RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5413
(285 letters)
>gnl|CDD|178323 PLN02721, PLN02721, threonine aldolase.
Length = 353
Score = 275 bits (704), Expect = 1e-91
Identities = 110/228 (48%), Positives = 146/228 (64%), Gaps = 15/228 (6%)
Query: 67 RTVDIRSDTISKPTMEMKNYMFNCEVGDDVYLEDPTCKELQEKAAKLAGKEAAIFVPSGT 126
R VD+RSDT++KPT M+ M N EV DDV DPT L+E+ AK+ GKEAA+FVPSGT
Sbjct: 6 RVVDLRSDTVTKPTDAMRAAMANAEVDDDVLGYDPTALRLEEEMAKIFGKEAALFVPSGT 65
Query: 127 MGNLIAIMTHCDRRDSEIIVGDCSHIMLWEQGGASQTSVYSQIGRVLMRGVTNQKDGTFD 186
MGNLI+++ HCD R SE+I+GD SHI L+E GG S +G V R V N +DGT D
Sbjct: 66 MGNLISVLVHCDVRGSEVILGDNSHIHLYENGGI------STLGGVHPRTVKNNEDGTMD 119
Query: 187 LDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGA 246
LD +EA + H +T L+C+ENTH CGG L +++ ++ + H + +H+DGA
Sbjct: 120 LDAIEAAIRPKGDDHFPTTRLICLENTHANCGGRCLSVEYTDKVGELAKRHGLKLHIDGA 179
Query: 247 RLPLAEVCASV---------DTVMFCLSKGLGAPVGSILAGPEEFIQK 285
R+ A V V D+V CLSKGLGAPVGS++ G + FI+K
Sbjct: 180 RIFNASVALGVPVHRLVKAADSVSVCLSKGLGAPVGSVIVGSKSFIRK 227
>gnl|CDD|216367 pfam01212, Beta_elim_lyase, Beta-eliminating lyase.
Length = 288
Score = 263 bits (675), Expect = 5e-88
Identities = 98/225 (43%), Positives = 139/225 (61%), Gaps = 16/225 (7%)
Query: 70 DIRSDTISKPTMEMKNYMFNCEVGDDVYLEDPTCKELQEKAAKLAGKEAAIFVPSGTMGN 129
D+RSDT++ PT M+ M VGD+VY DPT L+++ A+L GKEAA+FVPSGTM N
Sbjct: 1 DLRSDTVTGPTPAMREAMAAAMVGDEVYGGDPTVNRLEDRVAELFGKEAALFVPSGTMAN 60
Query: 130 LIAIMTHCDRRDSEIIVGDCSHIMLWEQGGASQTSVYSQIGRVLMRGVTNQKDGTFDLDE 189
+A+M HC RR E+I G+ +HI E GG +++G + + G DL++
Sbjct: 61 QLALMAHC-RRGDEVICGEPAHIYFDETGGH------AELGGAQPVPLPGAEAGKLDLED 113
Query: 190 MEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGARL- 248
+EA +IH T L+ +ENTHN GG V+ ++ LRE++A +EH IP+H+DGARL
Sbjct: 114 LEAAIRPVGDIHFPPTGLISLENTHNSAGGQVVSLEELREIRAIAREHGIPLHLDGARLA 173
Query: 249 --------PLAEVCASVDTVMFCLSKGLGAPVGSILAGPEEFIQK 285
+ E+ + D+V LSKGLGAPVGS+LAG ++FI
Sbjct: 174 NAAVALGVIVKEITSYADSVSMSLSKGLGAPVGSVLAGSDDFIAY 218
>gnl|CDD|99748 cd06502, TA_like, Low-specificity threonine aldolase (TA). This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). TA
catalyzes the conversion of L-threonine or
L-allo-threonine to glycine and acetaldehyde in a
secondary glycine biosynthetic pathway.
Length = 338
Score = 226 bits (579), Expect = 5e-73
Identities = 90/225 (40%), Positives = 127/225 (56%), Gaps = 19/225 (8%)
Query: 70 DIRSDTISKPTMEMKNYMFNCEVGDDVYLEDPTCKELQEKAAKLAGKEAAIFVPSGTMGN 129
D RSDT++ PT EM M VGDDVY EDPT +L+ +AA+L GKEAA+FVPSGT N
Sbjct: 1 DFRSDTVTGPTPEMLEAMAAANVGDDVYGEDPTTAKLEARAAELFGKEAALFVPSGTAAN 60
Query: 130 LIAIMTHCDRRDSEIIVGDCSHIMLWEQGGASQTSVYSQIGRVLMRGVTNQKDGTFDLDE 189
+A+ H +I + +HI E G S + + + G ++G ++
Sbjct: 61 QLALAAHTQPGG-SVICHETAHIYTDEAGAP---EFLSGVKLLPVPG----ENGKLTPED 112
Query: 190 MEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGARL- 248
+EA D+IH SLV +ENT GGTV P+ L+ + A +E+ +P+H+DGARL
Sbjct: 113 LEAAIRPRDDIHFPPPSLVSLENTTE--GGTVYPLDELKAISALAKENGLPLHLDGARLA 170
Query: 249 --------PLAEVCASVDTVMFCLSKGLGAPVGSILAGPEEFIQK 285
L + VD+V FCLSKG GAPVG+++ G +FI +
Sbjct: 171 NAAAALGVALKTYKSGVDSVSFCLSKGGGAPVGAVVVGNRDFIAR 215
>gnl|CDD|224919 COG2008, GLY1, Threonine aldolase [Amino acid transport and
metabolism].
Length = 342
Score = 222 bits (567), Expect = 5e-71
Identities = 88/228 (38%), Positives = 126/228 (55%), Gaps = 19/228 (8%)
Query: 68 TVDIRSDTISKPTMEMKNYMFNCE-VGDDVYLEDPTCKELQEKAAKLAGKEAAIFVPSGT 126
+D RSD ++ PT EM+ + VGDDVY EDPT L+++ A+L GKEAA+FVPSGT
Sbjct: 1 MIDFRSDNVAGPTPEMREALAAANAVGDDVYGEDPTTNALEQRIAELFGKEAALFVPSGT 60
Query: 127 MGNLIAIMTHCDRRDSEIIVGDCSHIMLWEQGGASQTSVYSQIGRVLMRGVTNQKDGTFD 186
N +A+ HC + +I + +HI E G + ++ + DG
Sbjct: 61 QANQLALAAHC-QPGESVICHETAHIYTDECGAP---EFFGGGQKLP---IVPGADGKLT 113
Query: 187 LDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGA 246
+++EA D H A T L +ENT GGTV P+ L + A C+EH +P+HMDGA
Sbjct: 114 PEDVEAAIRPDDIHH-APTPLAVLENTATE-GGTVYPLDELEAISAVCKEHGLPLHMDGA 171
Query: 247 RL---------PLAEVCASVDTVMFCLSKGLGAPVGSILAGPEEFIQK 285
RL L + + VD+V FCL+KG GAPVG+I+ G +F ++
Sbjct: 172 RLANALVALGVALKTIKSYVDSVSFCLTKGGGAPVGAIVFGNRDFAKR 219
>gnl|CDD|236710 PRK10534, PRK10534, L-threonine aldolase; Provisional.
Length = 333
Score = 208 bits (530), Expect = 9e-66
Identities = 95/226 (42%), Positives = 142/226 (62%), Gaps = 20/226 (8%)
Query: 69 VDIRSDTISKPTMEMKNYMFNCEVGDDVYLEDPTCKELQEKAAKLAGKEAAIFVPSGTMG 128
+D+RSDT+++P+ M M VGDDVY +DPT LQ+ AA+L+GKEAA+F+P+GT
Sbjct: 2 IDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAALFLPTGTQA 61
Query: 129 NLIAIMTHCDRRDSEIIVGDCSHIMLWEQGGASQTSVYSQIGRVLMRGVTNQKDGTFDLD 188
NL+A+++HC+R + E IVG +H L+E GGA + +G + + + DGT LD
Sbjct: 62 NLVALLSHCERGE-EYIVGQAAHNYLYEAGGA------AVLGSIQPQPIDAAADGTLPLD 114
Query: 189 EMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGARL 248
++ AK D+IH A T L+ +ENTHN G VLP ++L++ +E N+ +H+DGAR+
Sbjct: 115 KVAAKIK-PDDIHFARTRLLSLENTHN---GKVLPREYLKQAWEFTRERNLALHVDGARI 170
Query: 249 ---------PLAEVCASVDTVMFCLSKGLGAPVGSILAGPEEFIQK 285
L E+ D+ CLSKGLG PVGS+L G ++I++
Sbjct: 171 FNAVVAYGCELKEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKR 216
>gnl|CDD|99742 cd01494, AAT_I, Aspartate aminotransferase (AAT) superfamily (fold
type I) of pyridoxal phosphate (PLP)-dependent enzymes.
PLP combines with an alpha-amino acid to form a compound
called a Schiff base or aldimine intermediate, which
depending on the reaction, is the substrate in four
kinds of reactions (1) transamination (movement of amino
groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
Structure and sequence analysis has revealed that the
PLP dependent enzymes can be classified into four major
groups of different evolutionary origin: aspartate
aminotransferase superfamily (fold type I), tryptophan
synthase beta superfamily (fold type II), alanine
racemase superfamily (fold type III), and D-amino acid
superfamily (fold type IV) and Glycogen phophorylase
family (fold type V).
Length = 170
Score = 69.7 bits (171), Expect = 1e-14
Identities = 45/187 (24%), Positives = 72/187 (38%), Gaps = 32/187 (17%)
Query: 104 KELQEKAAKLA--GKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGDCSHIMLW---EQG 158
+EL+EK A+L G + A+FVPSGT N A++ D I+ + W E
Sbjct: 3 EELEEKLARLLQPGNDKAVFVPSGTGANEAALLALLGPGDEVIVDANGHGSRYWVAAELA 62
Query: 159 GASQTSVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCASTSLVCVENTHNYCG 218
GA V + V + G D+ +E + + +L+ + G
Sbjct: 63 GA---------KPVPVP-VDDAGYGGLDVAILE------ELKAKPNVALIVITPNTTSGG 106
Query: 219 GTVLPMQWLRELKARCQEHNIPVHMDGARL----PLAEVCASV---DTVMFCLSKGLGAP 271
V +E++ +E+ I + +D A P V D V F L K LG
Sbjct: 107 VLVPL----KEIRKIAKEYGILLLVDAASAGGASPAPGVLIPEGGADVVTFSLHKNLGGE 162
Query: 272 VGSILAG 278
G ++
Sbjct: 163 GGGVVIV 169
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 52.7 bits (127), Expect = 7e-08
Identities = 47/197 (23%), Positives = 77/197 (39%), Gaps = 38/197 (19%)
Query: 105 ELQEKAAKLAGKEAA---IFVPSGTMG-NLIA-IMTHCDRRDSEIIVGDCSH---IMLWE 156
+E A+ +++ +F T NL+A + + EI+V D H I+ W+
Sbjct: 70 AAREAVARFLNADSSDEIVFTRGTTEALNLVARGLGRSLKPGDEIVVSDLEHHSNIVPWQ 129
Query: 157 QGGASQTSVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCASTSLVC---VENT 213
+ + G + R + DG DLD +E + T LV V N
Sbjct: 130 ELAK-------RTGAKV-RVIPLDDDGLLDLDALEKLITP-------KTKLVALSHVSNV 174
Query: 214 HNYCGGTVLPMQWLRELKARCQEHNIPVHMDGAR----LPLAEVCASVDTVMFCLSKGLG 269
GTV P ++E+ EH V +D A+ LP+ D + F K L
Sbjct: 175 T----GTVNP---VKEIAELAHEHGALVLVDAAQAAGHLPIDVQELGCDFLAFSGHKWLL 227
Query: 270 APVGS-ILAGPEEFIQK 285
P G +L +E +++
Sbjct: 228 GPTGIGVLYVRKELLEE 244
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 48.5 bits (116), Expect = 2e-06
Identities = 46/202 (22%), Positives = 71/202 (35%), Gaps = 44/202 (21%)
Query: 104 KELQEKAAKLAG--------KEAAIFVPSGTMGNLIAIMT--HCDRRDSEIIVGD---CS 150
EL+E AK G +EAA+ SG N+ A++ + I+V S
Sbjct: 44 PELREALAKFLGRSPVLKLDREAAVVFGSGAGANIEALIFLLRLNP-GDAILVPAPTYPS 102
Query: 151 HIMLWEQGGASQTSVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCASTSLVCV 210
+I ++ + V + + D D D +EA A +V
Sbjct: 103 YIRIFR---------LAGGEVVRYP-LYSSNDFHLDFDALEAALKEA----TEGNKVVLH 148
Query: 211 ENTHNYCGGTVLPMQWLRELKARCQEHNIPV-----HMDGAR--LPLAEVCASVDT---- 259
+ HN G TV ++ L +L +EHNI + + L A +
Sbjct: 149 TSPHNPTG-TVATLEELEKLLDLAKEHNILLLVDEAYAGFVFGSLDAVATRALLAEGPNL 207
Query: 260 -VMFCLSKGLGAP---VGSILA 277
V+ SK G VG IL
Sbjct: 208 LVVGSFSKAFGLAGWRVGYILG 229
>gnl|CDD|99747 cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The major groups in this CD
corresponds to serine palmitoyltransferase (SPT),
5-aminolevulinate synthase (ALAS),
8-amino-7-oxononanoate synthase (AONS), and
2-amino-3-ketobutyrate CoA ligase (KBL). SPT is
responsible for the condensation of L-serine with
palmitoyl-CoA to produce 3-ketodihydrospingosine, the
reaction of the first step in sphingolipid biosynthesis.
ALAS is involved in heme biosynthesis; it catalyzes the
synthesis of 5-aminolevulinic acid from glycine and
succinyl-coenzyme A. AONS catalyses the decarboxylative
condensation of l-alanine and pimeloyl-CoA in the first
committed step of biotin biosynthesis. KBL catalyzes the
second reaction step of the metabolic degradation
pathway for threonine converting 2-amino-3-ketobutyrate,
to glycine and acetyl-CoA. The members of this CD are
widely found in all three forms of life.
Length = 349
Score = 44.1 bits (105), Expect = 4e-05
Identities = 42/200 (21%), Positives = 78/200 (39%), Gaps = 40/200 (20%)
Query: 100 DPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGD-CSHIMLWE-- 156
+EL+E+ A+ GKEAA+ SG N + T + D +I+ D +H + +
Sbjct: 45 SDLHEELEEELAEFHGKEAALVFSSGYAANDGVLSTLAGKGD--LIISDSLNHASIIDGI 102
Query: 157 QGGASQTSVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCASTSLVCVENTHNY 216
+ ++ ++ N D++++E + L+ E ++
Sbjct: 103 RLSGAKKRIFKH----------N------DMEDLEKLL--REARRPYGKKLIVTEGVYSM 144
Query: 217 CGGTVLPMQWLRELKARCQEHNIPVHMD-----------GARLPLAE-VCASVDTVMFCL 264
G + P L EL +++ + +D G + + VD +M L
Sbjct: 145 D-GDIAP---LPELVDLAKKYGAILFVDEAHSVGVYGPHGRGVEEFGGLTDDVDIIMGTL 200
Query: 265 SKGLGAPVGSILAGPEEFIQ 284
K GA VG +AG +E I
Sbjct: 201 GKAFGA-VGGYIAGSKELID 219
>gnl|CDD|237314 PRK13238, tnaA, tryptophanase/L-cysteine desulfhydrase,
PLP-dependent; Provisional.
Length = 460
Score = 44.0 bits (105), Expect = 5e-05
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 183 GTFDLDEMEAKFST--ADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIP 240
G FDL+++EA A+N+ + + T+N GG + M LR + +++ IP
Sbjct: 159 GNFDLEKLEALIEEVGAENV-----PFIVMTITNNSAGGQPVSMANLRAVYEIAKKYGIP 213
Query: 241 VHMDGARLPLAE 252
V +D AR AE
Sbjct: 214 VVIDAAR--FAE 223
>gnl|CDD|215829 pfam00266, Aminotran_5, Aminotransferase class-V. This domain is
found in amino transferases, and other enzymes including
cysteine desulphurase EC:4.4.1.-.
Length = 370
Score = 43.4 bits (103), Expect = 7e-05
Identities = 36/151 (23%), Positives = 55/151 (36%), Gaps = 35/151 (23%)
Query: 108 EKAAKLAGKEAA---IFVPSGTMG-NLIAI--MTHCDRRDSEIIVGDCSH---IMLWEQG 158
EK A+ + IF T NL+AI D EI+V + H ++ W++
Sbjct: 50 EKVAEFINAPSDEEIIFTSGTTEAINLVAISLGRSLKPGD-EILVTEMEHHANLVPWQEL 108
Query: 159 GASQTSVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCASTSLVC---VENTHN 215
+R + +G DLD +E + T LV V N
Sbjct: 109 AKRTG--------ATVRVIPVDPNGLLDLDALEKLLTP-------RTKLVAITHVSNVT- 152
Query: 216 YCGGTVLPMQWLRELKARCQEHNIPVHMDGA 246
GTV P++ E+ E+ V +D A
Sbjct: 153 ---GTVNPVE---EIGKLAHEYGALVVVDAA 177
>gnl|CDD|99743 cd06450, DOPA_deC_like, DOPA decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD correspond to DOPA/tyrosine decarboxylase
(DDC), histidine decarboxylase (HDC), and glutamate
decarboxylase (GDC). DDC is active as a dimer and
catalyzes the decarboxylation of tyrosine. GDC catalyzes
the decarboxylation of glutamate and HDC catalyzes the
decarboxylation of histidine.
Length = 345
Score = 39.9 bits (94), Expect = 0.001
Identities = 41/187 (21%), Positives = 70/187 (37%), Gaps = 37/187 (19%)
Query: 81 MEMKNYMFNCEVGDDVYLEDPTCKELQEK----AAKL--AGKEAA--IFVPSGTMGNLIA 132
+EM N D + E P E++ + AKL E A +F G+ NL+A
Sbjct: 16 LEMLTSAKNAI--DFTWDESPAATEMEAEVVNWLAKLFGLPSEDADGVFTSGGSESNLLA 73
Query: 133 IMTHCDR-------------RDSEIIVGDCSHIMLWEQGGASQTSVYSQIGRVLMRGVTN 179
++ DR I+ D +H+ E+ A V +R V
Sbjct: 74 LLAARDRARKRLKAGGGRGIDKLVIVCSDQAHVS-VEKAAA--------YLDVKVRLVPV 124
Query: 180 QKDGTFDLDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNI 239
+DG D + +EA +V T + G + P L E+ +++++
Sbjct: 125 DEDGRMDPEALEAAIDEDKAEGLNPIMVVATAGTTDT--GAIDP---LEEIADLAEKYDL 179
Query: 240 PVHMDGA 246
+H+D A
Sbjct: 180 WLHVDAA 186
>gnl|CDD|99734 cd00609, AAT_like, Aspartate aminotransferase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). Pyridoxal
phosphate combines with an alpha-amino acid to form a
compound called a Schiff base or aldimine intermediate,
which depending on the reaction, is the substrate in
four kinds of reactions (1) transamination (movement of
amino groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
The major groups in this CD corresponds to Aspartate
aminotransferase a, b and c, Tyrosine, Alanine,
Aromatic-amino-acid, Glutamine phenylpyruvate,
1-Aminocyclopropane-1-carboxylate synthase,
Histidinol-phosphate, gene products of malY and cobC,
Valine-pyruvate aminotransferase and Rhizopine
catabolism regulatory protein.
Length = 350
Score = 39.6 bits (93), Expect = 0.001
Identities = 44/211 (20%), Positives = 78/211 (36%), Gaps = 38/211 (18%)
Query: 97 YLEDPTCKELQEKAAKLAGK--------EAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGD 148
Y DP EL+E A+ G+ E + + + + D E++V D
Sbjct: 32 YYPDPGLPELREAIAEWLGRRGGVDVPPEEIVVTNGAQEALSLLLRALLNPGD-EVLVPD 90
Query: 149 CSHIMLWEQGGASQTSVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCASTSLV 208
++ + G + V ++G F LD + + T L+
Sbjct: 91 PTYPGY--------EAAARLAGAEV-VPVPLDEEGGFLLDLELLEAAKTPK-----TKLL 136
Query: 209 CVENTHNYCGGTVLPMQWLRELKARCQEHNIPV---------HMDGARLPLAEVCASVDT 259
+ N +N G VL + L EL ++H I + DG P + + +
Sbjct: 137 YLNNPNNPTG-AVLSEEELEELAELAKKHGILIISDEAYAELVYDGEPPPALALLDAYER 195
Query: 260 VMFC--LSKGLGAP---VGSILAGPEEFIQK 285
V+ SK G P +G ++A PEE +++
Sbjct: 196 VIVLRSFSKTFGLPGLRIGYLIAPPEELLER 226
>gnl|CDD|99741 cd00617, Tnase_like, Tryptophanase family (Tnase). This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD correspond to tryptophanase (Tnase) and
tyrosine phenol-lyase (TPL). Tnase and TPL are active as
tetramers and catalyze beta-elimination reactions. Tnase
catalyzes degradation of L-tryptophan to yield indole,
pyruvate and ammonia and TPL catalyzes degradation of
L-tyrosine to yield phenol, pyruvate and ammonia.
Length = 431
Score = 38.9 bits (91), Expect = 0.002
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 183 GTFDLDEMEAKFS--TADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIP 240
G D+ ++E A+NI + + T+N GG + M LRE++ ++ IP
Sbjct: 134 GNIDVAKLEKLIDEVGAENI-----PYIVLTITNNTAGGQPVSMANLREVRELAHKYGIP 188
Query: 241 VHMDGAR 247
V +D AR
Sbjct: 189 VVLDAAR 195
>gnl|CDD|131034 TIGR01979, sufS, cysteine desulfurases, SufSfamily. This model
represents a subfamily of NifS-related cysteine
desulfurases involved in FeS cluster formation needed
for nitrogen fixation among other vital functions. Many
cysteine desulfurases are also active as selenocysteine
lyase and/or cysteine sulfinate desulfinase. This
subfamily is associated with the six-gene SUF system
described in E. coli and Erwinia as an FeS cluster
formation system during oxidative stress. The active
site Cys is this subfamily resembles GHHC with one or
both His conserved [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 403
Score = 38.8 bits (91), Expect = 0.002
Identities = 47/193 (24%), Positives = 81/193 (41%), Gaps = 36/193 (18%)
Query: 108 EKAAKLAGKEAA---IFVPSGTMG-NLIAI---MTHCDRRDSEIIVGDCSH---IMLWEQ 157
EK AK + +F T NL+A ++ + EI++ + H I+ W+
Sbjct: 69 EKVAKFINAASDEEIVFTRGTTESINLVAYSWGDSN-LKAGDEIVISEMEHHANIVPWQL 127
Query: 158 GGASQTSVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCASTSLVCVENTHNYC 217
++ + G L + + DGT DLD++E + T LV + + N
Sbjct: 128 --LAERT-----GATL-KFIPLDDDGTLDLDDLEKLLT-------EKTKLVAITHVSNVL 172
Query: 218 GGTVLPMQWLRELKARCQEHNIPVHMDGAR----LPLAEVCASVDTVMFCLSKGLGAPVG 273
GTV P++ E+ + V +DGA+ +P+ D +F K G P G
Sbjct: 173 -GTVNPVE---EIAKLAHQVGAKVLVDGAQAVPHMPVDVQALDCDFYVFSGHKMYG-PTG 227
Query: 274 -SILAGPEEFIQK 285
+L G EE +++
Sbjct: 228 IGVLYGKEELLEQ 240
>gnl|CDD|131666 TIGR02617, tnaA_trp_ase, tryptophanase, leader peptide-associated.
Members of this family belong to the beta-eliminating
lyase family (pfam01212) and act as tryptophanase
(L-tryptophan indole-lyase). The tryptophanases of this
family, as a rule, are found with a tryptophanase leader
peptide (TnaC) encoded upstream. Both tryptophanases
(4.1.99.1) and tyrosine phenol-lyases (EC 4.1.99.2) are
found between trusted and noise cutoffs, but this model
captures nearly all tryptophanases for which the leader
peptide gene tnaC can be found upstream [Energy
metabolism, Amino acids and amines].
Length = 467
Score = 38.4 bits (89), Expect = 0.003
Identities = 41/181 (22%), Positives = 69/181 (38%), Gaps = 21/181 (11%)
Query: 80 TMEMKNYMFNCEVGDDVYLEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDR 139
T M+ M GD+ Y + L E + G + I G I I +
Sbjct: 56 TQSMQAAMM---RGDEAYSGSRSYYALAESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKK 112
Query: 140 RDSEIIVGDCSHIMLWEQGGASQTSVYSQIGRVLMRGVTNQK----------DGTFDLDE 189
R+ E + D S ++ + T +SQI R V ++ G FDL+
Sbjct: 113 REQEKGL-DRSKMVAFSNYFFDTTQGHSQINGCTARNVYTKEAFDTGVRYDFKGNFDLEG 171
Query: 190 MEAKFST--ADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGAR 247
+E +N+ ++ C N GG + + L+ + ++++IPV MD AR
Sbjct: 172 LERGIEEVGPNNVPYIVATITC-----NSAGGQPVSLANLKAVYEIAKKYDIPVVMDSAR 226
Query: 248 L 248
Sbjct: 227 F 227
>gnl|CDD|99735 cd00610, OAT_like, Acetyl ornithine aminotransferase family. This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). The
major groups in this CD correspond to ornithine
aminotransferase, acetylornithine aminotransferase,
alanine-glyoxylate aminotransferase, dialkylglycine
decarboxylase, 4-aminobutyrate aminotransferase,
beta-alanine-pyruvate aminotransferase,
adenosylmethionine-8-amino-7-oxononanoate
aminotransferase, and glutamate-1-semialdehyde
2,1-aminomutase. All the enzymes belonging to this
family act on basic amino acids and their derivatives
are involved in transamination or decarboxylation.
Length = 413
Score = 37.5 bits (88), Expect = 0.005
Identities = 45/215 (20%), Positives = 67/215 (31%), Gaps = 60/215 (27%)
Query: 105 ELQEKAAKLAGKEA--AIFVPSGTMGNLIAI---MTHCDRRDSEIIVGDCSHIMLWEQG- 158
EL E L + FV SGT A+ + R I+ +E
Sbjct: 83 ELAELLLALTPEGLDKVFFVNSGTEAVEAALKLARAYTGR----------KKIISFEGAY 132
Query: 159 -GASQTSV-------YSQIGRVLMRGVT---------NQKDGTFDLDEMEAKFSTADNIH 201
G + ++ Y L+ GV + DL+ +E
Sbjct: 133 HGRTLGALSLTGSKKYRGGFGPLLPGVLHVPYPYRYRPPAELADDLEALEEALEEHPEEV 192
Query: 202 CASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGARLPLAEV-------- 253
A V VE G V P +L+ L+ C++H I + D EV
Sbjct: 193 AA----VIVEPIQGEGGVIVPPPGYLKALRELCRKHGILLIAD-------EVQTGFGRTG 241
Query: 254 ----CASVDTV--MFCLSKGL--GAPVGSILAGPE 280
+ L KGL G P+G++L E
Sbjct: 242 KMFAFEHFGVEPDIVTLGKGLGGGLPLGAVLGREE 276
>gnl|CDD|178257 PLN02651, PLN02651, cysteine desulfurase.
Length = 364
Score = 37.3 bits (87), Expect = 0.005
Identities = 40/162 (24%), Positives = 60/162 (37%), Gaps = 44/162 (27%)
Query: 103 CKELQEKA----AKLAGKEAA--IFVPSGTMGNLIAI---MTHCDRRDSEII-------- 145
++ EKA A L G + IF T N +AI M + +I
Sbjct: 41 SEDAVEKARAQVAALIGADPKEIIFTSGATESNNLAIKGVMHFYKDKKKHVITTQTEHKC 100
Query: 146 -VGDCSHIMLWEQGGASQTSVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCAS 204
+ C H+ +Q G T + V + DG DLDE+ A
Sbjct: 101 VLDSCRHL---QQEGFEVTYL-----PV-------KSDGLVDLDELAAAIRPD------- 138
Query: 205 TSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGA 246
T+LV V +N G + P++ E+ C+E + H D A
Sbjct: 139 TALVSVMAVNNEIG-VIQPVE---EIGELCREKKVLFHTDAA 176
>gnl|CDD|237313 PRK13237, PRK13237, tyrosine phenol-lyase; Provisional.
Length = 460
Score = 37.4 bits (87), Expect = 0.007
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 183 GTFDLDEMEAKFST--ADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIP 240
G DLD+++A A+NI + +C+ T N GG + M +R ++ C +H I
Sbjct: 159 GNVDLDKLQALIDEVGAENI-----AYICLAVTVNLAGGQPVSMANMRAVRELCDKHGIK 213
Query: 241 VHMDGARL 248
V D R
Sbjct: 214 VFFDATRC 221
>gnl|CDD|225576 COG3033, TnaA, Tryptophanase [Amino acid transport and metabolism].
Length = 471
Score = 37.1 bits (86), Expect = 0.008
Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 9/94 (9%)
Query: 156 EQGGASQTSVYSQIGRVLMRGVTNQKDGTFDLDEMEA--KFSTADNIHCASTSLVCVENT 213
+ GA+ +VY V G FDL+++E ADN+ + + T
Sbjct: 142 QINGATPRNVYVDEAF--DTEVKYPFKGNFDLEKLERLIDEVGADNV-----PYIVLTIT 194
Query: 214 HNYCGGTVLPMQWLRELKARCQEHNIPVHMDGAR 247
+N GG + M ++ + ++++IPV MD AR
Sbjct: 195 NNSAGGQPVSMANMKAVYEIAKKYDIPVVMDAAR 228
>gnl|CDD|99739 cd00615, Orn_deC_like, Ornithine decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD corresponds to ornithine decarboxylase (ODC),
arginine decarboxylase (ADC) and lysine decarboxylase
(LDC). ODC is a dodecamer composed of six homodimers and
catalyzes the decarboxylation of tryptophan. ADC
catalyzes the decarboxylation of arginine and LDC
catalyzes the decarboxylation of lysine. Members of this
family are widely found in all three forms of life.
Length = 294
Score = 35.7 bits (83), Expect = 0.021
Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 8/67 (11%)
Query: 91 EVGDDVYLEDPT--CKELQEKAAKLAGKEAAIFVPSGT-MGNLIAIMTHCDRRDSEIIVG 147
+ D L DPT KE QE AA+ G + F+ +GT N I+ C D +I
Sbjct: 50 GLDD---LLDPTGPIKEAQELAARAFGAKHTFFLVNGTSSSNKAVILAVCGPGDKILIDR 106
Query: 148 DC--SHI 152
+C S I
Sbjct: 107 NCHKSVI 113
>gnl|CDD|131667 TIGR02618, tyr_phenol_ly, tyrosine phenol-lyase. This model
describes a group of tyrosine phenol-lyase (4.1.99.2)
(beta-tyrosinase), a pyridoxal-phosphate enzyme closely
related to tryptophanase (4.1.99.1) (see model
TIGR02617). Both belong to the beta-eliminating lyase
family (pfam01212) [Energy metabolism, Amino acids and
amines].
Length = 450
Score = 35.7 bits (82), Expect = 0.023
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 183 GTFDLDEMEAKFST--ADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIP 240
G DL +++ AD I +C+ T N GG + M +RE++ C+ H I
Sbjct: 152 GNVDLKKLQKLIDEVGADKI-----PYICLAVTVNLAGGQPVSMANMREVRELCEAHGIK 206
Query: 241 VHMDGAR 247
V D R
Sbjct: 207 VFYDATR 213
>gnl|CDD|181005 PRK07503, PRK07503, methionine gamma-lyase; Provisional.
Length = 403
Score = 35.5 bits (82), Expect = 0.025
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 73 SDTISKPTMEMKNYMFNCEVGDDVY--LEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNL 130
+ T + PT E F E Y + +PT L+++ A L G EAA+ + SG MG +
Sbjct: 35 TATFAFPTAEYGAECFAGEEEGHFYSRISNPTLALLEQRMASLEGGEAAVALASG-MGAI 93
Query: 131 IAIMTHCDRRDSEIIVG 147
A + R E+IV
Sbjct: 94 TATLWTLLRPGDEVIVD 110
>gnl|CDD|129937 TIGR00858, bioF, 8-amino-7-oxononanoate synthase.
7-keto-8-aminopelargonic acid synthetase is an alternate
name. This model represents 8-amino-7-oxononanoate
synthase, the BioF protein of biotin biosynthesis. This
model is based on a careful phylogenetic analysis to
separate members of this family from
2-amino-3-ketobutyrate and other related pyridoxal
phosphate-dependent enzymes. In several species,
including Staphylococcus and Coxiella, a candidate
8-amino-7-oxononanoate synthase is confirmed by location
in the midst of a biotin biosynthesis operon but scores
below the trusted cutoff of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 360
Score = 35.3 bits (82), Expect = 0.030
Identities = 41/197 (20%), Positives = 70/197 (35%), Gaps = 46/197 (23%)
Query: 105 ELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGD-CSHIMLWEQGGAS-- 161
EL+E+ A+ G EAA+ SG + N+ I + D +I+ D +H L + S
Sbjct: 65 ELEEELAEWKGTEAALLFSSGYLANVGVISALVGKGD--LILSDALNHASLIDGCRLSGA 122
Query: 162 QTSVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTV 221
+ Y D++ +E + + V + G +
Sbjct: 123 RVRRYRHN----------------DVEHLERLLEK----NRGERRKLIVTDGVFSMDGDI 162
Query: 222 LPMQWLRELKARCQEHNIPVHMDGA---------------RLPLAEVCASVDTVMFCLSK 266
P L +L A + + + +D A L VD + LSK
Sbjct: 163 AP---LPQLVALAERYGAWLMVDDAHGTGVLGEDGRGTLEHFGLKP--EPVDIQVGTLSK 217
Query: 267 GLGAPVGSILAGPEEFI 283
LG+ G+ +AG + I
Sbjct: 218 ALGS-YGAYVAGSQALI 233
>gnl|CDD|223238 COG0160, GabT, 4-aminobutyrate aminotransferase and related
aminotransferases [Amino acid transport and metabolism].
Length = 447
Score = 35.3 bits (82), Expect = 0.035
Identities = 20/80 (25%), Positives = 30/80 (37%), Gaps = 25/80 (31%)
Query: 218 GGTVLPMQWLRELKARCQEHNIPVHMDGARLPLAEV---CASVDTVMF------------ 262
G V P +L+ L+ C+EH I + D EV MF
Sbjct: 236 GIIVPPKGFLKALRKLCREHGILLIAD-------EVQTGFGRTGK-MFAFEHFGVEPDIV 287
Query: 263 CLSKGLGA--PVGSILAGPE 280
L+K LG P+ +++ E
Sbjct: 288 TLAKSLGGGLPLSAVVGRAE 307
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 34.9 bits (81), Expect = 0.037
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 96 VYLEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGD 148
+ EL+E+ A G EAA+ SG + NL + + D +I D
Sbjct: 79 ISGTSDLHVELEEELADFLGAEAALLFSSGFVANLGLLSALLKKGD--LIFSD 129
>gnl|CDD|224090 COG1168, MalY, Bifunctional PLP-dependent enzyme with
beta-cystathionase and maltose regulon repressor
activities [Amino acid transport and metabolism].
Length = 388
Score = 35.0 bits (81), Expect = 0.039
Identities = 34/143 (23%), Positives = 47/143 (32%), Gaps = 37/143 (25%)
Query: 116 KEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGDCSHIMLWEQGGASQTSVYSQI------ 169
E +FVP G +AI D +I QT VY
Sbjct: 83 PEWIVFVPGVVPGISLAIRALTKPGDGVVI----------------QTPVYPPFYNAIKL 126
Query: 170 -GRVLMRGVTNQKDGTF--DLDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQW 226
GR ++ + DG + D D +E F L + N HN G V +
Sbjct: 127 NGRKVIENPLVEDDGRYEIDFDALEKAFVDE------RVKLFILCNPHNPTG-RVWTKEE 179
Query: 227 LRELKARCQEHNIPV-----HMD 244
LR++ C H + V H D
Sbjct: 180 LRKIAELCLRHGVRVISDEIHAD 202
>gnl|CDD|236517 PRK09440, avtA, valine--pyruvate transaminase; Provisional.
Length = 416
Score = 34.8 bits (81), Expect = 0.046
Identities = 30/92 (32%), Positives = 41/92 (44%), Gaps = 13/92 (14%)
Query: 204 STSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGAR-LPLAEVCASVDT--- 259
T +CV N G VL + L +L A ++HNIP+ +D A P + S T
Sbjct: 179 DTGAICVSRPTNPTG-NVLTDEELEKLDALARQHNIPLLIDNAYGPPFPGIIFSEATPLW 237
Query: 260 -----VMFCLSK-GL-GAPVGSILAGPEEFIQ 284
+ LSK GL G G I+ EE I+
Sbjct: 238 NPNIILCMSLSKLGLPGVRCG-IVIADEEIIE 268
>gnl|CDD|223476 COG0399, WecE, Predicted pyridoxal phosphate-dependent enzyme
apparently involved in regulation of cell wall
biogenesis [Cell envelope biogenesis, outer membrane].
Length = 374
Score = 34.1 bits (79), Expect = 0.070
Identities = 32/152 (21%), Positives = 54/152 (35%), Gaps = 34/152 (22%)
Query: 101 PTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGDCSHIMLWEQGGA 160
P + ++ A+ G + A+ V SGT +A++ E+IV
Sbjct: 34 PFVRRFEQAFAEYLGVKYAVAVSSGTAALHLALLALAIGPGDEVIV-------------P 80
Query: 161 SQTSVYSQIGRVLMRGVT------NQKDGTFDLDEMEAKFSTADNIHCASTSLVCVENTH 214
S T V + VL+ G + D D +EA + + +++ V H
Sbjct: 81 SFTFVATANA-VLLVGAKPVFVDIDPDTLNIDPDLIEAAITP------RTKAIIPV---H 130
Query: 215 NYCGGTVLPMQWLRELKARCQEHNIPVHMDGA 246
G M + L + H +PV D A
Sbjct: 131 LA--GQPCDMDAIMAL---AKRHGLPVIEDAA 157
>gnl|CDD|224832 COG1921, SelA, Selenocysteine synthase [seryl-tRNASer selenium
transferase] [Amino acid transport and metabolism].
Length = 395
Score = 33.9 bits (78), Expect = 0.072
Identities = 31/101 (30%), Positives = 38/101 (37%), Gaps = 19/101 (18%)
Query: 201 HCASTSLVCVENT--------HNYCGGTVLPMQWLRELKARCQEHNIPVHMD---GARLP 249
H L ENT NY +L EL E +PV +D GA +
Sbjct: 145 HLKDYELAINENTALLLKVHSSNYGFTGMLS---EEELVEIAHEKGLPVIVDLASGALVD 201
Query: 250 ----LAEVCAS-VDTVMFCLSKGLGAPVGSILAGPEEFIQK 285
L E A D V F K LG P I+ G +E I+K
Sbjct: 202 KEPDLREALALGADLVSFSGDKLLGGPQAGIIVGKKELIEK 242
>gnl|CDD|130395 TIGR01328, met_gam_lyase, methionine gamma-lyase. This model
describes a methionine gamma-lyase subset of a family of
PLP-dependent trans-sulfuration enzymes. The member from
the parasite Trichomonas vaginalis is described as
catalyzing alpha gamma- and alpha-beta eliminations and
gamma-replacement reactions on methionine, cysteine, and
some derivatives. Likewise, the enzyme from Pseudomonas
degrades cysteine as well as methionine [Energy
metabolism, Amino acids and amines].
Length = 391
Score = 33.7 bits (77), Expect = 0.082
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 3/79 (3%)
Query: 73 SDTISKPTMEMKNYMFNCEVGDDVY--LEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNL 130
+ T + E F + +Y L +PT L+ + A L G EAA+ SG MG +
Sbjct: 29 TSTFVFDSCEQGGNRFAGQESGYIYSRLGNPTVSNLEGRIAFLEGTEAAVATSSG-MGAI 87
Query: 131 IAIMTHCDRRDSEIIVGDC 149
A + + +I +C
Sbjct: 88 AATLLTILKAGDHLISDEC 106
>gnl|CDD|99746 cd06453, SufS_like, Cysteine desulfurase (SufS)-like. This family
belongs to the pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). The
major groups in this CD correspond to cysteine
desulfurase (SufS) and selenocysteine lyase. SufS
catalyzes the removal of elemental sulfur and selenium
atoms from L-cysteine, L-cystine, L-selenocysteine, and
L-selenocystine to produce L-alanine; and selenocysteine
lyase catalyzes the decomposition of L-selenocysteine.
Length = 373
Score = 33.6 bits (78), Expect = 0.089
Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 15/72 (20%)
Query: 177 VTNQKDGTFDLDEMEAKFSTADNIHCASTSLVCVENTH--NYCGGTVLPMQWLRELKARC 234
V DG DL+ +E + T LV V TH N G T+ P+ +E+
Sbjct: 119 VPVDDDGQLDLEALEKLLTE-------RTKLVAV--THVSNVLG-TINPV---KEIGEIA 165
Query: 235 QEHNIPVHMDGA 246
E +PV +DGA
Sbjct: 166 HEAGVPVLVDGA 177
>gnl|CDD|224029 COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase
and related enzymes [Amino acid transport and
metabolism].
Length = 386
Score = 33.7 bits (78), Expect = 0.092
Identities = 37/170 (21%), Positives = 60/170 (35%), Gaps = 48/170 (28%)
Query: 104 KELQEKA----AKLAGKEAA--IFVPSGTMGNLIAIMTHC-----DRRDSEIIVGDCSH- 151
++ E+A AKL G + IF T N +AI ++ II H
Sbjct: 43 RKAVEEAREQIAKLLGADPEEIIFTSGATESNNLAIKGAALAYRNAQKGKHIITSAIEHP 102
Query: 152 -----IMLWEQGGASQT--SVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCAS 204
E+ G T V +G DL+++E
Sbjct: 103 AVLNTCRYLERQGFEVTYLPV--------------DSNGLVDLEQLEEALR-------PD 141
Query: 205 TSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGA----RLPL 250
T LV + + +N G T+ P + E+ C+E I H+D ++P+
Sbjct: 142 TILVSIMHANNETG-TIQP---IAEIGEICKERGILFHVDAVQAVGKIPI 187
>gnl|CDD|235655 PRK05958, PRK05958, 8-amino-7-oxononanoate synthase; Reviewed.
Length = 385
Score = 33.2 bits (77), Expect = 0.12
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 105 ELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGD 148
L+E+ A+ G E A+ SG NL + + D +IV D
Sbjct: 88 ALEEELAEWFGAERALLFSSGYAANLAVLTALAGKGD--LIVSD 129
>gnl|CDD|232992 TIGR00474, selA, seryl-tRNA(sec) selenium transferase. In
bacteria, the incorporation of selenocysteine as the
21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes SelA.
This model excludes homologs that appear to differ in
function from Frankia alni, Helicobacter pylori,
Methanococcus jannaschii and other archaea, and so on
[Protein synthesis, tRNA aminoacylation].
Length = 454
Score = 33.3 bits (77), Expect = 0.13
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 15/74 (20%)
Query: 227 LRELKARCQEHNIPVHMD---GARLPLAE------------VCASVDTVMFCLSKGLGAP 271
+ EL A +EH +PV D G+ + L+ + A VD V F K LG P
Sbjct: 234 IAELVALGREHGLPVMEDLGSGSLVDLSRYGLPDEPTVQEVIAAGVDLVTFSGDKLLGGP 293
Query: 272 VGSILAGPEEFIQK 285
I+ G +E I++
Sbjct: 294 QAGIIVGKKELIER 307
>gnl|CDD|130881 TIGR01822, 2am3keto_CoA, 2-amino-3-ketobutyrate coenzyme A ligase.
This model represents a narrowly defined clade of animal
and bacterial (almost exclusively Proteobacterial)
2-amino-3-ketobutyrate--CoA ligase. This enzyme can act
in threonine catabolism. The closest homolog from
Bacillus subtilis, and sequences like it, may be
functionally equivalent but were not included in the
model because of difficulty in finding reports of
function [Energy metabolism, Amino acids and amines].
Length = 393
Score = 32.9 bits (75), Expect = 0.18
Identities = 22/111 (19%), Positives = 41/111 (36%), Gaps = 17/111 (15%)
Query: 186 DLDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMD- 244
D+ ++EA+ A A L+ + + G + P+ + +L +++ V +D
Sbjct: 153 DMADLEAQLKEARA-AGARHRLIATDGVFSM-DGVIAPLDEICDL---ADKYDALVMVDE 207
Query: 245 -------GAR----LPLAEVCASVDTVMFCLSKGLGAPVGSILAGPEEFIQ 284
G L V VD + L K LG G +E ++
Sbjct: 208 CHATGFLGPTGRGSHELCGVMGRVDIITGTLGKALGGASGGFTTARKEVVE 258
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 32.7 bits (75), Expect = 0.22
Identities = 40/186 (21%), Positives = 66/186 (35%), Gaps = 43/186 (23%)
Query: 84 KNYMFNCEVGDDVYLEDPTCKELQEKAAKLAGK-----EAA--IFVPSGTMGNLIAIMTH 136
+ + E P EL+E+ + E A F GT NL+A++
Sbjct: 80 ELLVSALNKNLGDPDESPAAAELEERVVNMLSDLLGAPEEASGTFTSGGTEANLLALLAA 139
Query: 137 CDRRDSEIIVGDCSHIMLWEQGG--------ASQTSVYS--QIGRVL---MRGV-TNQKD 182
+R L E G S+T+ +S + R L +R V T D
Sbjct: 140 RER---------WRKRALAESGKPGGKPNIVCSETAHFSFEKAARYLGLGLRRVPTVPTD 190
Query: 183 GTFDLDEMEAKFS--TADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIP 240
D+D +E T + +V T + G++ + EL +E+ I
Sbjct: 191 YRIDVDALEEAIDENTIGGV------VVGTAGTTDT--GSIDD---IEELADIAEEYGIW 239
Query: 241 VHMDGA 246
+H+D A
Sbjct: 240 LHVDAA 245
>gnl|CDD|168478 PRK06234, PRK06234, methionine gamma-lyase; Provisional.
Length = 400
Score = 32.5 bits (74), Expect = 0.24
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 98 LEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGD 148
L +PT E++ K A L G EAA+ SG MG + + + + ++ D
Sbjct: 61 LGNPTSTEVENKLALLEGGEAAVVAASG-MGAISSSLWSALKAGDHVVASD 110
>gnl|CDD|130393 TIGR01326, OAH_OAS_sulfhy, OAH/OAS sulfhydrylase. This model
describes a distinct clade of the Cys/Met metabolism
pyridoxal phosphate-dependent enzyme superfamily.
Members include examples of OAH/OAS sulfhydrylase, an
enzyme with activity both as O-acetylhomoserine (OAH)
sulfhydrylase (EC 2.5.1.49) and O-acetylserine (OAS)
sulphydrylase (EC 2.5.1.47). An alternate name for OAH
sulfhydrylase is homocysteine synthase. This model is
designated subfamily because it may or may not have both
activities [Amino acid biosynthesis, Aspartate family,
Amino acid biosynthesis, Serine family].
Length = 418
Score = 32.3 bits (74), Expect = 0.25
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 87 MFNCEVGDDVY--LEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMT 135
+F + ++Y L +PT L+++ A L G AA+ V SG AI+
Sbjct: 41 LFGLQEAGNIYSRLMNPTTDVLEQRIAALEGGVAALAVASGQAAITYAILN 91
>gnl|CDD|188131 TIGR01325, O_suc_HS_sulf, O-succinylhomoserine sulfhydrylase. This
model describes O-succinylhomoserine sulfhydrylase, one
of several related pyridoxal phosphate-dependent enzymes
of cysteine and methionine metabolism. This enzyme is
part of an alternative pathway of homocysteine
biosynthesis, a step in methionine biosynthesis [Amino
acid biosynthesis, Aspartate family].
Length = 381
Score = 32.1 bits (73), Expect = 0.30
Identities = 58/214 (27%), Positives = 83/214 (38%), Gaps = 48/214 (22%)
Query: 88 FNCEVGDDVY--LEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEII 145
F E+ VY +PT +E+ A L G EAA+ SG A+M D
Sbjct: 39 FAGELPGFVYSRYGNPTVSVFEERLALLEGAEAAVATASGMAAIFAALMALLGAGD---- 94
Query: 146 VGDCSHIMLWEQGGASQTSVYSQIGRVLMR-GV-TNQKDGTFDLDEMEAKFSTADNIHCA 203
H++ S V S+I L R GV T DGT DL EA
Sbjct: 95 -----HVVASRSLFGSCFVVCSEI---LPRFGVQTVFVDGT-DLSAWEAALK-------P 138
Query: 204 STSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGARLPLAEVCAS------- 256
+T V VE N P+Q L ++ A + H GA++ + V A+
Sbjct: 139 NTKAVFVETPSN-------PLQELVDIAAVAE----LAHAAGAKVVVDNVFATPLLQQPL 187
Query: 257 ---VDTVMFCLSK---GLGAPVGSILAGPEEFIQ 284
D V++ +K G G +G + G EE++
Sbjct: 188 KLGADVVVYSATKHIDGQGRVLGGAILGSEEYMD 221
>gnl|CDD|224893 COG1982, LdcC, Arginine/lysine/ornithine decarboxylases [Amino acid
transport and metabolism].
Length = 557
Score = 32.3 bits (74), Expect = 0.31
Identities = 25/81 (30%), Positives = 33/81 (40%), Gaps = 10/81 (12%)
Query: 91 EVGDDVYLEDPT--CKELQEKAAKLAGKEAAIFVPSGT-MGNLIAIMTHCDRRDSEIIVG 147
E+ L DP KE QE AA++ G + FV +GT N I D ++
Sbjct: 61 ELDS---LLDPEGPIKEAQELAARVFGADHTYFVVNGTSTANKAVINAVLTPGDKVLVDR 117
Query: 148 DC--SHIMLWEQGGASQTSVY 166
+C S GA T VY
Sbjct: 118 NCHKSIHHGLILAGA--TPVY 136
>gnl|CDD|234361 TIGR03812, tyr_de_CO2_Arch, tyrosine decarboxylase MnfA. Members
of this protein family are the archaeal form, MnfA, of
tyrosine decarboxylase, and are involved in methanofuran
biosynthesis. Members show clear homology to the
Enterococcus form, Tdc, that is involved in tyrosine
decarboxylation for resistance to acidic conditions
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 373
Score = 31.9 bits (73), Expect = 0.31
Identities = 28/130 (21%), Positives = 53/130 (40%), Gaps = 25/130 (19%)
Query: 122 VPSGTMGNLIAI-----MTHCDRRDSEIIVGDCSHIMLWEQGGASQTSVYSQIGRVLMRG 176
V GT N+ A+ + ++R IIV + +H S +G + +R
Sbjct: 82 VSGGTEANIQAVRAAKNLAREEKRTPNIIVPESAHF--------SFEKAAEMLG-LELRY 132
Query: 177 VTNQKDGTFDLDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQE 236
+D T D+ ++E DN + +V + T G + ++ L ++ E
Sbjct: 133 APLDEDYTVDVKDVEDLID--DN----TIGIVGIAGTTEL--GQIDDIEELSKI---ALE 181
Query: 237 HNIPVHMDGA 246
+ I +H+D A
Sbjct: 182 NGIYLHVDAA 191
>gnl|CDD|216267 pfam01053, Cys_Met_Meta_PP, Cys/Met metabolism PLP-dependent
enzyme. This family includes enzymes involved in
cysteine and methionine metabolism. The following are
members: Cystathionine gamma-lyase, Cystathionine
gamma-synthase, Cystathionine beta-lyase, Methionine
gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine
sulfhydrylase All of these members participate is
slightly different reactions. All these enzymes use PLP
(pyridoxal-5'-phosphate) as a cofactor.
Length = 382
Score = 31.8 bits (73), Expect = 0.38
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 100 DPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGDC 149
+PT L+E+ A L G EAA+ SG M + A + + ++ D
Sbjct: 51 NPTRDALEERIAALEGGEAALAFSSG-MAAIFAALLALLKAGDHVVATDD 99
>gnl|CDD|180685 PRK06767, PRK06767, methionine gamma-lyase; Provisional.
Length = 386
Score = 31.3 bits (71), Expect = 0.57
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 98 LEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIV 146
L +PT K +E+ A L G E A+ SG M + A + + II
Sbjct: 58 LGNPTVKLFEERMAVLEGGEEALAFGSG-MAAISATLIGFLKAGDHIIC 105
>gnl|CDD|171585 PRK12566, PRK12566, glycine dehydrogenase; Provisional.
Length = 954
Score = 31.4 bits (71), Expect = 0.65
Identities = 49/185 (26%), Positives = 74/185 (40%), Gaps = 34/185 (18%)
Query: 105 ELQEKAAKLAGKEAAIFVP-SGTMGN---LIAIMT-HCDRRDSEIIVGDCSHIMLWEQGG 159
EL+ + G +A P SG G L+AI H R S+ I L
Sbjct: 547 ELEAWLCAITGFDAICMQPNSGAQGEYAGLLAIRRYHRSRGQSQ------RDICLIPSSA 600
Query: 160 ASQTSVYSQIGRVLMRGVTNQKDGTFDLDEMEAKFSTA-DNIHCASTSLVCVENTHN-YC 217
+Q+ + + V DG DLD+++AK + A D + C ++ +TH Y
Sbjct: 601 HGTNPASAQMAGMRVVIVECDPDGNVDLDDLKAKAAAAGDRLSCL---MITYPSTHGVYE 657
Query: 218 GGTVLPMQWLRELKARCQEHNIPVHMDGARLPL-------AEVCASVDTV----MFCLSK 266
G +RE+ +H V+MDGA L A++ A V + FC+
Sbjct: 658 EG-------IREICEVVHQHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPH 710
Query: 267 GLGAP 271
G G P
Sbjct: 711 GGGGP 715
>gnl|CDD|235599 PRK05769, PRK05769, 4-aminobutyrate aminotransferase; Provisional.
Length = 441
Score = 30.7 bits (70), Expect = 0.87
Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 24/80 (30%)
Query: 218 GGTVLP-MQWLRELKARCQEHNIPVHMDGARLPLAEVCASVDTV--MF------------ 262
GG V+P + +EL+ ++ I + D EV + MF
Sbjct: 234 GGYVVPPKNFFKELRKLADKYGILLIDD-------EVQTGMGRTGKMFAIEHFGVEPDII 286
Query: 263 CLSKGLGA--PVGSILAGPE 280
L+K + P+G+++ E
Sbjct: 287 TLAKAIAGGLPLGAVIGRAE 306
>gnl|CDD|129792 TIGR00709, dat, 2,4-diaminobutyrate 4-transaminases. This family
consists of L-diaminobutyric acid transaminases. This
general designation covers both 2.6.1.76
(diaminobutyrate-2-oxoglutarate transaminase, which uses
glutamate as the amino donor in DABA biosynthesis), and
2.6.1.46 (diaminobutyrate--pyruvate transaminase, which
uses alanine as the amino donor). Most members with
known function are 2.6.1.76, and at least some
annotations as 2.6.1.46 in current databases at time of
model revision are incorrect. A distinct branch of this
family contains examples of 2.6.1.76 nearly all of which
are involved in ectoine biosynthesis. A related enzyme
is 4-aminobutyrate aminotransferase (EC 2.6.1.19), also
called GABA transaminase. These enzymes all are
pyridoxal phosphate-containing class III
aminotransferase [Central intermediary metabolism,
Other].
Length = 442
Score = 30.7 bits (69), Expect = 0.93
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 16/76 (21%)
Query: 218 GGTV-LPMQWLRELKARCQEHNIPVHMDGARLPLAEVC----------ASVDTVMFCLSK 266
GG V P +WL++++ ++H+I + +D + A A ++ +SK
Sbjct: 219 GGVVAAPSEWLQKIREVTRKHDIKLILDEVQ---AGFGRSGTMFAFEHAGIEPDFVVMSK 275
Query: 267 --GLGAPVGSILAGPE 280
G G P+ +L PE
Sbjct: 276 AVGGGLPLAVLLIAPE 291
>gnl|CDD|235278 PRK04311, PRK04311, selenocysteine synthase; Provisional.
Length = 464
Score = 30.6 bits (70), Expect = 0.96
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 15/74 (20%)
Query: 227 LRELKARCQEHNIPVHMD---GARLPLA-----------EVCAS-VDTVMFCLSKGLGAP 271
L EL A +EH +PV D G+ + L+ E+ A+ VD V F K LG P
Sbjct: 239 LAELAALGKEHGLPVVYDLGSGSLVDLSQYGLPDEPTVQELLAAGVDLVTFSGDKLLGGP 298
Query: 272 VGSILAGPEEFIQK 285
I+ G +E I +
Sbjct: 299 QAGIIVGKKELIAR 312
>gnl|CDD|236159 PRK08134, PRK08134, O-acetylhomoserine
aminocarboxypropyltransferase; Validated.
Length = 433
Score = 30.5 bits (69), Expect = 1.1
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 11/68 (16%)
Query: 87 MFNCEVGDDVY--LEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEI 144
+FN E VY + +PT L+E+ A L G AI SG +AI T
Sbjct: 48 LFNLERAGHVYSRISNPTVAVLEERVAALEGGVGAIATASGQAALHLAIAT--------- 98
Query: 145 IVGDCSHI 152
++G SHI
Sbjct: 99 LMGAGSHI 106
>gnl|CDD|102505 PRK06702, PRK06702, O-acetylhomoserine
aminocarboxypropyltransferase; Validated.
Length = 432
Score = 30.4 bits (68), Expect = 1.1
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 87 MFNCEVGDDVY--LEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRD 141
+FN E +Y + +PT ++K A+L G A+ SG ++A++ C D
Sbjct: 45 LFNLEAEGYIYTRIGNPTLAAFEQKLAELEGGVGAVATASGQAAIMLAVLNICSSGD 101
>gnl|CDD|102071 PRK05937, PRK05937, 8-amino-7-oxononanoate synthase; Provisional.
Length = 370
Score = 30.1 bits (68), Expect = 1.1
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 105 ELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGDCS-HI 152
+L+ K A G A VPSG M NL + H ++ ++ D HI
Sbjct: 60 DLEHKIAHFHGAPEAFIVPSGYMANL-GLCAHLS-SVTDYVLWDEQVHI 106
>gnl|CDD|240647 cd12170, 2-Hacid_dh_9, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 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 subdomain 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.
Length = 294
Score = 30.0 bits (68), Expect = 1.2
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 245 GARLPLAEVCASVDTVMFCLSKGLGAPVGSILAGPEEF 282
LPL E+ +VD + CL K + IL G EEF
Sbjct: 180 IRYLPLNELLKTVDVICTCLPKNV------ILLGEEEF 211
>gnl|CDD|211833 TIGR03531, selenium_SpcS, O-phosphoseryl-tRNA(Sec) selenium
transferase. In the archaea and eukaryotes, the
conversion of the mischarged serine to selenocysteine
(Sec) on its tRNA is accomplished in two steps. This
enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase,
acts second, after a phosphophorylation step catalyzed
by a homolog of the bacterial SelA protein [Protein
synthesis, tRNA aminoacylation].
Length = 444
Score = 30.0 bits (68), Expect = 1.3
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 12/70 (17%)
Query: 227 LRELKARCQEHNIPVHMDGA----------RLPLAEVCASVDTVMFCLSKGLGAPV-GSI 275
+ E+ C ++IP ++ A + A VD V+ K PV G+I
Sbjct: 224 IEEIAKICANYDIPHIVNNAYGLQSNKYMELINKAIKVGRVDAVVSSTDKNFMVPVGGAI 283
Query: 276 LAGP-EEFIQ 284
+ E FIQ
Sbjct: 284 IYSFDENFIQ 293
>gnl|CDD|130884 TIGR01825, gly_Cac_T_rel, pyridoxal phosphate-dependent
acyltransferase, putative. This model represents an
enzyme subfamily related to three known enzymes; it
appears closest to glycine C-acteyltransferase, shows no
overlap with it in species distribution, and may share
that function. The three closely related enzymes are
glycine C-acetyltransferase (2-amino-3-ketobutyrate
coenzyme A ligase), 5-aminolevulinic acid synthase, and
8-amino-7-oxononanoate synthase. All transfer the
R-group (acetyl, succinyl, or 6-carboxyhexanoyl) from
coenzyme A to an amino acid (Gly, Gly, Ala,
respectively), with release of CO2 for the latter two
reactions.
Length = 385
Score = 30.2 bits (68), Expect = 1.4
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 105 ELQEKAAKLAGKEAAIFVPSG---TMGNLIAIMTHCDRRDSEIIVGD 148
EL+EK AK EAA+ SG G L A++ R +I++ D
Sbjct: 82 ELEEKLAKFKKTEAALVFQSGFNTNQGVLSALL-----RKGDIVLSD 123
>gnl|CDD|218796 pfam05889, SLA_LP_auto_ag, Soluble liver antigen/liver pancreas
antigen (SLA/LP autoantigen). This family consists of
several eukaryotic and archaeal proteins which are
related to the human soluble liver antigen/liver
pancreas antigen (SLA/LP autoantigen). Autoantibodies
are a hallmark of autoimmune hepatitis, but most are not
disease specific. Autoantibodies to soluble liver
antigen (SLA) and to liver and pancreas antigen (LP)
have been described as disease specific, occurring in
about 30% of all patients with autoimmune hepatitis. The
function of SLA/LP is unknown, however, it has been
suggested that the protein may function as a serine
hydroxymethyltransferase and may be an important enzyme
in the thus far poorly understood selenocysteine
pathway. The archaeal sequences Methanopyrus kandleri
spcS and MK0229 are annotated as being pyridoxal
phosphate-dependent enzymes.
Length = 386
Score = 29.9 bits (67), Expect = 1.6
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 227 LRELKARCQEHNIPVHMDGA----------RLPLAEVCASVDTVMFCLSKGLGAPVG-SI 275
++E+ C E+++P ++GA + A +D V+ L K PVG +I
Sbjct: 174 VKEIAKICAEYDVPHLVNGAYGIQSEKYIHLIQQAAKVGRIDAVVQSLDKNFIVPVGGAI 233
Query: 276 LAGP-EEFIQ 284
+A E FIQ
Sbjct: 234 IAAFDESFIQ 243
>gnl|CDD|188122 TIGR01264, tyr_amTase_E, tyrosine aminotransferase, eukaryotic.
This model describes tyrosine aminotransferase as found
in animals and Trypanosoma cruzi. It is the first enzyme
of a pathway of tyrosine degradation via homogentisate.
Several plant enzyme designated as probable tyrosine
aminotransferases are very closely related to an
experimentally demonstrated nicotianamine
aminotransferase, an enzyme in a siderophore (iron
uptake chelator) biosynthesis pathway. These plant
sequences are excluded from the model seed and score
between the trusted an noise cutoffs [Energy metabolism,
Amino acids and amines].
Length = 401
Score = 29.8 bits (67), Expect = 1.7
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 8/59 (13%)
Query: 186 DLDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMD 244
DL ++E S D T+ + V N N CG V Q L E+ A + +P+ D
Sbjct: 157 DLKQLE---SLIDE----KTAALVVNNPSNPCGS-VFSRQHLEEILAVAERQCLPIIAD 207
>gnl|CDD|102374 PRK06434, PRK06434, cystathionine gamma-lyase; Validated.
Length = 384
Score = 29.5 bits (66), Expect = 2.0
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 65 NIRTVDIRSDTISKPTMEMKNYMFNCEVGDDVYLE--DPTCKELQEKAAKLAGKEAAIFV 122
N+ T + T P E + YM + +Y +PT + +EK A L E A+
Sbjct: 26 NVTTPIFETSTFVYPNSEKEAYMDSTRGMPYIYTRWGNPTVQAFEEKYAVLENAEHALSF 85
Query: 123 PSGTMGNLIAIMTHCDRRDSEII 145
SG MG + + + ++ I+
Sbjct: 86 SSG-MGAITSAILSLIKKGKRIL 107
>gnl|CDD|237409 PRK13520, PRK13520, L-tyrosine decarboxylase; Provisional.
Length = 371
Score = 29.5 bits (67), Expect = 2.0
Identities = 33/160 (20%), Positives = 59/160 (36%), Gaps = 39/160 (24%)
Query: 101 PTCKELQEKAAKLAG-----KEAAIFVPSG-TMGNLIAIMT---HCDRRDSEIIVGDCSH 151
P +L+E+A ++ G +A ++ SG T N+ A+ I+V + +H
Sbjct: 55 PGTAKLEEEAVEMLGELLHLPDAYGYITSGGTEANIQAVRAARNLAKAEKPNIVVPESAH 114
Query: 152 IMLWEQGGASQTSVYS-----QIGRVLMRGVTNQKDGTFDLDEMEAKFSTADNIHCASTS 206
+S + V +R D D+ +E DN
Sbjct: 115 --------------FSFDKAADMLGVELRRAPLDDDYRVDVKAVEDLID--DNTIG---- 154
Query: 207 LVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGA 246
+V + T G V P+ L ++ E+ I +H+D A
Sbjct: 155 IVGIAGTTEL--GQVDPIPELSKI---ALENGIFLHVDAA 189
>gnl|CDD|152304 pfam11868, DUF3388, Protein of unknown function (DUF3388). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 261 to 275 amino acids in
length. This protein is found associated with pfam01842.
Length = 192
Score = 29.0 bits (65), Expect = 2.1
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 1 SLVSFREYSDSHRQTKIAREVLTLPTPALVE 31
+VS R ++ H Q + RE++ LP +VE
Sbjct: 113 GIVSTRRSNEKHWQ--LVREIMRLPATKVVE 141
>gnl|CDD|99738 cd00614, CGS_like, CGS_like: Cystathionine gamma-synthase is a PLP
dependent enzyme and catalyzes the committed step of
methionine biosynthesis. This pathway is unique to
microorganisms and plants, rendering the enzyme an
attractive target for the development of antimicrobials
and herbicides. This subgroup also includes
cystathionine gamma-lyases (CGL), O-acetylhomoserine
sulfhydrylases and O-acetylhomoserine thiol lyases.
CGL's are very similar to CGS's. Members of this group
are widely distributed among all three forms of life.
Length = 369
Score = 29.5 bits (67), Expect = 2.3
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 88 FNCEVGDDVY--LEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEII 145
F G +Y + +PT L++K A L G EAA+ SG M + ++ + ++
Sbjct: 25 FALREGGYIYSRIGNPTVDALEKKLAALEGGEAALAFSSG-MAAISTVLLALLKAGDHVV 83
Query: 146 VGDC 149
D
Sbjct: 84 ASDD 87
>gnl|CDD|226485 COG3977, COG3977, Alanine-alpha-ketoisovalerate (or
valine-pyruvate) aminotransferase [Amino acid transport
and metabolism].
Length = 417
Score = 29.3 bits (66), Expect = 2.4
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 204 STSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDGA 246
ST +CV N G VL + L +L A ++H IP+ +D A
Sbjct: 179 STGAICVSRPTNPTG-NVLTDEELAKLDALARQHGIPLIIDNA 220
>gnl|CDD|225428 COG2873, MET17, O-acetylhomoserine sulfhydrylase [Amino acid
transport and metabolism].
Length = 426
Score = 29.2 bits (66), Expect = 2.5
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 88 FNCEVGDDVY--LEDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMT 135
F + ++Y + +PT L+E+ A L G AA+ V SG AI+
Sbjct: 47 FGLKEPGNIYTRIMNPTTDVLEERIAALEGGVAALAVASGQAAITYAILN 96
>gnl|CDD|233359 TIGR01329, cysta_beta_ly_E, cystathionine beta-lyase, eukaryotic.
This model represents cystathionine beta-lyase
(alternate name: beta-cystathionase), one of several
pyridoxal-dependent enzymes of cysteine, methionine, and
homocysteine metabolism. This enzyme is involved in the
biosynthesis of Met from Cys.
Length = 378
Score = 29.0 bits (65), Expect = 2.9
Identities = 18/49 (36%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 100 DPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGD 148
+PT L+ AKL + A SG M L I T EII GD
Sbjct: 46 NPTRTALESLLAKLDKADRAFAFSSG-MAALDVI-TRLLNNGDEIIAGD 92
>gnl|CDD|223699 COG0626, MetC, Cystathionine beta-lyases/cystathionine
gamma-synthases [Amino acid transport and metabolism].
Length = 396
Score = 29.1 bits (66), Expect = 3.0
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 101 PTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGD 148
PT L+E A+L G E A SG M + + + +++ D
Sbjct: 63 PTRDALEEALAELEGGEDAFAFSSG-MAAISTALLALLKAGDHVLLPD 109
>gnl|CDD|132315 TIGR03271, methan_mark_5, putative methanogenesis marker protein 5.
Members of this protein family, to date, are found in a
completed prokaryotic genome if and only if the species
is one of the archaeal methanogens. The exact function
is unknown, but likely is linked to methanogenesis or a
process closely connected to it [Energy metabolism,
Methanogenesis].
Length = 142
Score = 27.8 bits (62), Expect = 3.6
Identities = 12/41 (29%), Positives = 19/41 (46%)
Query: 108 EKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGD 148
+ K K AA+ VPSG G + + ++ IIV +
Sbjct: 48 PEDPKKGLKYAAVEVPSGVRGRMSLFGPLIEEAEAAIIVRE 88
>gnl|CDD|163313 TIGR03537, DapC, succinyldiaminopimelate transaminase. The four
sequences which make up the seed for this model are not
closely related, although they are all members of the
pfam00155 family of aminotransferases and are more
closely related to each other than to anything else.
Additionally, all of them are found in the vicinity of
genes involved in the biosynthesis of lysine via the
diaminopimelate pathway (GenProp0125), although this
amount to a separation of 12 genes in the case of
Sulfurihydrogenibium azorense Az-Fu1. None of these
genomes contain another strong candidate for this role
in the pathway. Note: the detailed information included
in the EC:2.6.1.17 record includes the assertions that
the enzyme uses the pyridoxal pyrophosphate cofactor,
which is consistent with the pfam00155 family, and the
assertion that the amino group donor is L-glutamate,
which is undetermined for the sequences in this clade.
Length = 350
Score = 28.3 bits (63), Expect = 4.2
Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 12/90 (13%)
Query: 205 TSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMDG--ARLPLAEVCASV----- 257
T +V + HN G T P +L+E A C+EH I + D + E S
Sbjct: 137 TKIVWINYPHNPTGATA-PRSYLKETIAMCREHGIILCSDECYTEIYFGEPPHSALEVGI 195
Query: 258 -DTVMFC-LSK--GLGAPVGSILAGPEEFI 283
+ + F LSK G+ +AG E+ I
Sbjct: 196 ENVLAFHSLSKRSGMTGYRSGFVAGDEKLI 225
>gnl|CDD|107206 cd01563, Thr-synth_1, Threonine synthase is a pyridoxal phosphate
(PLP) dependent enzyme that catalyses the last reaction
in the synthesis of threonine from aspartate. It
proceeds by converting O-phospho-L-homoserine (OPH) into
threonine and inorganic phosphate. In plants, OPH is an
intermediate between the methionine and
threonine/isoleucine pathways. Thus threonine synthase
competes for OPH with cystathionine-gamma-synthase, the
first enzyme in the methionine pathway. These enzymes
are in general dimers. Members of this CD, Thr-synth_1,
are widely distributed in bacteria, archaea and higher
plants.
Length = 324
Score = 28.3 bits (64), Expect = 4.3
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 110 AAKLAGKEAAIFVPSGT-MGNLIAIMTH 136
AA+ AG + +F+P+G +G L + +
Sbjct: 89 AAR-AGIKCVVFLPAGKALGKLAQALAY 115
>gnl|CDD|179868 PRK04612, argD, acetylornithine transaminase protein; Provisional.
Length = 408
Score = 28.4 bits (63), Expect = 4.5
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 11/73 (15%)
Query: 219 GTVLPMQ--WLRELKARCQEHNIPVHMDGARLPLAEVCA-------SVDTVMFCLSKGLG 269
G V+P +L ++A C +H+ + +D + + V + L+K LG
Sbjct: 200 GGVMPAAPGFLARVRALCDQHDALLVLDEIQCGMGRTGTLFAHWQEQVTPDIVTLAKALG 259
Query: 270 A--PVGSILAGPE 280
P+G++LAGP+
Sbjct: 260 GGFPIGAMLAGPK 272
>gnl|CDD|146802 pfam04354, ZipA_C, ZipA, C-terminal FtsZ-binding domain. This
family represents the ZipA C-terminal domain. ZipA is
involved in septum formation in bacterial cell division.
Its C-terminal domain binds FtsZ, a major component of
the bacterial septal ring. The structure of this domain
is an alpha-beta fold with three alpha helices and a
beta sheet of six antiparallel beta strands. The major
loops protruding from the beta sheet surface are thought
to form a binding site for FtsZ.
Length = 130
Score = 27.1 bits (61), Expect = 5.1
Identities = 12/16 (75%), Positives = 12/16 (75%), Gaps = 1/16 (6%)
Query: 181 KDGTFDLDEMEAKFST 196
K GTFDLD ME FST
Sbjct: 59 KPGTFDLDNMEQ-FST 73
>gnl|CDD|223513 COG0436, COG0436, Aspartate/tyrosine/aromatic aminotransferase
[Amino acid transport and metabolism].
Length = 393
Score = 28.4 bits (64), Expect = 5.1
Identities = 27/128 (21%), Positives = 49/128 (38%), Gaps = 23/128 (17%)
Query: 172 VLMRGVTNQKDGTFDLDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELK 231
V + + DL+++EA + T + + + +N G V + L+ +
Sbjct: 138 VPVPLDEEENGFKPDLEDLEAAIT-------PKTKAIILNSPNN-PTGAVYSKEELKAIV 189
Query: 232 ARCQEHNIPV---------HMDGAR-LPLAEVC-ASVDTVMF-CLSKGLGAP---VGSIL 276
+EH+I + DGA + E+ A T+ SK G +G ++
Sbjct: 190 ELAREHDIIIISDEIYEELVYDGAEHPSILELAGARDRTITINSFSKTYGMTGWRIGWVV 249
Query: 277 AGPEEFIQ 284
PEE I
Sbjct: 250 GPPEELIA 257
>gnl|CDD|236796 PRK10922, PRK10922, 3-octaprenyl-4-hydroxybenzoate decarboxylase;
Provisional.
Length = 497
Score = 28.3 bits (63), Expect = 5.1
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 5 FREYSDSHRQTKIAREVLTLPTPALVESTPLSRSWS-DNGNLS-IPAMYCW 53
FR+ D Q K +VL +PT L + + WS D+ +L+ IP M CW
Sbjct: 104 FRDLFDKLPQFK---QVLNMPTKRLRGAPCQQKIWSGDDVDLNRIPIMTCW 151
>gnl|CDD|184024 PRK13393, PRK13393, 5-aminolevulinate synthase; Provisional.
Length = 406
Score = 28.1 bits (63), Expect = 5.3
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 104 KELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIVGD 148
L+ + A L GKEAA+ SG + N A+ T R +I+ D
Sbjct: 93 VLLEAELADLHGKEAALLFTSGYVSNWAALSTLGSRLPGCVILSD 137
>gnl|CDD|236437 PRK09264, PRK09264, diaminobutyrate--2-oxoglutarate
aminotransferase; Validated.
Length = 425
Score = 28.2 bits (64), Expect = 5.8
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 221 VLPMQWLRELKARCQEHNI 239
V +WL+ L C++H+I
Sbjct: 215 VASAEWLQRLAKLCRKHDI 233
>gnl|CDD|131061 TIGR02006, IscS, cysteine desulfurase IscS. This model represents
IscS, one of several cysteine desulfurases from a larger
protein family designated (misleadingly, in this case)
class V aminotransferases. IscS is one of at least 6
enzymes characteristic of the IscSUA-hscAB-fsx system of
iron-sulfur cluster assembly. Scoring almost as well as
proteobacterial sequences included in the model are
mitochondrial cysteine desulfurases, apparently from an
analogous system in eukaryotes. The sulfur, taken from
cysteine, may be used in other systems as well, such as
tRNA base modification and biosynthesis of other
cofactors [Biosynthesis of cofactors, prosthetic groups,
and carriers, Other, Protein synthesis, tRNA and rRNA
base modification].
Length = 402
Score = 27.9 bits (62), Expect = 6.1
Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 11/68 (16%)
Query: 180 QKDGTFDLDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNI 239
+ +G DL+E++A D+ T LV + + +N G +Q + + C+E +
Sbjct: 125 KSNGLIDLEELKAAIR--DD-----TILVSIMHVNNEIG----VIQDIAAIGEICRERKV 173
Query: 240 PVHMDGAR 247
H+D A+
Sbjct: 174 FFHVDAAQ 181
>gnl|CDD|236298 PRK08574, PRK08574, cystathionine gamma-synthase; Provisional.
Length = 385
Score = 28.1 bits (63), Expect = 6.3
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 99 EDPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHCDRRDSEIIV 146
E+PT + L+E AKL G A+ SG M + + + +++
Sbjct: 51 ENPTLRPLEEALAKLEGGVDALAFNSG-MAAISTLFFSLLKAGDRVVL 97
>gnl|CDD|201705 pfam01276, OKR_DC_1, Orn/Lys/Arg decarboxylase, major domain.
Length = 417
Score = 27.8 bits (62), Expect = 6.5
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 104 KELQEKAAKLAGKEAAIFVPSGTMG-NLIAIMTHCDRRDSEIIVGDC 149
KE Q+ AA++ G + + FV +GT G N M C D+ +I +C
Sbjct: 69 KEAQKYAARVFGADKSYFVVNGTSGANKTVGMAVCTPGDTVLIDRNC 115
>gnl|CDD|112645 pfam03841, SelA, L-seryl-tRNA selenium transferase.
Length = 367
Score = 28.1 bits (63), Expect = 6.6
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 15/74 (20%)
Query: 227 LRELKARCQEHNIPVHMD---GARLPLAE------------VCASVDTVMFCLSKGLGAP 271
L EL A +EH +PV+ D G+ + L++ + VD V F K LG P
Sbjct: 159 LAELVALGKEHGLPVYYDLGSGSLVDLSQYGLPKEPTVQELLALGVDLVSFSGDKLLGGP 218
Query: 272 VGSILAGPEEFIQK 285
I+ G +E I++
Sbjct: 219 QAGIIVGKKELIER 232
>gnl|CDD|130298 TIGR01231, lacC, tagatose-6-phosphate kinase. This enzyme is part
of the tagatose-6-phosphate pathway of lactose
degradation [Energy metabolism, Biosynthesis and
degradation of polysaccharides].
Length = 309
Score = 27.9 bits (62), Expect = 6.7
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 222 LPMQWLRELKARCQEHNIPVHMDGARLPLAEV 253
LP + ++ RCQ +PV +D + L V
Sbjct: 140 LPQDYYAQIIERCQNKGVPVVLDCSGATLQTV 171
>gnl|CDD|221207 pfam11754, Velvet, Velvet factor. The velvet factor is conserved
in many fungal species and is found to have gained
different roles depending on the organism's need,
expanding the conserved role in developmental
programmes. The velvet factor orthologues can be adapted
to the fungal-specific life cycle and may be involved in
diverse functions such as sclerotia formation and toxin
production, as in A. parasiticus, nutrition-dependent
sporulation, as in A. fumigatus, or the
microconidia-to-macroconidia ratio and cell wall
formation, as in the heterothallic fungus Fusarium
verticilloides.
Length = 189
Score = 27.2 bits (61), Expect = 7.0
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 27 PALVESTPLSRSWSDNG 43
P + ESTPLSRS+++ G
Sbjct: 162 PGMAESTPLSRSFAEQG 178
>gnl|CDD|181244 PRK08133, PRK08133, O-succinylhomoserine sulfhydrylase; Validated.
Length = 390
Score = 27.7 bits (62), Expect = 7.7
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 100 DPTCKELQEKAAKLAGKEAAIFVPSGTMGNLIAIMTHC 137
+PT QE+ A L G EA + SG L +M
Sbjct: 60 NPTVTMFQERLAALEGAEACVATASGMAAILAVVMALL 97
>gnl|CDD|217370 pfam03102, NeuB, NeuB family. NeuB is the prokaryotic
N-acetylneuraminic acid (Neu5Ac) synthase. It catalyzes
the direct formation of Neu5Ac (the most common sialic
acid) by condensation of phosphoenolpyruvate (PEP) and
N-acetylmannosamine (ManNAc). This reaction has only
been observed in prokaryotes; eukaryotes synthesise the
9-phosphate form, Neu5Ac-9-P, and utilise ManNAc-6-P
instead of ManNAc. Such eukaryotic enzymes are not
present in this family. This family also contains SpsE
spore coat polysaccharide biosynthesis proteins.
Length = 240
Score = 27.4 bits (62), Expect = 8.0
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 222 LPMQWLRELKARCQEHNIP 240
LP +W +EL C+E I
Sbjct: 52 LPEEWHKELFEYCKEKGIE 70
>gnl|CDD|181402 PRK08363, PRK08363, alanine aminotransferase; Validated.
Length = 398
Score = 27.5 bits (61), Expect = 9.3
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 186 DLDEMEAKFSTADNIHCASTSLVCVENTHNYCGGTVLPMQWLRELKARCQEHNIPVHMD 244
D+D++ K + T + V N +N G + + L+E+ EH++PV D
Sbjct: 155 DIDDIRKKITE-------KTKAIAVINPNNPTG-ALYEKKTLKEILDIAGEHDLPVISD 205
>gnl|CDD|182372 PRK10310, PRK10310, PTS system galactitol-specific transporter
subunit IIB; Provisional.
Length = 94
Score = 26.0 bits (57), Expect = 9.4
Identities = 17/45 (37%), Positives = 19/45 (42%), Gaps = 13/45 (28%)
Query: 217 CGGTV-LPMQWLRELKARCQEHNIPV------------HMDGARL 248
CGG V E+K CQ HNIPV +MDG L
Sbjct: 9 CGGAVATSTMAAEEIKELCQSHNIPVELIQCRVNEIETYMDGVHL 53
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 0.134 0.407
Gapped
Lambda K H
0.267 0.0662 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,210,974
Number of extensions: 1302697
Number of successful extensions: 1331
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1299
Number of HSP's successfully gapped: 90
Length of query: 285
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 189
Effective length of database: 6,679,618
Effective search space: 1262447802
Effective search space used: 1262447802
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: 58 (26.3 bits)