERLKEIQPDIRVNALRERLTAENAVELL--------NGVDLVL 136
Query: 120 SCVDNFEARMTINMACNQLGQ--TW------------FESGVSENAVSGHIQLIIPGESA 165
D+F + + A G W F SG V G
Sbjct: 137 DGSDSFATKFLVADAAEITGTPLVWGTVLRFHGELAVFNSGPDHRGV---------GLRD 187
Query: 166 CFACAPPLIVASSIDEKTLKKDGVCAASLPTTMGIVAGFLVQNALKKLLKFGEV--SWYL 223
F P SI D A L T ++ + A+K L G+V L
Sbjct: 188 LFPEQP---SGDSI------PDCATAGVLGATTAVIGALMATEAIKFLTGIGDVQPGTVL 238
Query: 224 GYSALTDFFPKMKLKPNPSCDDSYCVQRQKEFNARPVEVKLEAAKPEAQVVHADNDWGEY 283
Y ALT ++ +P+ ++ E ++A + + D E
Sbjct: 239 SYDALTATTRSFRVGADPARPLVTRLRPSYEAARTDTTSLIDATLNGSATLL---DVREP 295
Query: 284 H 284
H
Sbjct: 296 H 296
>gnl|CDD|235526 PRK05597, PRK05597, molybdopterin biosynthesis protein MoeB;
Validated.
Length = 355
Score = 66.8 bits (163), Expect = 1e-12
Identities = 40/139 (28%), Positives = 63/139 (45%), Gaps = 10/139 (7%)
Query: 2 ALKRMGIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLF 61
L +G + + + V V+G GG+GS L G+G + + D D V+L+N++R
Sbjct: 14 MLGEIG-QQGQQSLFDAKVAVIGAGGLGSPALLYLAGAGVGHITIIDDDTVDLSNLHRQV 72
Query: 62 FQPDQ-CGLSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLS 120
G K E+AR + +NPDV + V +T AL D++L
Sbjct: 73 IHSTAGVGQPKAESAREAMLALNPDVKVTVSVRRLTW---SNAL----DELRD-ADVILD 124
Query: 121 CVDNFEARMTINMACNQLG 139
DNF+ R + A +LG
Sbjct: 125 GSDNFDTRHLASWAAARLG 143
>gnl|CDD|180967 PRK07411, PRK07411, hypothetical protein; Validated.
Length = 390
Score = 59.7 bits (145), Expect = 3e-10
Identities = 74/289 (25%), Positives = 119/289 (41%), Gaps = 56/289 (19%)
Query: 9 VENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR-LFFQPDQC 67
+E + ++ +V+ +G GG+GS L GIG++ + D+D V+ +N+ R +
Sbjct: 30 LEGQKRLKAASVLCIGTGGLGSPLLLYLAAAGIGRIGIVDFDVVDSSNLQRQVIHGTSWV 89
Query: 68 GLSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEA 127
G K+E+A+ + INP ++++ T L AL + P D+V+ DNF
Sbjct: 90 GKPKIESAKNRILEINPYCQVDLYE---TRLSSENALDIL-----APYDVVVDGTDNFPT 141
Query: 128 RMTINMACNQLGQTWFESGVSENAVSGHIQLIIPGESACF-------------ACAPPLI 174
R +N AC L + V G I G++ F PP +
Sbjct: 142 RYLVNDACVLLNKP---------NVYGSI-FRFEGQATVFNYEGGPNYRDLYPEPPPPGM 191
Query: 175 VASSIDEKTLKKDGVCAASLPTTMGIVAGFLVQNALKKLLKFGEV--SWYLGYSALTDFF 232
V S + L G+ LP GI+ +K +L G L Y+AL F
Sbjct: 192 VPSCAEGGVL---GI----LP---GIIGVIQATETIKIILGAGNTLSGRLLLYNALDMKF 241
Query: 233 PKMKLKPNPSCD--------DSYCVQRQKEFNARPVEVKLEAAKPEAQV 273
++KL+PNP + +C Q A+ E +A PE V
Sbjct: 242 RELKLRPNPERPVIEKLIDYEQFCGIPQ----AKAAEAAQKAEIPEMTV 286
>gnl|CDD|130475 TIGR01408, Ube1, ubiquitin-activating enzyme E1. This model
represents the full length, over a thousand amino acids,
of a multicopy family of eukaryotic proteins, many of
which are designated ubiquitin-activating enzyme E1.
Members have two copies of the ThiF family domain
(pfam00899), a repeat found in ubiquitin-activating
proteins (pfam02134), and other regions.
Length = 1008
Score = 59.5 bits (144), Expect = 6e-10
Identities = 44/166 (26%), Positives = 72/166 (43%), Gaps = 34/166 (20%)
Query: 13 EHIRTLTVIVVGVGGVGSVTAEMLTRCGI--------GKLILFDYDKVELANMNRLF-FQ 63
+ ++ L + +VG G +G EML + G + + D D +E +N+NR F F+
Sbjct: 415 QKLQNLNIFLVGCGAIG---CEMLKNFALMGVGTGKKGMITVTDPDLIEKSNLNRQFLFR 471
Query: 64 PDQCGLSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEG--------PV 115
P G K A INP + I+ H +VG TE +
Sbjct: 472 PHHIGKPKSYTAADATLKINPQIKIDAH------QNRVGPE------TETIFNDEFYEKL 519
Query: 116 DLVLSCVDNFEARMTINMACNQLGQTWFESGVSENAVSGHIQLIIP 161
D+V++ +DN EAR ++ C + ESG G+ Q+++P
Sbjct: 520 DVVINALDNVEARRYVDSRCLAFLKPLLESGTL--GTKGNTQVVVP 563
Score = 36.4 bits (84), Expect = 0.016
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 3/84 (3%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANM-NRLFFQPDQCGLSKVEAARIT 78
V++ G+GG+G A+ L G+ + L D +K + ++ + F D G ++ EA
Sbjct: 27 VLISGMGGLGLEIAKNLVLAGVKSVTLHDTEKCQAWDLSSNFFLSEDDVGRNRAEAVVKK 86
Query: 79 LQNINPDVTIEVHN--FNITLLRK 100
L +NP V + + FN L K
Sbjct: 87 LAELNPYVHVSSSSVPFNEEFLDK 110
>gnl|CDD|238765 cd01488, Uba3_RUB, Ubiquitin activating enzyme (E1) subunit UBA3.
UBA3 is part of the heterodimeric activating enzyme
(E1), specific for the Rub family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins. consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin(-like) by C-terminal adenylation, and
subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis. UBA3
contains both the nucleotide-binding motif involved in
adenylation and the catalytic cysteine involved in the
thioester intermediate and Ublp transfer to E2.
Length = 291
Score = 58.5 bits (142), Expect = 6e-10
Identities = 41/163 (25%), Positives = 71/163 (43%), Gaps = 28/163 (17%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLF-FQPDQCGLSKVEAARIT 78
++V+G GG+G + L G + + D D ++++N+NR F F+ G K E A
Sbjct: 2 ILVIGAGGLGCELLKNLALSGFRNIHVIDMDTIDVSNLNRQFLFREKDIGKPKAEVAAKF 61
Query: 79 LQNINPDVTIEVHN-----FNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTIN- 132
+ + P V + H + R+ ++++ +D+ EAR IN
Sbjct: 62 VNDRVPGVNVTPHFGKIQDKDEEFYRQ--------------FNIIICGLDSIEARRWING 107
Query: 133 MACNQLGQTWFES------GVSENAVSGHIQLIIPGESACFAC 169
+ L ES G +E GH ++I+PG +AC C
Sbjct: 108 TLVSLLLYEDPESIIPLIDGGTE-GFKGHARVILPGITACIEC 149
>gnl|CDD|181302 PRK08223, PRK08223, hypothetical protein; Validated.
Length = 287
Score = 57.0 bits (138), Expect = 2e-09
Identities = 41/141 (29%), Positives = 59/141 (41%), Gaps = 25/141 (17%)
Query: 9 VENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLFFQP-DQC 67
+ +R V + G+GGVG + L R GIGK + D+D EL N NR
Sbjct: 19 PTEQQRLRNSRVAIAGLGGVGGIHLLTLARLGIGKFTIADFDVFELRNFNRQAGAMMSTL 78
Query: 68 GLSKVEAARITLQNINPDVTIEV-------HNFNITLLRKVGALAVQGSLTEGPVDLVLS 120
G K E +++INP++ I N + L +G VD+ +
Sbjct: 79 GRPKAEVLAEMVRDINPELEIRAFPEGIGKENADAFL--------------DG-VDVYVD 123
Query: 121 CVDNFE--ARMTINMACNQLG 139
+D FE AR + AC Q G
Sbjct: 124 GLDFFEFDARRLVFAACQQRG 144
>gnl|CDD|185071 PRK15116, PRK15116, sulfur acceptor protein CsdL; Provisional.
Length = 268
Score = 56.0 bits (135), Expect = 4e-09
Identities = 30/67 (44%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR-LFFQPDQCGLSKVEAARIT 78
+ VVG+GGVGS AE L R GIG + L D D V + N NR + D GL+K E
Sbjct: 33 ICVVGIGGVGSWAAEALARTGIGAITLIDMDDVCVTNTNRQIHALRDNVGLAKAEVMAER 92
Query: 79 LQNINPD 85
++ INP+
Sbjct: 93 IRQINPE 99
>gnl|CDD|238767 cd01490, Ube1_repeat2, Ubiquitin activating enzyme (E1), repeat 2.
E1, a highly conserved small protein present universally
in eukaryotic cells, is part of cascade to attach
ubiquitin (Ub) covalently to substrate proteins. This
cascade consists of activating (E1), conjugating (E2),
and/or ligating (E3) enzymes and then targets them for
degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Ubiquitin-E1 is a
single-chain protein with a weakly conserved two-fold
repeat. This CD represents the second repeat of Ub-E1.
Length = 435
Score = 55.8 bits (135), Expect = 8e-09
Identities = 45/160 (28%), Positives = 70/160 (43%), Gaps = 36/160 (22%)
Query: 20 VIVVGVGGVGSVTAEML---------TRCGIGKLILFDYDKVELANMNRLF-FQPDQCGL 69
V +VG G +G E+L T G++ + D D +E +N+NR F F+P G
Sbjct: 2 VFLVGAGAIG---CELLKNFALMGVGTGES-GEITVTDMDNIEKSNLNRQFLFRPHDVGK 57
Query: 70 SKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTE--------GPVDLVLSC 121
K E A ++ +NPD+ I +VG TE +D V +
Sbjct: 58 PKSEVAAAAVKAMNPDLKITAL------QNRVGPE------TEHIFNDEFWEKLDGVANA 105
Query: 122 VDNFEARMTINMACNQLGQTWFESGVSENAVSGHIQLIIP 161
+DN +ARM ++ C + ESG G+ Q++IP
Sbjct: 106 LDNVDARMYVDRRCVYYRKPLLESGTL--GTKGNTQVVIP 143
>gnl|CDD|163448 TIGR03736, PRTRC_ThiF, PRTRC system ThiF family protein. A novel
genetic system characterized by six major proteins,
included a ParB homolog and a ThiF homolog, is
designated PRTRC, or ParB-Related,ThiF-Related Cassette.
This family is the PRTRC system ThiF family protein.
Length = 244
Score = 48.1 bits (115), Expect = 1e-06
Identities = 33/126 (26%), Positives = 48/126 (38%), Gaps = 22/126 (17%)
Query: 16 RTLTVIVVGVGGVGSVTAEMLTRCGIGKLIL----------FDYDKVELANMNRLFFQPD 65
R ++V++VG GG GS L R L +D D V AN+ R F P
Sbjct: 10 RPVSVVLVGAGGTGSQVIAGLARLHHALKALGHPGGLAVTVYDDDTVSEANVGRQAFYPA 69
Query: 66 QCGLSKVEAARITLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNF 125
G +K A + + +N + +L D+V+ CVDN
Sbjct: 70 DVGQNK---AIVLVNRLN-------QAMGTDWTAHPERVERSSTL--HRPDIVIGCVDNR 117
Query: 126 EARMTI 131
AR+ I
Sbjct: 118 AARLAI 123
>gnl|CDD|184853 PRK14851, PRK14851, hypothetical protein; Provisional.
Length = 679
Score = 47.5 bits (113), Expect = 4e-06
Identities = 38/120 (31%), Positives = 54/120 (45%), Gaps = 14/120 (11%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLFFQ--PDQCGLSKVEAARI 77
V + G+GGVG V + R GIG+ + D+D+ E N+NR F P G K+ +
Sbjct: 46 VAIPGMGGVGGVHLITMVRTGIGRFHIADFDQFEPVNVNRQFGARVPS-FGRPKLAVMKE 104
Query: 78 TLQNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFE---ARMTINMA 134
+INP + I I A + L VD+VL +D F+ R NMA
Sbjct: 105 QALSINPFLEITPFPAGIN------ADNMDAFLDG--VDVVLDGLDFFQFEIRRTLFNMA 156
>gnl|CDD|238763 cd01486, Apg7, Apg7 is an E1-like protein, that activates two
different ubiquitin-like proteins, Apg12 and Apg8, and
assigns them to specific E2 enzymes, Apg10 and Apg3,
respectively. This leads to the covalent conjugation of
Apg8 with phosphatidylethanolamine, an important step
in autophagy. Autophagy is a dynamic membrane
phenomenon for bulk protein degradation in the
lysosome/vacuole.
Length = 307
Score = 43.1 bits (102), Expect = 8e-05
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 3/82 (3%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR--LF-FQPDQCGLSKVEAAR 76
+++G G +G A L G+ + D KV +N R LF F+ + G K EAA
Sbjct: 2 CLLLGAGTLGCNVARNLLGWGVRHITFVDSGKVSYSNPVRQSLFTFEDCKGGKPKAEAAA 61
Query: 77 ITLQNINPDVTIEVHNFNITLL 98
L+ I P + +I +
Sbjct: 62 ERLKEIFPSIDATGIVLSIPMP 83
>gnl|CDD|238762 cd01485, E1-1_like, Ubiquitin activating enzyme (E1), repeat
1-like. E1, a highly conserved small protein present
universally in eukaryotic cells, is part of cascade to
attach ubiquitin (Ub) covalently to substrate proteins.
This cascade consists of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes and then targets them
for degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. The E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. A set of novel molecules
with a structural similarity to Ub, called Ub-like
proteins (Ubls), have similar conjugation cascades. In
contrast to ubiquitin-E1, which is a single-chain
protein with a weakly conserved two-fold repeat, many of
the Ubls-E1are a heterodimer where each subunit
corresponds to one half of a single-chain E1. This CD
represents the family homologous to the first repeat of
Ub-E1.
Length = 198
Score = 40.1 bits (94), Expect = 4e-04
Identities = 21/96 (21%), Positives = 45/96 (46%), Gaps = 4/96 (4%)
Query: 13 EHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLFFQP---DQCGL 69
+R+ V+++G G +G+ A+ L GI + + D+ V ++ FF G+
Sbjct: 15 NKLRSAKVLIIGAGALGAEIAKNLVLAGIDSITIVDHRLVSTEDLGSNFFLDAEVSNSGM 74
Query: 70 SKVEAARITLQNINPDVTIE-VHNFNITLLRKVGAL 104
++ A+ LQ +NP+V + V +++ +
Sbjct: 75 NRAAASYEFLQELNPNVKLSIVEEDSLSNDSNIEEY 110
>gnl|CDD|238768 cd01491, Ube1_repeat1, Ubiquitin activating enzyme (E1), repeat
1. E1, a highly conserved small protein present
universally in eukaryotic cells, is part of cascade to
attach ubiquitin (Ub) covalently to substrate proteins.
This cascade consists of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes and then targets
them for degradation by the 26S proteasome. E1
activates ubiquitin by C-terminal adenylation, and
subsequently forms a highly reactive thioester bond
between its catalytic cysteine and ubiquitin's
C-terminus. E1 also associates with E2 and promotes
ubiquitin transfer to the E2's catalytic cysteine.
Ubiquitin-E1 is a single-chain protein with a weakly
conserved two-fold repeat. This CD represents the first
repeat of Ub-E1.
Length = 286
Score = 40.3 bits (95), Expect = 6e-04
Identities = 22/96 (22%), Positives = 47/96 (48%), Gaps = 10/96 (10%)
Query: 2 ALKRMGIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLF 61
A+K++ + V++ G+GG+G A+ L G+ + L D ++++ F
Sbjct: 13 AMKKL---------QKSNVLISGLGGLGVEIAKNLILAGVKSVTLHDTKPCSWSDLSSQF 63
Query: 62 F-QPDQCGLSKVEAARITLQNINPDVTIEVHNFNIT 96
+ + + G ++ EA++ L +NP V + V +T
Sbjct: 64 YLREEDIGKNRAEASQARLAELNPYVPVTVSTGPLT 99
>gnl|CDD|238769 cd01492, Aos1_SUMO, Ubiquitin activating enzyme (E1) subunit
Aos1. Aos1 is part of the heterodimeric activating
enzyme (E1), specific for the SUMO family of
ubiquitin-like proteins (Ubls). E1 enzymes are part of
a conjugation cascade to attach Ub or Ubls, covalently
to substrate proteins consisting of activating (E1),
conjugating (E2), and/or ligating (E3) enzymes. E1
activates ubiquitin by C-terminal adenylation, and
subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. The
E1 also associates with E2 and promotes ubiquitin
transfer to the E2's catalytic cysteine.
Post-translational modification by SUMO family of
ubiquitin-like proteins (Ublps) is involved in cell
division, nuclear transport, the stress response and
signal transduction. Aos1 contains part of the
adenylation domain.
Length = 197
Score = 39.6 bits (93), Expect = 8e-04
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 13 EHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLFFQPDQC-GLSK 71
+ +R+ ++++G+ G+G+ A+ L GIG L + D V ++ F P + G ++
Sbjct: 17 KRLRSARILLIGLKGLGAEIAKNLVLSGIGSLTILDDRTVTEEDLGAQFLIPAEDLGQNR 76
Query: 72 VEAARITLQNINPDVTIEV 90
EA+ L+ +NP V + V
Sbjct: 77 AEASLERLRALNPRVKVSV 95
>gnl|CDD|238770 cd01493, APPBP1_RUB, Ubiquitin activating enzyme (E1) subunit
APPBP1. APPBP1 is part of the heterodimeric activating
enzyme (E1), specific for the Rub family of
ubiquitin-like proteins (Ubls). E1 enzymes are part of
a conjugation cascade to attach Ub or Ubls, covalently
to substrate proteins consisting of activating (E1),
conjugating (E2), and/or ligating (E3) enzymes. E1
activates ubiquitin(-like) by C-terminal adenylation,
and subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis.
ABPP1 contains part of the adenylation domain.
Length = 425
Score = 39.2 bits (92), Expect = 0.002
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 19 TVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANM-NRLFFQPDQCGLSKVEAARI 77
V ++ G+ + L GIG + D KV+ ++ N F G S+ EA
Sbjct: 22 HVCLLNATATGTEILKNLVLPGIGSFTIVDGSKVDEEDLGNNFFLDASSLGKSRAEATCE 81
Query: 78 TLQNINPDVT 87
LQ +NPDV
Sbjct: 82 LLQELNPDVN 91
>gnl|CDD|184854 PRK14852, PRK14852, hypothetical protein; Provisional.
Length = 989
Score = 39.3 bits (91), Expect = 0.002
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 4 KRMGIVENYEHIRTLT--VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLF 61
+ +G+V+ R L V + G+GGVG + L R GIG L D+D N+NR +
Sbjct: 317 RNLGLVDYAGQRRLLRSRVAIAGLGGVGGIHLMTLARTGIGNFNLADFDAYSPVNLNRQY 376
>gnl|CDD|236122 PRK07877, PRK07877, hypothetical protein; Provisional.
Length = 722
Score = 37.7 bits (88), Expect = 0.006
Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 14/85 (16%)
Query: 13 EHIRTLTVIVVGVGGVGSVTAEMLTRCGI-GKLILFDYDKVELANMNR----LFFQPDQC 67
E + L + VVG+ VG A L G+ G+L L D+D +EL+N+NR +F
Sbjct: 103 ERLGRLRIGVVGLS-VGHAIAHTLAAEGLCGELRLADFDTLELSNLNRVPAGVF----DL 157
Query: 68 GLSKVEAA--RITLQNINPDVTIEV 90
G++K A RI ++P + +EV
Sbjct: 158 GVNKAVVAARRIA--ELDPYLPVEV 180
>gnl|CDD|233388 TIGR01381, E1_like_apg7, E1-like protein-activating enzyme
Gsa7p/Apg7p. This model represents a family of
eukaryotic proteins found in animals, plants, and
yeasts, including Apg7p (YHR171W) from Saccharomyces
cerevisiae and GSA7 from Pichia pastoris. Members are
about 650 to 700 residues in length and include a
central domain of about 150 residues shared with the
ThiF/MoeB/HesA family of proteins. A low level of
similarity to ubiquitin-activating enzyme E1 is
described in a paper on peroxisome autophagy mediated by
GSA7, and is the basis of the name ubiquitin activating
enzyme E1-like protein. Members of the family appear to
be involved in protein lipidation events analogous to
ubiquitination and required for membrane fusion events
during autophagy.
Length = 664
Score = 36.8 bits (85), Expect = 0.012
Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 4/89 (4%)
Query: 11 NYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRL-FFQPDQC-- 67
E L V+++G G +G A L G+ + D KV +N R + C
Sbjct: 332 QLERYSQLKVLLLGAGTLGCNVARCLIGWGVRHITFVDNGKVSYSNPVRQSLSNFEDCLL 391
Query: 68 -GLSKVEAARITLQNINPDVTIEVHNFNI 95
G K E A+ L+ I P + H +
Sbjct: 392 GGRGKAETAQKALKRIFPSIQATGHRLTV 420
>gnl|CDD|176224 cd08263, Zn_ADH10, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and 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. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 367
Score = 35.4 bits (82), Expect = 0.024
Identities = 21/59 (35%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 2 ALKRMGIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRL 60
ALK V E TV V+GVGGVGS ++ G +I D +LA L
Sbjct: 178 ALKHAADVRPGE-----TVAVIGVGGVGSSAIQLAKAFGASPIIAVDVRDEKLAKAKEL 231
>gnl|CDD|217556 pfam03435, Saccharop_dh, Saccharopine dehydrogenase. This family
comprised of three structural domains that can not be
separated in the linear sequence. In some organisms this
enzyme is found as a bifunctional polypeptide with
lysine ketoglutarate reductase. The saccharopine
dehydrogenase can also function as a saccharopine
reductase.
Length = 380
Score = 33.0 bits (76), Expect = 0.17
Identities = 25/120 (20%), Positives = 43/120 (35%), Gaps = 30/120 (25%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLFFQPDQCGLSKVEAARITL 79
V+++G GGVG A +L R G ++ + D + + + A +
Sbjct: 1 VLIIGAGGVGQGVAPLLARHGDLEITVADRSLEKAQAL------AAPKLGLRFIAIAVDA 54
Query: 80 QNINPDVTIEVHNFNITLLRKVGALAVQGSLTEGPVDLVLSCVDNFEARMTINMACNQLG 139
N A+ L EG DLV++ F + +T+ AC + G
Sbjct: 55 DNY---------------------EALVALLKEG--DLVINLAPPFLS-LTVLKACIETG 90
>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 = 32.9 bits (76), Expect = 0.18
Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 15 IRTLTVIVVGVGGVGSVTAEMLTRCGIG-KLILFD 48
IR LTV ++G G +GS A++ G G K+I +D
Sbjct: 143 IRDLTVGIIGTGRIGSAAAKIFK--GFGAKVIAYD 175
>gnl|CDD|176198 cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases. This
group contains proteins identified as sorbitol
dehydrogenases and other sugar dehydrogenases of the
medium-chain dehydrogenase/reductase family (MDR), which
includes zinc-dependent alcohol dehydrogenase and
related proteins. Sorbitol and aldose reductase are
NAD(+) binding proteins of the polyol pathway, which
interconverts glucose and fructose. Sorbitol
dehydrogenase is tetrameric and has a single catalytic
zinc per subunit. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes, or ketones. Related proteins include
threonine dehydrogenase, formaldehyde dehydrogenase, and
butanediol dehydrogenase. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit. Horse
liver alcohol dehydrogenase is a dimeric enzyme and each
subunit has two domains. The NAD binding domain is in a
Rossmann fold and the catalytic domain contains a zinc
ion to which substrates bind. There is a cleft between
the domains that closes upon formation of the ternary
complex.
Length = 343
Score = 32.2 bits (74), Expect = 0.26
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 7/75 (9%)
Query: 19 TVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRL----FFQPDQCGLSKVEA 74
TV+V+G G +G + + L G ++I D D +LA L P + + KV
Sbjct: 162 TVVVIGAGTIGLLAIQWLKILGAKRVIAVDIDDEKLAVARELGADDTINPKEEDVEKVRE 221
Query: 75 ARITLQNINPDVTIE 89
+ D+ IE
Sbjct: 222 L---TEGRGADLVIE 233
>gnl|CDD|236887 PRK11259, solA, N-methyltryptophan oxidase; Provisional.
Length = 376
Score = 31.7 bits (73), Expect = 0.41
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 20 VIVVGVGGVGSVTAEMLTRCG 40
VIV+G+G +GS L R G
Sbjct: 6 VIVIGLGSMGSAAGYYLARRG 26
>gnl|CDD|224662 COG1748, LYS9, Saccharopine dehydrogenase and related proteins
[Amino acid transport and metabolism].
Length = 389
Score = 31.5 bits (72), Expect = 0.45
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFD 48
++V+G GGVGSV A L + G G++ + D
Sbjct: 4 ILVIGAGGVGSVVAHKLAQNGDGEVTIAD 32
>gnl|CDD|223411 COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino
acid transport and metabolism].
Length = 411
Score = 31.1 bits (71), Expect = 0.65
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 2 ALKRMGIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLI 45
ALK +G + V V G G VG AE L G K++
Sbjct: 197 ALKALGD-----DLEGARVAVQGFGNVGQYAAEKLHELG-AKVV 234
>gnl|CDD|133409 cd04782, HTH_BltR, Helix-Turn-Helix DNA binding domain of the
BltR transcription regulator. Helix-turn-helix (HTH)
multidrug-efflux transporter transcription regulator,
BltR (BmrR-like transporter) of Bacillus subtilis, and
related proteins; N-terminal domain. Blt, like Bmr, is
a membrane protein which causes the efflux of a variety
of toxic substances and antibiotics. These regulators
are comprised of two distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their conserved N-terminal domains
contain predicted winged HTH motifs that mediate DNA
binding, while the C-terminal domains are often
unrelated and bind specific coactivator molecules. They
share the N-terminal DNA binding domain with other
transcription regulators of the MerR superfamily that
promote transcription by reconfiguring the spacer
between the -35 and -10 promoter elements.
Length = 97
Score = 29.1 bits (66), Expect = 0.84
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 7/34 (20%)
Query: 32 TAEMLTRCGIGKLILFDYDKVELANMNRLFFQPD 65
T E CGI K LF YDK+ L F+P+
Sbjct: 3 TGEFAKLCGISKQTLFHYDKIGL-------FKPE 29
>gnl|CDD|240635 cd12158, ErythrP_dh, D-Erythronate-4-Phosphate Dehydrogenase
NAD-binding and catalytic domains.
D-Erythronate-4-phosphate Dehydrogenase (E. coli gene
PdxB), a D-specific 2-hydroxyacid dehydrogenase family
member, catalyzes the NAD-dependent oxidation of
erythronate-4-phosphate, which is followed by
transamination to form 4-hydroxy-L-threonine-4-phosphate
within the de novo biosynthesis pathway of vitamin B6.
D-Erythronate-4-phosphate dehydrogenase has the common
architecture shared with D-isomer specific 2-hydroxyacid
dehydrogenases but contains an additional C-terminal
dimerization domain in addition to an NAD-binding domain
and the "lid" domain. The lid domain corresponds to the
catalytic domain of phosphoglycerate dehydrogenase and
other proteins of the D-isomer specific 2-hydroxyacid
dehydrogenase family, which include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence.
Length = 343
Score = 30.6 bits (70), Expect = 0.90
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 13 EHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFD 48
++ TV +VGVG VGS A L G+ ++L D
Sbjct: 111 FSLKGKTVGIVGVGNVGSRLARRLEALGM-NVLLCD 145
>gnl|CDD|133424 cd01339, LDH-like_MDH, L-lactate dehydrogenase-like malate
dehydrogenase proteins. Members of this subfamily have
an LDH-like structure and an MDH enzymatic activity.
Some members, like MJ0490 from Methanococcus
jannaschii, exhibit both MDH and LDH activities.
Tetrameric MDHs, including those from phototrophic
bacteria, are more similar to LDHs than to other MDHs.
LDH catalyzes the last step of glycolysis in which
pyruvate is converted to L-lactate. MDH is one of the
key enzymes in the citric acid cycle, facilitating both
the conversion of malate to oxaloacetate and
replenishing levels of oxalacetate by reductive
carboxylation of pyruvate. The LDH-like MDHs are part
of the NAD(P)-binding Rossmann fold superfamily, which
includes a wide variety of protein families including
the NAD(P)-binding domains of alcohol dehydrogenases,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate dehydrogenases,
formate/glycerate dehydrogenases, siroheme synthases,
6-phosphogluconate dehydrogenases, aminoacid
dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 300
Score = 30.5 bits (70), Expect = 1.0
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFD 48
+ ++G G VG+ A++L +G ++L D
Sbjct: 1 ISIIGAGNVGATLAQLLALKELGDVVLLD 29
>gnl|CDD|183586 PRK12549, PRK12549, shikimate 5-dehydrogenase; Reviewed.
Length = 284
Score = 30.2 bits (69), Expect = 1.0
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFDYD---KVELA-NMNRLFFQPDQC 67
V+ +G GG G+ A L G+ +L +FD D LA +N F P
Sbjct: 130 VVQLGAGGAGAAVAHALLTLGVERLTIFDVDPARAAALADELNARF--PAAR 179
>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 = 28.1 bits (63), Expect = 1.4
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 2 ALKRMGIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYD 50
LK G V N + ++ TV+V+G G VG A++L G K++L D D
Sbjct: 9 LLKAAGKVTN-KSLKGKTVVVLGAGEVGKGIAKLLADEGGKKVVLCDRD 56
>gnl|CDD|176217 cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like,
2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and
other MDR family members. This subgroup of the medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family has members identified
as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A
dehydrogenase and alcohol dehydrogenases. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 277
Score = 29.9 bits (68), Expect = 1.4
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 19 TVIVVGVGGVGSVTAEMLTRCGIGKLILFDYD--KVELA 55
V VVG+G VG + A++ G +++ D D + ELA
Sbjct: 100 RVAVVGLGLVGLLAAQLAKAAGAREVVGVDPDAARRELA 138
>gnl|CDD|236190 PRK08220, PRK08220, 2,3-dihydroxybenzoate-2,3-dehydrogenase;
Validated.
Length = 252
Score = 29.9 bits (68), Expect = 1.5
Identities = 16/65 (24%), Positives = 22/65 (33%), Gaps = 5/65 (7%)
Query: 19 TVIVVGVG-GVGSVTAEMLTRCGIGKLILFDYDKVELANMNRLFFQPDQCGLSKVEAARI 77
TV V G G+G A G K+I FD + + F +S A
Sbjct: 10 TVWVTGAAQGIGYAVALAFVEAGA-KVIGFDQAFLTQEDYP---FATFVLDVSDAAAVAQ 65
Query: 78 TLQNI 82
Q +
Sbjct: 66 VCQRL 70
>gnl|CDD|176216 cd08254, hydroxyacyl_CoA_DH, 6-hydroxycyclohex-1-ene-1-carboxyl-CoA
dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase,
and other MDR family members. This group contains
enzymes of the zinc-dependent alcohol dehydrogenase
family, including members (aka MDR) identified as
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and
N-benzyl-3-pyrrolidinol dehydrogenase.
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase
catalyzes the conversion of
6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to
6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This
group displays the characteristic catalytic and
structural zinc sites of the zinc-dependent alcohol
dehydrogenases. NAD(P)(H)-dependent oxidoreductases are
the major enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and 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. NAD(H)-binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 338
Score = 29.9 bits (68), Expect = 1.7
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 19 TVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNRL 60
TV+V+G+GG+G ++ G +I D + +L L
Sbjct: 168 TVLVIGLGGLGLNAVQIAKAMG-AAVIAVDIKEEKLELAKEL 208
>gnl|CDD|172521 PRK14027, PRK14027, quinate/shikimate dehydrogenase; Provisional.
Length = 283
Score = 29.6 bits (66), Expect = 2.0
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 7 GIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYD 50
G+ E + + +V+ VG GGVG+ A L G+ KL + D D
Sbjct: 117 GMEEGLPNAKLDSVVQVGAGGVGNAVAYALVTHGVQKLQVADLD 160
>gnl|CDD|214833 smart00822, PKS_KR, This enzymatic domain is part of bacterial
polyketide synthases. It catalyses the first step in
the reductive modification of the beta-carbonyl centres
in the growing polyketide chain. It uses NADPH to
reduce the keto group to a hydroxy group.
Length = 180
Score = 29.0 bits (66), Expect = 2.1
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 19 TVIVVG-VGGVGSVTAEMLTRCGIGKLIL 46
T ++ G +GG+G A L G +L+L
Sbjct: 2 TYLITGGLGGLGRALARWLAERGARRLVL 30
>gnl|CDD|240625 cd05300, 2-Hacid_dh_1, Putative D-isomer specific 2-hydroxyacid
dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomains but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric. Formate dehydrogenase (FDH) catalyzes the
NAD+-dependent oxidation of formate ion to carbon
dioxide with the concomitant reduction of NAD+ to NADH.
FDHs of this family contain no metal ions or prosthetic
groups. Catalysis occurs though direct transfer of the
hydride ion to NAD+ without the stages of acid-base
catalysis typically found in related dehydrogenases.
FDHs are found in all methylotrophic microorganisms in
energy production and in the stress responses of plants.
Length = 313
Score = 29.0 bits (66), Expect = 2.4
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 10 ENYEHIRTLTVIVVGVGGVGSVTAEML 36
+ TV++VG+G +G A
Sbjct: 127 GPVRELAGKTVLIVGLGDIGREIARRA 153
>gnl|CDD|179251 PRK01216, PRK01216, DNA polymerase IV; Validated.
Length = 351
Score = 29.4 bits (66), Expect = 2.6
Identities = 10/32 (31%), Positives = 21/32 (65%), Gaps = 3/32 (9%)
Query: 25 VGGVGSVTAEMLTRCGIGKL---ILFDYDKVE 53
+ G+G +TAE L + G+ KL + ++D+++
Sbjct: 183 IPGIGDITAEKLKKLGVNKLVDTLRIEFDELK 214
>gnl|CDD|223117 COG0039, Mdh, Malate/lactate dehydrogenases [Energy production
and conversion].
Length = 313
Score = 29.1 bits (66), Expect = 2.6
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGK-LILFD 48
V V+G G VGS A +L G+G L+L D
Sbjct: 3 VAVIGAGNVGSSLAFLLLLQGLGSELVLID 32
>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 = 28.7 bits (65), Expect = 3.1
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 2 ALKRMGIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCG 40
ALK++GI + V + G G VGS A L G
Sbjct: 21 ALKKLGI-----GLAGARVAIQGFGNVGSHAARFLHEAG 54
>gnl|CDD|178152 PLN02537, PLN02537, diaminopimelate decarboxylase.
Length = 410
Score = 29.0 bits (65), Expect = 3.3
Identities = 27/71 (38%), Positives = 34/71 (47%), Gaps = 15/71 (21%)
Query: 37 TRC---GIGKLILFDYDKVELANMNRLFFQPD-QCGLSK-VEAARIT------LQNINPD 85
TRC G GKL+ + + LA +F D + L VEAARI L INPD
Sbjct: 88 TRCIFNGNGKLL----EDLVLAAQEGVFVNVDSEFDLENIVEAARIAGKKVNVLLRINPD 143
Query: 86 VTIEVHNFNIT 96
V +VH + T
Sbjct: 144 VDPQVHPYVAT 154
>gnl|CDD|180477 PRK06223, PRK06223, malate dehydrogenase; Reviewed.
Length = 307
Score = 28.6 bits (65), Expect = 3.9
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 20 VIVVGVGGVGSVTAEMLTRCGIGKLILFD 48
+ ++G G VG+ A +L +G ++LFD
Sbjct: 5 ISIIGAGNVGATLAHLLALKELGDVVLFD 33
>gnl|CDD|235717 PRK06153, PRK06153, hypothetical protein; Provisional.
Length = 393
Score = 28.4 bits (64), Expect = 4.2
Identities = 14/55 (25%), Positives = 26/55 (47%)
Query: 5 RMGIVENYEHIRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELANMNR 59
R GI + + ++G+GG GS +++ + + ++ LFD D N R
Sbjct: 164 RAGIGALSAKLEGQRIAIIGLGGTGSYILDLVAKTPVREIHLFDGDDFLQHNAFR 218
>gnl|CDD|133452 cd05213, NAD_bind_Glutamyl_tRNA_reduct, NADP-binding domain of
glutamyl-tRNA reductase. Glutamyl-tRNA reductase
catalyzes the conversion of glutamyl-tRNA to
glutamate-1-semialdehyde, initiating the synthesis of
tetrapyrrole. Whereas tRNAs are generally associated
with peptide bond formation in protein translation, here
the tRNA activates glutamate in the initiation of
tetrapyrrole biosynthesis in archaea, plants and many
bacteria. In the first step, activated glutamate is
reduced to glutamate-1-semi-aldehyde via the NADPH
dependent glutamyl-tRNA reductase. Glutamyl-tRNA
reductase forms a V-shaped dimer. Each monomer has 3
domains: an N-terminal catalytic domain, a classic
nucleotide binding domain, and a C-terminal dimerization
domain. Although the representative structure 1GPJ lacks
a bound NADPH, a theoretical binding pocket has been
described. (PMID 11172694). Amino acid dehydrogenase
(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 = 311
Score = 28.4 bits (64), Expect = 5.0
Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 15 IRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILF--DYDK-VELANM 57
++ V+V+G G +G + A+ L G+ ++ + Y++ ELA
Sbjct: 176 LKGKKVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELAKE 221
>gnl|CDD|216530 pfam01494, FAD_binding_3, FAD binding domain. This domain is
involved in FAD binding in a number of enzymes.
Length = 349
Score = 28.1 bits (63), Expect = 5.4
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 19 TVIVVGVGGVGSVTAEMLTRCGIGKLIL 46
V++VG G G + A +L R G+ +++
Sbjct: 3 DVLIVGGGPAGLMLALLLARAGVRVVLV 30
>gnl|CDD|113988 pfam05237, MoeZ_MoeB, MoeZ/MoeB domain. This putative domain is
found in the MoeZ protein and the MoeB protein. The
domain has two CXXC motifs that are only partly
conserved.
Length = 77
Score = 26.1 bits (58), Expect = 6.4
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 194 LPTTMGIVAGFLVQNALKKLLKFGEVSW--YLGYSALTDFFPKMKLKPNPSC 243
L +G + A+K L GE L + A T F K++L+ +P C
Sbjct: 22 LGPVVGTIGSLQALEAIKLLTGIGEPLSGRLLLFDAWTMHFRKIRLRRDPDC 73
>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 = 27.6 bits (62), Expect = 6.9
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 18 LTVIVVGVGGVGSVTAEMLTRCGIGKLILFDYDKVELA 55
TV V G+G VG AE L G KLI+ D ++ +A
Sbjct: 29 KTVAVQGLGKVGYKLAEHLLEEG-AKLIVADINEEAVA 65
>gnl|CDD|238695 cd01401, PncB_like, Nicotinate phosphoribosyltransferase
(NAPRTase), related to PncB. Nicotinate
phosphoribosyltransferase catalyses the formation of
NAMN and PPi from 5-phosphoribosy -1-pyrophosphate
(PRPP) and nicotinic acid, this is the first, and also
rate limiting, reaction in the NAD salvage synthesis.
This salvage pathway serves to recycle NAD degradation
products. This subgroup is present in bacteria, archea
and funghi.
Length = 377
Score = 28.0 bits (63), Expect = 7.2
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 268 KPEAQVVHADNDWGEYHYQVQGS 290
PE VV D G+ ++ G
Sbjct: 87 NPEEVVVRLDTGKGQLDIRISGP 109
>gnl|CDD|181499 PRK08605, PRK08605, D-lactate dehydrogenase; Validated.
Length = 332
Score = 27.8 bits (62), Expect = 7.9
Identities = 9/34 (26%), Positives = 18/34 (52%)
Query: 15 IRTLTVIVVGVGGVGSVTAEMLTRCGIGKLILFD 48
I+ L V V+G G +G A++ + ++ +D
Sbjct: 144 IKDLKVAVIGTGRIGLAVAKIFAKGYGSDVVAYD 177
>gnl|CDD|187548 cd05237, UDP_invert_4-6DH_SDR_e, UDP-Glcnac (UDP-linked
N-acetylglucosamine) inverting 4,6-dehydratase,
extended (e) SDRs. UDP-Glcnac inverting
4,6-dehydratase was identified in Helicobacter pylori
as the hexameric flaA1 gene product (FlaA1). FlaA1 is
hexameric, possesses UDP-GlcNAc-inverting
4,6-dehydratase activity, and catalyzes the first step
in the creation of a pseudaminic acid derivative in
protein glycosylation. Although this subgroup has the
NADP-binding motif characteristic of extended SDRs, its
members tend to have a Met substituted for the active
site Tyr found in most SDR families. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet) core region typical of all SDRs,
extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids. Extended
SDRs are a diverse collection of proteins, and include
isomerases, epimerases, oxidoreductases, and lyases;
they typically have a TGXXGXXG cofactor binding motif.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 287
Score = 27.6 bits (62), Expect = 8.3
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 19 TVIVVGVGG-VGSVTAEMLTRCGIGKLILFDYDKVELANMNR 59
T++V G G +GS + + G KLI+FD D+ +L + R
Sbjct: 4 TILVTGGAGSIGSELVRQILKFGPKKLIVFDRDENKLHELVR 45
>gnl|CDD|234094 TIGR03026, NDP-sugDHase, nucleotide sugar dehydrogenase. Enzymes
in this family catalyze the NAD-dependent
alcohol-to-acid oxidation of nucleotide-linked sugars.
Examples include UDP-glucose 6-dehydrogenase (1.1.1.22)
, GDP-mannose 6-dehydrogenase (1.1.1.132) ,
UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136),
UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase
and UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase.
These enzymes are most often involved in the
biosynthesis of polysaccharides and are often found in
operons devoted to that purpose. All of these enzymes
contain three Pfam domains, pfam03721, pfam00984, and
pfam03720 for the N-terminal, central, and C-terminal
regions respectively.
Length = 409
Score = 27.6 bits (62), Expect = 8.5
Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 7/84 (8%)
Query: 19 TVIVVGVGGVGSVTAEMLTRCGIGKLILFDYD--KVELANMNRLFFQPDQCGLSKVEAAR 76
+ V+G+G VG A +L G + D D KV+ N + + GL ++ A
Sbjct: 2 KIAVIGLGYVGLPLAALLADLGH-DVTGVDIDQEKVDKLNKGKSPI--YEPGLDELLAKA 58
Query: 77 ITLQNIN--PDVTIEVHNFNITLL 98
+ + D + + ++ ++
Sbjct: 59 LKAGRLRATTDYEEAIRDADVIII 82
>gnl|CDD|148068 pfam06239, ECSIT, Evolutionarily conserved signalling intermediate
in Toll pathway. Activation of NF-kappaB as a
consequence of signaling through the Toll and IL-1
receptors is a major element of innate immune responses.
ECSIT plays an important role in signalling to
NF-kappaB, functioning as the intermediate in the
signaling pathways between TRAF-6 and MEKK-1.
Length = 229
Score = 27.3 bits (61), Expect = 8.8
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 205 LVQNALKKLLKFGEVSWYLGYSALTDFFPKMKLKP 239
+ ALKK+ ++G Y+AL D FPK P
Sbjct: 71 FIYAALKKMEEYGVEKDLEVYNALLDVFPKGVFIP 105
>gnl|CDD|223990 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
[Energy production and conversion].
Length = 366
Score = 27.6 bits (62), Expect = 9.4
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 19 TVIVVGVGGVGSVTAEMLTRCGIGKLILFDY--DKVELA 55
TV V G+GGVG + G G++I D +K+ELA
Sbjct: 188 TVAVFGLGGVGLAAIQGAKAAGAGRIIAVDINPEKLELA 226
>gnl|CDD|216777 pfam01905, DevR, CRISPR-associated negative auto-regulator
DevR/Csa2. This group of families is one of several
protein families that are always found associated with
prokaryotic CRISPRs, themselves a family of clustered
regularly interspaced short palindromic repeats, DNA
repeats found in nearly half of all bacterial and
archaeal genomes. These DNA repeat regions have a
remarkably regular structure: unique sequences of
constant size, called spacers, sit between each pair of
repeats. It has been shown that the CRISPRs are
virus-derived sequences acquired by the host to enable
them to resist viral infection. The Cas proteins from
the host use the CRISPRs to mediate an antiviral
response. After transcription of the CRISPR, a complex
of Cas proteins termed Cascade cleaves a CRISPR RNA
precursor in each repeat and retains the cleavage
products containing the virus-derived sequence. Assisted
by the helicase Cas3, these mature CRISPR RNAs then
serve as small guide RNAs that enable Cascade to
interfere with virus proliferation. Cas5 contains an
endonuclease motif, whose inactivation leads to loss of
resistance, even in the presence of phage-derived
spacers. This family used to be known as DUF73. DevR
appears to be negative auto-regulator within the system.
Length = 258
Score = 27.3 bits (61), Expect = 9.6
Identities = 21/111 (18%), Positives = 31/111 (27%), Gaps = 22/111 (19%)
Query: 2 ALKRMGIVENYEHIRTLTVIVVGVGGVGSVTA---EMLTRCGIGKLILFDY--------- 49
AL V NY R V++ V V A E L K +
Sbjct: 10 ALNMDESVGNYTRHRKAPVVLKTGYKVRYVPAISGESL------KHAYQETLVKLALENG 63
Query: 50 ----DKVELANMNRLFFQPDQCGLSKVEAARITLQNINPDVTIEVHNFNIT 96
+ + +R F + K + + I V +V F T
Sbjct: 64 LPLCELCKRGIGDRGFIKFATDKDLKKDDRDDEDEIILKCVVEDVFGFLYT 114
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
0.320 0.135 0.404
Gapped
Lambda K H
0.267 0.0845 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,610,279
Number of extensions: 1375958
Number of successful extensions: 1545
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1487
Number of HSP's successfully gapped: 96
Length of query: 292
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 196
Effective length of database: 6,679,618
Effective search space: 1309205128
Effective search space used: 1309205128
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 (21.8 bits)
S2: 59 (26.3 bits)