RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3048
(367 letters)
>gnl|CDD|215836 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase
conserved domain.
Length = 373
Score = 320 bits (821), Expect = e-107
Identities = 133/291 (45%), Positives = 178/291 (61%), Gaps = 34/291 (11%)
Query: 1 MVSILAAKRKKILDLTSAGPTVSENDIKSRLVAYASDQSNSSVEKSAIIGDVPVRQLRSD 60
++++LAA+ K I + +AG +LVAY SDQ++SS+EK+A+I V +R++ +D
Sbjct: 117 LLALLAARTKWIRRMKAAGK--PSLG---KLVAYTSDQAHSSIEKAALIAGVELREIPTD 171
Query: 61 DNGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDNLEELGPICQEYNIWLHVDA 120
+NG +RG L A++ED GLIP + ATLGTTG+ AFD L+ELG IC +Y++WLHVDA
Sbjct: 172 ENGKMRGMDLEKAIEEDKENGLIPFFVCATLGTTGSGAFDPLQELGDICNKYDLWLHVDA 231
Query: 121 AYAGSALLLPEYAHLKRGLEYVDSFAFNAHKWLLTNHDCSAMWVKNANHLTNTFFTDRVY 180
AYAGSA + PE+ H G+E DSF+FN HKW+L DCSA+WV++ L + Y
Sbjct: 232 AYAGSAFICPEFRHWLFGIERADSFSFNPHKWMLVLLDCSALWVRDKGALQQALQFNPEY 291
Query: 181 LKHTDAPMNTQSPDYTVMNWLGKALGLPEEFLNCSKGPGGGVIQHWQTPLSRRFRALKLW 240
L H D + + DY WQ PLSRRFR LKLW
Sbjct: 292 LGHNDKQSDV-AVDY----------------------------GDWQIPLSRRFRILKLW 322
Query: 241 MTLRSYGLKGLQAYLRKHISLAKKFADLVEKDDRFELVCPPSMGLVCFRLK 291
LRSYG++GLQ +R+H+ LAK F LV KD RFE+ +GLVCFRLK
Sbjct: 323 FVLRSYGVEGLQNQIRRHVELAKYFEALVRKDSRFEICAERGLGLVCFRLK 373
Score = 41.2 bits (97), Expect = 5e-04
Identities = 18/28 (64%), Positives = 21/28 (75%), Gaps = 2/28 (7%)
Query: 197 VMNWLGKALGLPEEFLNCSKGPGGGVIQ 224
VM+WL K LGLP+EFL G GGGV+Q
Sbjct: 84 VMDWLAKMLGLPKEFL--GSGEGGGVLQ 109
>gnl|CDD|215475 PLN02880, PLN02880, tyrosine decarboxylase.
Length = 490
Score = 263 bits (674), Expect = 3e-84
Identities = 145/363 (39%), Positives = 199/363 (54%), Gaps = 49/363 (13%)
Query: 1 MVSILAAKRKKILDLTSAGPTVSENDIKSRLVAYASDQSNSSVEKSAIIGDV---PVRQL 57
+V +LAA+ + L G E +LV YASDQ++S+++K+ I + R L
Sbjct: 160 LVVLLAARDRV---LRKVGKNALE-----KLVVYASDQTHSALQKACQIAGIHPENCRLL 211
Query: 58 RSDD--NGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDNLEELGPICQEYNIW 115
++D N L + L A+ DL+ GLIP L AT+GTT + A D L ELG I + +W
Sbjct: 212 KTDSSTNYALAPELLSEAISTDLSSGLIPFFLCATVGTTSSTAVDPLLELGKIAKSNGMW 271
Query: 116 LHVDAAYAGSALLLPEYAHLKRGLEYVDSFAFNAHKWLLTNHDCSAMWVKNANHLTNTFF 175
HVDAAYAGSA + PEY H G+E DSF NAHKW LTN DCS +WVK+ N L +
Sbjct: 272 FHVDAAYAGSACICPEYRHYIDGVEEADSFNMNAHKWFLTNFDCSLLWVKDRNALIQSLS 331
Query: 176 TDRVYLKHTDAPMNTQSPDYTVMNWLGKALGLPEEFLNCSKGPGGGVIQHWQTPLSRRFR 235
T+ +LK N S +V+++ + WQ PL RRFR
Sbjct: 332 TNPEFLK------NKASQANSVVDY-----------------------KDWQIPLGRRFR 362
Query: 236 ALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEKDDRFELVCPPSMGLVCFRL---KG 292
+LKLWM LR YG++ LQ+Y+R HI LAK+F LV +D RFE+V P LVCFRL K
Sbjct: 363 SLKLWMVLRLYGVENLQSYIRNHIKLAKEFEQLVAQDSRFEVVTPRIFSLVCFRLVPPKN 422
Query: 293 DNDLTNQLYERLM----SHKQIYIIKASFQGRPFLRFVVTSPETNQCDVAFAWNEISHQS 348
+ D N+L L+ S +I+I G+ LRF V +P T + V AW + ++
Sbjct: 423 NEDNGNKLNHDLLDAVNSSGKIFISHTVLSGKYVLRFAVGAPLTEERHVTAAWKVLQDEA 482
Query: 349 SEM 351
S++
Sbjct: 483 SKL 485
Score = 41.4 bits (97), Expect = 6e-04
Identities = 18/28 (64%), Positives = 21/28 (75%), Gaps = 2/28 (7%)
Query: 197 VMNWLGKALGLPEEFLNCSKGPGGGVIQ 224
V++WL K L LPE+FL S G GGGVIQ
Sbjct: 127 VLDWLAKLLNLPEQFL--STGNGGGVIQ 152
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 219 bits (560), Expect = 7e-67
Identities = 141/363 (38%), Positives = 193/363 (53%), Gaps = 49/363 (13%)
Query: 1 MVSILAAKRKKILDLTSAGPTVSENDIKSRLVAYASDQSNSSVEKSAIIGDV---PVRQL 57
+V +LAA R +IL G T + +LV Y SDQ++SS K+ +IG + +R L
Sbjct: 208 LVVVLAA-RDRIL--KKVGKT-----LLPQLVVYGSDQTHSSFRKACLIGGIHEENIRLL 259
Query: 58 RSDD--NGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDNLEELGPICQEYNIW 115
++D N + ++L A+ DLAKG IP + AT+GTT + A D L LG I ++Y IW
Sbjct: 260 KTDSSTNYGMPPESLEEAISHDLAKGFIPFFICATVGTTSSAAVDPLVPLGNIAKKYGIW 319
Query: 116 LHVDAAYAGSALLLPEYAHLKRGLEYVDSFAFNAHKWLLTNHDCSAMWVKNANHLTNTFF 175
LHVDAAYAG+A + PEY G+E DSF NAHKWL N CS +WVK+ L +
Sbjct: 320 LHVDAAYAGNACICPEYRKFIDGIENADSFNMNAHKWLFANQTCSPLWVKDRYSLIDALK 379
Query: 176 TDRVYLKHTDAPMNTQSPDYTVMNWLGKALGLPEEFLNCSKGPGGGVIQHWQTPLSRRFR 235
T+ YL+ S TV+N+ + WQ LSRRFR
Sbjct: 380 TNPEYLEFK------VSKKDTVVNY-----------------------KDWQISLSRRFR 410
Query: 236 ALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEKDDRFELVCPPSMGLVCFRL---KG 292
+LKLWM LR YG + L+ ++R H++LAK F D V +D FE+V LVCFRL G
Sbjct: 411 SLKLWMVLRLYGSENLRNFIRDHVNLAKHFEDYVAQDPSFEVVTTRYFSLVCFRLAPVDG 470
Query: 293 DNDLTNQLYERLM----SHKQIYIIKASFQGRPFLRFVVTSPETNQCDVAFAWNEISHQS 348
D D N+ L+ S +I+I + G+ LRF V +P T + V AW I +
Sbjct: 471 DEDQCNERNRELLAAVNSTGKIFISHTALSGKFVLRFAVGAPLTEEKHVTEAWQIIQKHA 530
Query: 349 SEM 351
S+
Sbjct: 531 SKF 533
Score = 35.1 bits (80), Expect = 0.064
Identities = 17/28 (60%), Positives = 20/28 (71%), Gaps = 2/28 (7%)
Query: 197 VMNWLGKALGLPEEFLNCSKGPGGGVIQ 224
V++WL K L LP+ FL S G GGGVIQ
Sbjct: 175 VLDWLAKLLQLPDHFL--STGNGGGVIQ 200
>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 = 197 bits (503), Expect = 2e-60
Identities = 69/165 (41%), Positives = 100/165 (60%), Gaps = 5/165 (3%)
Query: 1 MVSILAAKRKKILDLTSAGPTVSENDIKSRLVAYASDQSNSSVEKSAIIGDVPVRQLRSD 60
++++LAA+ + L + G +LV SDQ++ SVEK+A DV VR + D
Sbjct: 71 LLALLAARDRARKRLKAGGG-----RGIDKLVIVCSDQAHVSVEKAAAYLDVKVRLVPVD 125
Query: 61 DNGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDNLEELGPICQEYNIWLHVDA 120
++G + +AL A+ ED A+GL P +VAT GTT T A D LEE+ + ++Y++WLHVDA
Sbjct: 126 EDGRMDPEALEAAIDEDKAEGLNPIMVVATAGTTDTGAIDPLEEIADLAEKYDLWLHVDA 185
Query: 121 AYAGSALLLPEYAHLKRGLEYVDSFAFNAHKWLLTNHDCSAMWVK 165
AY G L PE HL G+E VDS + + HK+ L CSA+ V+
Sbjct: 186 AYGGFLLPFPEPRHLDFGIERVDSISVDPHKYGLVPLGCSAVLVR 230
Score = 111 bits (281), Expect = 5e-28
Identities = 44/114 (38%), Positives = 61/114 (53%), Gaps = 3/114 (2%)
Query: 234 FRALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEKDDRFELVCPPSMGLVCFRLKGD 293
RALKLW TLR +G G ++ + + LAK A+L+ D FEL+ P++ LVCFRLK
Sbjct: 229 VRALKLWATLRRFGRDGYGEHIDRIVDLAKYLAELIRADPGFELLGEPNLSLVCFRLKPS 288
Query: 294 --NDLTNQ-LYERLMSHKQIYIIKASFQGRPFLRFVVTSPETNQCDVAFAWNEI 344
D N L +RL ++ + G LRFVVT+P T + D +I
Sbjct: 289 VKLDELNYDLSDRLNERGGWHVPATTLGGPNVLRFVVTNPLTTRDDADALLEDI 342
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 173 bits (441), Expect = 5e-50
Identities = 84/314 (26%), Positives = 128/314 (40%), Gaps = 57/314 (18%)
Query: 34 YASDQSNSSVEKSAIIGDVPVRQLRSD-DNGVLRGDALLTAVKEDLAKGLIPCCLVATLG 92
S+ ++ S EK+A + +R++ + + + DAL A+ E+ G +V T G
Sbjct: 161 VCSETAHFSFEKAARYLGLGLRRVPTVPTDYRIDVDALEEAIDENTIGG----VVVGTAG 216
Query: 93 TTGTCAFDNLEELGPICQEYNIWLHVDAAYAGSALLLPEYAHLK-RGLEYVDSFAFNAHK 151
TT T + D++EEL I +EY IWLHVDAA+ G L E GLE VDS + HK
Sbjct: 217 TTDTGSIDDIEELADIAEEYGIWLHVDAAFGGFLLPFLEPDGRWDFGLEGVDSITVDGHK 276
Query: 152 WLLTNHDCSAMWVKNANHLTNTFFTDRVYLKHTDAPMNTQSPDYTVMNWLGKALGLPEEF 211
+ L C + ++ L
Sbjct: 277 YGLAPIGCGVVLFRDEEAL------------------------------------RRILI 300
Query: 212 LNCSKGPGGGVIQ--HWQTPLSRRFRALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLV 269
PGGG+ + R +AL L+ LR G +G + L + + LA+ A+ +
Sbjct: 301 FADYYLPGGGIPNFTILGSRPGR--QALALYANLRRLGREGYRKLLDRTLELARYLAEEL 358
Query: 270 EKDDRFELVCPPSMGLVCFRLKGDND-----------LTNQLYERLMSHKQIYIIKASFQ 318
EK FELV P + +V FRLK D D Q+ +L+ +
Sbjct: 359 EKLGDFELVNEPELPIVAFRLKDDEDTLADLSERLDRRGWQVPAQLLPKGLAIVFGTHVT 418
Query: 319 GRPFLRFVVTSPET 332
GR L+F+V +
Sbjct: 419 GRQGLKFIVANLLI 432
>gnl|CDD|163511 TIGR03799, NOD_PanD_pyr, putative pyridoxal-dependent aspartate
1-decarboxylase. This enzyme is proposed here to be a
form of aspartate 1-decarboxylase, pyridoxal-dependent,
that represents a non-orthologous displacement to the
more widely distributed pyruvoyl-dependent form
(TIGR00223). Aspartate 1-decarboxylase makes
beta-alanine, used usually in pathothenate biosynthesis,
by decarboxylation from asparatate. A number of species
with the PanB and PanC enzymes, however, lack PanD. This
protein family occurs in a number of Proteobacteria that
lack PanD. This enzyme family appears to be a
pyridoxal-dependent enzyme (see pfam00282). The family
was identified by Partial Phylogenetic Profiling;
members in Geobacter sulfurreducens, G. metallireducens,
and Pseudoalteromonas atlantica are clustered with the
genes for PanB and PanC. We suggest the gene symbol panP
(panthothenate biosynthesis enzyme, Pyridoxal-dependent)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pantothenate and coenzyme A].
Length = 522
Score = 76.7 bits (189), Expect = 3e-15
Identities = 43/121 (35%), Positives = 63/121 (52%), Gaps = 3/121 (2%)
Query: 36 SDQSNSSVEKSAI---IGDVPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLVATLG 92
S++ + S+ K+A IG + +++D N + DAL E + + P +V G
Sbjct: 215 SERGHYSLGKAADVLGIGRDNLIAIKTDANNRIDVDALRDKCAELAEQNIKPLAIVGVAG 274
Query: 93 TTGTCAFDNLEELGPICQEYNIWLHVDAAYAGSALLLPEYAHLKRGLEYVDSFAFNAHKW 152
TT T D L+E+ I QE HVDAA+ G+ LL Y HL +G+E DS +AHK
Sbjct: 275 TTETGNIDPLDEMADIAQELGCHFHVDAAWGGATLLSNTYRHLLKGIERADSVTIDAHKQ 334
Query: 153 L 153
L
Sbjct: 335 L 335
Score = 37.0 bits (86), Expect = 0.013
Identities = 21/59 (35%), Positives = 33/59 (55%)
Query: 231 SRRFRALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEKDDRFELVCPPSMGLVCFR 289
SR A+ ++ L G KG + + + I AK FADL+++ FELV P + L+ +R
Sbjct: 378 SRPGMAMLVYAGLHIIGRKGYELLIDQSIEKAKYFADLIQQQPDFELVTEPELCLLTYR 436
>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 = 65.5 bits (160), Expect = 8e-13
Identities = 35/146 (23%), Positives = 47/146 (32%), Gaps = 8/146 (5%)
Query: 21 TVSENDIKSRLVAYASDQSNSSVEKSAI-IGDVPVRQLRSDDNGVLRGDALLTAVKEDLA 79
+ + S A + + DD G L A+ E+L
Sbjct: 32 AALLALLGPGDEVIVDANGHGSRYWVAAELAGAKPVPVPVDDAG---YGGLDVAILEELK 88
Query: 80 KGLIPCCLVATLGTTGTCAFDNLEELGPICQEYNIWLHVDAAYAGSALLLPEYAHLKRGL 139
+V T TT L+E+ I +EY I L VDAA AG A P
Sbjct: 89 AKPNVALIVITPNTTSGGVLVPLKEIRKIAKEYGILLLVDAASAGGASPAPGV---LIPE 145
Query: 140 EYVDSFAFNAHKWLLTNHDCSAMWVK 165
D F+ HK L + VK
Sbjct: 146 GGADVVTFSLHKNLGGE-GGGVVIVK 170
>gnl|CDD|235068 PRK02769, PRK02769, histidine decarboxylase; Provisional.
Length = 380
Score = 60.4 bits (147), Expect = 4e-10
Identities = 38/131 (29%), Positives = 65/131 (49%), Gaps = 6/131 (4%)
Query: 32 VAYASDQSNSSVEKSAIIGDVPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLVATL 91
Y S ++ SV K A + + R + S NG + D L++ +KE+ + I + A +
Sbjct: 112 TLYYSKDTHYSVSKIARLLRIKSRVITSLPNGEIDYDDLISKIKENKNQPPI---IFANI 168
Query: 92 GTTGTCAFDNLEELGPICQEYNI---WLHVDAAYAGSALLLPEYAHLKRGLEYVDSFAFN 148
GTT T A DN++E+ I ++ I ++H DAA +G L + +DS A +
Sbjct: 169 GTTMTGAIDNIKEIQEILKKIGIDDYYIHADAALSGMILPFVNNPPPFSFADGIDSIAIS 228
Query: 149 AHKWLLTNHDC 159
HK++ + C
Sbjct: 229 GHKFIGSPMPC 239
>gnl|CDD|130848 TIGR01788, Glu-decarb-GAD, glutamate decarboxylase. This model
represents the pyridoxal phosphate-dependent glutamate
(alpha) decarboxylase found in bacteria (low and hi-GC
gram positive, proteobacteria and cyanobacteria),
plants, fungi and at least one archaon (Methanosarcina).
The product of the enzyme is gamma-aminobutyrate (GABA).
Length = 431
Score = 56.6 bits (137), Expect = 8e-09
Identities = 67/280 (23%), Positives = 113/280 (40%), Gaps = 66/280 (23%)
Query: 44 EKSAIIGDVPVRQLRSD-DNGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDNL 102
EK A DV +R++ D V+ + ++ AV E+ +V LGTT T ++++
Sbjct: 152 EKFARYFDVELREVPMDPGRYVIDPEQVVEAVDEN------TIGVVCILGTTYTGEYEDV 205
Query: 103 EELGPICQEYN------IWLHVDAAYAG--SALLLPEYAHLKRGLEYVDSFAFNAHKWLL 154
+ L EYN I +HVDAA G + + P+ R L V S + HK+ L
Sbjct: 206 KALNDALDEYNAKTGWDIPIHVDAASGGFIAPFVYPDLEWDFR-LPRVKSINVSGHKYGL 264
Query: 155 TNHDCSAMWV--KNANHLTNTFFTDRVYLKHTDAPMNTQSPDYTV--MNWLGKALGLPEE 210
WV ++ L P+ + +N+LG G
Sbjct: 265 VYPGVG--WVIWRDEEAL----------------------PEELIFHVNYLG---GDEPT 297
Query: 211 F-LNCSKGPGGGVIQHWQTPLSRRFRALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLV 269
F LN S+ + Q++ G +G + ++ + +A+ A+ +
Sbjct: 298 FTLNFSRPANQVIAQYYN---------------FLRLGREGYRKIMQNSLDVARYLAEEI 342
Query: 270 EKDDRFELVCP-PSMGLVCFRLKGDNDLTNQLYERLMSHK 308
K FE++ + LV F+LK D D LY+ +SH+
Sbjct: 343 AKLGPFEIISDGSGIPLVAFKLKDDADPGYTLYD--LSHR 380
>gnl|CDD|237409 PRK13520, PRK13520, L-tyrosine decarboxylase; Provisional.
Length = 371
Score = 54.9 bits (133), Expect = 2e-08
Identities = 62/265 (23%), Positives = 102/265 (38%), Gaps = 51/265 (19%)
Query: 42 SVEKSAIIGDVPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDN 101
S +K+A + V +R+ DD+ R D + AV++ + I +V GTT D
Sbjct: 116 SFDKAADMLGVELRRAPLDDD--YRVD--VKAVEDLIDDNTI--GIVGIAGTTELGQVDP 169
Query: 102 LEELGPICQEYNIWLHVDAAYAGSAL-LLPEYAHLKRGLEYVDSFAFNAHKWLLTNHDCS 160
+ EL I E I+LHVDAA+ G + L + + L VDS + HK L
Sbjct: 170 IPELSKIALENGIFLHVDAAFGGFVIPFLDDPPNFDFSLPGVDSITIDPHKMGLAPIPAG 229
Query: 161 AMWVKNANHLTNTFFTDRVYLKH--TDAPMNTQSPDYTVMNWLGKALGLPEEFLNCSKGP 218
+ F D YL D P T T+ G
Sbjct: 230 GI-----------LFRDESYLDALAVDTPYLTSKKQATL---TGTR-------------S 262
Query: 219 GGGVIQHWQTPLSRRFRALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEKDDRFELV 278
G GV + A+ ++ G +G + + + + + A+ +++ FE V
Sbjct: 263 GAGVAATY---------AV-----MKYLGREGYRKVVERCMENTRWLAEELKERG-FEPV 307
Query: 279 CPPSMGLVCFRLKGDNDLTNQLYER 303
P + +V F +++ +L ER
Sbjct: 308 IEPVLNIVAFDDPNPDEVREKLRER 332
>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 = 55.0 bits (133), Expect = 2e-08
Identities = 33/116 (28%), Positives = 51/116 (43%), Gaps = 14/116 (12%)
Query: 42 SVEKSAIIGDVPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDN 101
S EK+A + + +R D++ D + V++ + I +V GTT D+
Sbjct: 118 SFEKAAEMLGLELRYAPLDED--YTVD--VKDVEDLIDDNTI--GIVGIAGTTELGQIDD 171
Query: 102 LEELGPICQEYNIWLHVDAAYAGSALLLP------EYAHLKRGLEYVDSFAFNAHK 151
+EEL I E I+LHVDAA+ G ++P L V S + HK
Sbjct: 172 IEELSKIALENGIYLHVDAAFGG--FVIPFLKKGYNPPPFDFSLPGVQSITIDPHK 225
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 48.5 bits (116), Expect = 3e-06
Identities = 32/113 (28%), Positives = 50/113 (44%), Gaps = 12/113 (10%)
Query: 54 VRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDNLEELGPICQEYN 113
VR + DD+G+L DAL + K L+ L TGT ++E+ + E+
Sbjct: 139 VRVIPLDDDGLLDLDALEKLITPK-TK-LV--ALSHVSNVTGTVN--PVKEIAELAHEHG 192
Query: 114 IWLHVDAAYAGSALLLPEYAHLKRGLEYVDSFAFNAHKWLLTNHDCSAMWVKN 166
+ VDAA A L + ++ D AF+ HKWLL ++V+
Sbjct: 193 ALVLVDAAQAAGHLPID----VQE--LGCDFLAFSGHKWLLGPTGIGVLYVRK 239
>gnl|CDD|224029 COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase
and related enzymes [Amino acid transport and
metabolism].
Length = 386
Score = 46.0 bits (110), Expect = 1e-05
Identities = 42/157 (26%), Positives = 66/157 (42%), Gaps = 39/157 (24%)
Query: 16 TSAGPTVSEND---IKSRLVAYASDQSN-----SSVEKSAIIGDVPVRQLRS-------- 59
TS +E++ IK +AY + Q S++E A++ R L
Sbjct: 67 TSGA---TESNNLAIKGAALAYRNAQKGKHIITSAIEHPAVLN--TCRYLERQGFEVTYL 121
Query: 60 --DDNGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDNLEELGPICQEYNIWLH 117
D NG++ + L A++ D L+ ++ TGT + E+G IC+E I H
Sbjct: 122 PVDSNGLVDLEQLEEALRPDTI--LV--SIMHANNETGTIQ--PIAEIGEICKERGILFH 175
Query: 118 VDAAYAGSALLLPEYAHLKRGLE--YVDSFAFNAHKW 152
VDA A + LE VD +F+AHK+
Sbjct: 176 VDAVQA--------VGKIPIDLEELGVDLLSFSAHKF 204
>gnl|CDD|216367 pfam01212, Beta_elim_lyase, Beta-eliminating lyase.
Length = 288
Score = 44.9 bits (107), Expect = 3e-05
Identities = 31/120 (25%), Positives = 47/120 (39%), Gaps = 16/120 (13%)
Query: 47 AIIGDVPVRQLRSDDNGVLRGDALLTAVKEDLAK-----GLIPCCLVATLGTT-GTC-AF 99
A +G L + G L + L A++ GLI L T + G +
Sbjct: 91 AELGGAQPVPLPGAEAGKLDLEDLEAAIRPVGDIHFPPTGLI--SLENTHNSAGGQVVSL 148
Query: 100 DNLEELGPICQEYNIWLHVDAA---YAGSALLLPEYAHLKRGLEYVDSFAFNAHKWLLTN 156
+ L E+ I +E+ I LH+D A A AL + +K Y DS + + K L
Sbjct: 149 EELREIRAIAREHGIPLHLDGARLANAAVALGVI----VKEITSYADSVSMSLSKGLGAP 204
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 43.5 bits (103), Expect = 1e-04
Identities = 55/322 (17%), Positives = 92/322 (28%), Gaps = 75/322 (23%)
Query: 32 VAYASDQSNSSVEKSAIIGDVPVRQ--LRSDDNGVLRGDALLTAVKEDLA--KGLIPCCL 87
+ S + + V + L S ++ L DAL A+KE K ++
Sbjct: 92 AILVPAPTYPSYIRIFRLAGGEVVRYPLYSSNDFHLDFDALEAALKEATEGNKVVLHTSP 151
Query: 88 VATLGTTGTCAFDNLEELGPICQEYNIWLHVDAAYAGSALLLPEYAHLKRGLEYVDSFAF 147
GT T LE+L + +E+NI L VD AYAG F F
Sbjct: 152 HNPTGTVATLEE--LEKLLDLAKEHNILLLVDEAYAG--------------------FVF 189
Query: 148 NAHKWLLTNHDCSAMWVKNANHLTNTFFTDRVYLKHTDAPMNTQSPDYTVMNWLGKALGL 207
+ R L + S KA GL
Sbjct: 190 GSLD----------------------AVATRALLAEGPNLLVVGS--------FSKAFGL 219
Query: 208 PEE---FLNCSKGPGGGVIQHWQTPLSRRF-------RALKLWMTLRSYGLKGLQAYLRK 257
++ + + L+R F A ++ L+ ++
Sbjct: 220 AGWRVGYILGNA-----AVISQLRKLARPFYSSTHLQAAAAAALSDPLLVASELEEMRQR 274
Query: 258 HISLAKKFADLVEKDDRFELVCPPSMGLVCFRLKGDNDLTNQLYERLMSHKQIYIIKAS- 316
D +E ++ + G D + L + L+ +Y+ S
Sbjct: 275 IKERRDYLRDGLEAAG-LSVLPSQA-GFFLLTG-LDPEAALALAQVLLEEVGVYVTPGSS 331
Query: 317 FQGRPFLRFVVTSPETNQCDVA 338
F G +LR V + +
Sbjct: 332 FGGPGWLRITVAGGTEEELEEL 353
>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 = 41.6 bits (98), Expect = 5e-04
Identities = 28/105 (26%), Positives = 47/105 (44%), Gaps = 21/105 (20%)
Query: 64 VLRGDALLTAVK------EDLAKGLIPCCLVATLGTTGTC----AFDNLEELGPICQEYN 113
VL GD L T V+ E++ I C L +T +C + D++EE+ IC Y+
Sbjct: 181 VLDGDELTTDVEDIERAIEEIGPDNILCVL-----STTSCFAPRSPDDIEEIAKICANYD 235
Query: 114 IWLHVDAAYAGSALLLPEYAH-LKRGLEY--VDSFAFNAHKWLLT 155
I V+ AY L +Y + + ++ VD+ + K +
Sbjct: 236 IPHIVNNAY---GLQSNKYMELINKAIKVGRVDAVVSSTDKNFMV 277
>gnl|CDD|131032 TIGR01977, am_tr_V_EF2568, cysteine desulfurase family protein.
This model describes a subfamily of probable pyridoxal
phosphate-dependent enzymes in the aminotransferase
class V family. Related families contain members active
as cysteine desulfurases, selenocysteine lyases, or
both. The members of this family form a distinct clade
and all are shorter at the N-terminus. The function of
this subfamily is unknown [Unknown function, Enzymes of
unknown specificity].
Length = 376
Score = 38.9 bits (91), Expect = 0.003
Identities = 25/99 (25%), Positives = 46/99 (46%), Gaps = 14/99 (14%)
Query: 57 LRSDDNGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDNLEELGPICQEYNIWL 116
++ D+ G++ + + A+K + +V + + T +EE+G + QE I+
Sbjct: 117 VKCDNEGLISPERIKRAIKTN------TKLIVVSHASNVTGTILPIEEIGELAQENGIFF 170
Query: 117 HVDAA-YAGSALLLPEYAHLKRGLEYVDSFAFNAHKWLL 154
+DAA AG ++P + +D AF HK LL
Sbjct: 171 ILDAAQTAG---VIP----IDMTELAIDMLAFTGHKGLL 202
>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 = 38.4 bits (90), Expect = 0.005
Identities = 32/102 (31%), Positives = 43/102 (42%), Gaps = 20/102 (19%)
Query: 54 VRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLVA-TLGTTGTCAFDNLEELGPICQEY 112
VR + D NG+L DAL + LVA T + T + +EE+G + EY
Sbjct: 116 VRVIPVDPNGLLDLDALEKLLTPR-------TKLVAITHVSNVTGTVNPVEEIGKLAHEY 168
Query: 113 NIWLHVDAAYAGSALLLPEYAHLK---RGLEYVDSFAFNAHK 151
+ VDAA A H + L VD AF+ HK
Sbjct: 169 GALVVVDAAQA--------VGHRPIDVQALG-VDFLAFSGHK 201
>gnl|CDD|224919 COG2008, GLY1, Threonine aldolase [Amino acid transport and
metabolism].
Length = 342
Score = 37.3 bits (87), Expect = 0.008
Identities = 27/100 (27%), Positives = 40/100 (40%), Gaps = 18/100 (18%)
Query: 62 NGVLRGDALLTAVKEDLA----KGLIPCCLVATLGTTGTC-AFDNLEELGPICQEYNIWL 116
+G L + + A++ D L L T GT D LE + +C+E+ + L
Sbjct: 109 DGKLTPEDVEAAIRPDDIHHAPTPLA--VLENTATEGGTVYPLDELEAISAVCKEHGLPL 166
Query: 117 HVDAAYAGSAL-----LLPEYAHLKRGLEYVDSFAFNAHK 151
H+D A +AL L YVDS +F K
Sbjct: 167 HMDGARLANALVALGVALKTIK------SYVDSVSFCLTK 200
>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 = 37.6 bits (87), Expect = 0.009
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 64 VLRGDALLTAVK--EDLAKGLIPCCLVATLGTTGTCAF----DNLEELGPICQEYNIWLH 117
VL GD L+T V E + + ++A L TT +C D ++E+ IC EY++
Sbjct: 131 VLEGDYLITDVNDVETIIEEKGEEVILAVLSTT-SCFAPRSPDRVKEIAKICAEYDVPHL 189
Query: 118 VDAAYA 123
V+ AY
Sbjct: 190 VNGAYG 195
>gnl|CDD|132443 TIGR03402, FeS_nifS, cysteine desulfurase NifS. Members of this
protein family are NifS, one of several related families
of cysteine desulfurase involved in iron-sulfur (FeS)
cluster biosynthesis. NifS is part of the NIF system,
usually associated with other nif genes involved in
nitrogenase expression and nitrogen fixation. The
protein family is given a fairly broad interpretation
here. It includes a clade nearly always found in
extended nitrogen fixation genomic regions, plus a
second clade more closely related to the first than to
IscS and also part of NifS-like/NifU-like systems. This
model does not extend to a more distantly clade found in
the epsilon proteobacteria such as Helicobacter pylori,
also named NifS in the literature, built instead in
TIGR03403.
Length = 379
Score = 33.7 bits (78), Expect = 0.15
Identities = 35/126 (27%), Positives = 51/126 (40%), Gaps = 32/126 (25%)
Query: 16 TSAGPTVSEND---IKSRLVAYASDQSN----SSVEKSAIIG--------DVPVRQLRSD 60
TS G +E+D IKS A + ++VE A++ V L D
Sbjct: 65 TSGG---TESDNTAIKS--ALAAQPEKRHIITTAVEHPAVLSLCQHLEKQGYKVTYLPVD 119
Query: 61 DNGVLRGDALLTAVKEDLAKGLIPCCLVATL---GTTGTCAFDNLEELGPICQEYNIWLH 117
+ G L + L A+ +D A LV+ + TGT +EE+G I +E H
Sbjct: 120 EEGRLDLEELRAAITDDTA-------LVSVMWANNETGTIF--PIEEIGEIAKERGALFH 170
Query: 118 VDAAYA 123
DA A
Sbjct: 171 TDAVQA 176
>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 = 33.1 bits (76), Expect = 0.20
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 11/53 (20%)
Query: 100 DNLEELGPICQEYNIWLHVDA-----AYAGSALLLPEYAHLKRGLEYVDSFAF 147
D L+ + + +E + LH+D A A + L Y VDS +F
Sbjct: 146 DELKAISALAKENGLPLHLDGARLANAAAALGVALKTYK------SGVDSVSF 192
>gnl|CDD|163191 TIGR03235, DNA_S_dndA, cysteine desulfurase DndA. This model
describes DndA, a protein related to IscS and part of a
larger family of cysteine desulfurases. It is encoded,
typically, divergently from a conserved, sparsely
distributed operon for sulfur modification of DNA. This
modification system is designated dnd, after the
phenotype of DNA degradation during electrophoresis. The
system is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndB is described
as a putative ATPase [DNA metabolism,
Restriction/modification].
Length = 353
Score = 31.3 bits (71), Expect = 0.69
Identities = 27/121 (22%), Positives = 48/121 (39%), Gaps = 31/121 (25%)
Query: 12 ILDLTSAGPTVSENDIKSRLVAYASDQSNSSVEKSAIIGDVPVRQLRS----------DD 61
IL L AG + I + S++E A++ P+R L D+
Sbjct: 76 ILGLARAGEQKGKKHIIT-----------SAIEHPAVLE--PIRALERNGFTVTYLPVDE 122
Query: 62 NGVLRGDALLTAVKEDLAKGLIPCCLVATL-GTTGTCAFDNLEELGPICQEYNIWLHVDA 120
+G + D L A++ D LV+ + T + + E+ + + + + HVDA
Sbjct: 123 SGRIDVDELADAIRPDTL-------LVSIMHVNNETGSIQPIREIAEVLEAHEAFFHVDA 175
Query: 121 A 121
A
Sbjct: 176 A 176
>gnl|CDD|184450 PRK14012, PRK14012, cysteine desulfurase; Provisional.
Length = 404
Score = 31.1 bits (71), Expect = 0.85
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 6/50 (12%)
Query: 102 LEELGPICQEYNIWLHVDAAYAGSALLLPEYAHLKRGLEYVDSFAFNAHK 151
+ +G IC+E I HVDAA + + + + + LK VD +F+AHK
Sbjct: 163 IAAIGEICRERGIIFHVDAAQSVGKVPI-DLSKLK-----VDLMSFSAHK 206
>gnl|CDD|181320 PRK08247, PRK08247, cystathionine gamma-synthase; Reviewed.
Length = 366
Score = 31.2 bits (71), Expect = 0.92
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 240 WMTLRSYGLKGLQAYLRKHISLAKKFADLVEKDDRFELVCPPSM-GLVCFRLKGDN 294
W+ +R G+K L +R+H AK A + + V P G++ FRL+ +
Sbjct: 238 WLLIR--GMKTLALRMRQHEENAKAIAAFLNEQPGVTDVLYPGRGGMLSFRLQDEE 291
>gnl|CDD|132444 TIGR03403, nifS_epsilon, cysteine desulfurase, NifS family, epsilon
proteobacteria type. Members of this family are the
NifS-like cysteine desulfurase of the epsilon division
of the Proteobacteria, similar to the NifS protein of
nitrogen-fixing bacteria. Like NifS, and unlike IscS,
this protein is found as part of a system of just two
proteins, a cysteine desulfurase and a scaffold, for
iron-sulfur cluster biosynthesis. This protein is called
NifS by Olsen, et al. (PMID:11123951), so we use this
designation.
Length = 382
Score = 31.0 bits (70), Expect = 0.95
Identities = 27/103 (26%), Positives = 45/103 (43%), Gaps = 16/103 (15%)
Query: 52 VPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLVATL-GTTGTCAFDNLEELGPICQ 110
V V L ++ G + + + A+ E A LV+ + T ++E+G IC+
Sbjct: 115 VEVTYLPINEQGTITAEQVREAITEKTA-------LVSVMWANNETGMIFPIKEIGEICK 167
Query: 111 EYNIWLHVDAAYA-GSALLLPEYAHLKRGLEYVDSFAFNAHKW 152
E + H DA A G + + A VD +F+AHK+
Sbjct: 168 ERGVLFHTDAVQAIGKIPVDVQKAG-------VDFLSFSAHKF 203
>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 = 31.0 bits (71), Expect = 0.98
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 87 LVATLG---TTGTCAFDNLEELGPICQEYNIWLHVDAAYA 123
L+ T G G A L EL + ++Y L VD A++
Sbjct: 135 LIVTEGVYSMDGDIA--PLPELVDLAKKYGAILFVDEAHS 172
>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 = 30.2 bits (69), Expect = 1.5
Identities = 22/82 (26%), Positives = 32/82 (39%), Gaps = 19/82 (23%)
Query: 240 WMTLRSYGLKGLQAYLRKHISLAKKFADLVEKDDRFELVCPPSM---------------- 283
W+ LR GLK L + +H A K A+ +EK + E V P +
Sbjct: 227 WLLLR--GLKTLPLRMERHSENALKVAEFLEKHPKVERVYYPGLPSHPQHELAKKQMSGY 284
Query: 284 -GLVCFRLKGDNDLTNQLYERL 304
G+ F LKG + + L
Sbjct: 285 GGVFSFELKGGLEAAKKFLNAL 306
>gnl|CDD|178257 PLN02651, PLN02651, cysteine desulfurase.
Length = 364
Score = 30.4 bits (69), Expect = 1.6
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 13/73 (17%)
Query: 52 VPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTG-TCAFDNLEELGPICQ 110
+PV +G++ D L A++ D LV+ + +EE+G +C+
Sbjct: 118 LPV-----KSDGLVDLDELAAAIRPD-------TALVSVMAVNNEIGVIQPVEEIGELCR 165
Query: 111 EYNIWLHVDAAYA 123
E + H DAA A
Sbjct: 166 EKKVLFHTDAAQA 178
>gnl|CDD|223513 COG0436, COG0436, Aspartate/tyrosine/aromatic aminotransferase
[Amino acid transport and metabolism].
Length = 393
Score = 29.9 bits (68), Expect = 2.1
Identities = 7/32 (21%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 94 TGTCA-FDNLEELGPICQEYNIWLHVDAAYAG 124
TG + L+ + + +E++I + D Y
Sbjct: 176 TGAVYSKEELKAIVELAREHDIIIISDEIYEE 207
>gnl|CDD|239796 cd04268, ZnMc_MMP_like, Zinc-dependent metalloprotease, MMP_like
subfamily. This group contains matrix metalloproteinases
(MMPs), serralysins, and the astacin_like family of
proteases.
Length = 165
Score = 29.0 bits (65), Expect = 2.3
Identities = 16/65 (24%), Positives = 25/65 (38%)
Query: 147 FNAHKWLLTNHDCSAMWVKNANHLTNTFFTDRVYLKHTDAPMNTQSPDYTVMNWLGKALG 206
++ +W+ N + + LT RVYL + + T + LG ALG
Sbjct: 48 YSVIRWIPYNDGTWSYGPSQVDPLTGEILLARVYLYSSFVEYSGARLRNTAEHELGHALG 107
Query: 207 LPEEF 211
L F
Sbjct: 108 LRHNF 112
>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 = 29.6 bits (67), Expect = 2.5
Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 16/72 (22%)
Query: 60 DDNGVLRGDALLTAVKEDLAKGLI------PCCLVATLGTTGTCA-FDNLEELGPICQEY 112
++ G L LL A K K L P TG + LEEL + +++
Sbjct: 114 EEGGFLLDLELLEAAKTPKTKLLYLNNPNNP---------TGAVLSEEELEELAELAKKH 164
Query: 113 NIWLHVDAAYAG 124
I + D AYA
Sbjct: 165 GILIISDEAYAE 176
>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 = 29.5 bits (67), Expect = 2.7
Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 16/86 (18%)
Query: 68 DALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDNLEELGPICQEYNIWLHVDAAYA-GSA 126
D + A+ K +IP V G C D + + + + + + DAA A G+
Sbjct: 113 DLIEAAITPRT-KAIIP---VHLAGQP--CDMDAIMA---LAKRHGLPVIEDAAQAHGA- 162
Query: 127 LLLPEYAHLKRG-LEYVDSFAFNAHK 151
Y K G + +F+F+A K
Sbjct: 163 ----TYKGKKVGSFGDIGAFSFHATK 184
>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11),
splicing regulatory glutamine/lysine-rich protein 1
(SREK1) and similar proteins. This subfamily
corresponds to the RRM domain of SRSF11 (SRp54 or p54),
SREK1 ( SFRS12 or SRrp86) and similar proteins, a group
of proteins containing regions rich in serine-arginine
dipeptides (SR protein family). These are involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SR proteins have been identified as crucial
regulators of alternative splicing. Different SR
proteins display different substrate specificity, have
distinct functions in alternative splicing of different
pre-mRNAs, and can even negatively regulate splicing.
All SR family members are characterized by the presence
of one or two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and the C-terminal regions
rich in serine and arginine dipeptides (SR domains). The
RRM domain is responsible for RNA binding and
specificity in both alternative and constitutive
splicing. In contrast, SR domains are thought to be
protein-protein interaction domains that are often
interchangeable. .
Length = 76
Score = 27.2 bits (61), Expect = 3.2
Identities = 9/12 (75%), Positives = 9/12 (75%)
Query: 167 ANHLTNTFFTDR 178
A HLTNT F DR
Sbjct: 59 ALHLTNTVFIDR 70
>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 = 29.0 bits (65), Expect = 4.4
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 102 LEELGPICQEYNIWLHVDAAYAGSALLLPEYAHLKRGLEYVDSFAFNAHK 151
+ +G IC+E ++ HVDAA + + + LK VD + + HK
Sbjct: 161 IAAIGEICRERKVFFHVDAAQSVGKIPI-NVNELK-----VDLMSISGHK 204
>gnl|CDD|239463 cd03347, eu_PheOH, Eukaryotic phenylalanine-4-hydroxylase
(eu_PheOH); a member of the biopterin-dependent aromatic
amino acid hydroxylase family of non-heme,
iron(II)-dependent enzymes that also includes
prokaryotic phenylalanine-4-hydroxylase (pro_PheOH),
eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic
tryptophan hydroxylase (TrpOH). PheOH catalyzes the
first and rate-limiting step in the metabolism of the
amino acid L-phenylalanine (L-Phe), the hydroxylation of
L-Phe to L-tyrosine (L-Tyr). It uses
(6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the
physiological electron donor. The catalytic activity of
the tetrameric enzyme is tightly regulated by the
binding of L-Phe and BH4 as well as by phosphorylation.
Mutations in the human enzyme are linked to a severe
variant of phenylketonuria.
Length = 306
Score = 29.0 bits (65), Expect = 4.4
Identities = 30/114 (26%), Positives = 38/114 (33%), Gaps = 30/114 (26%)
Query: 94 TGTCAFDNLEELGPI--CQEYNIWLHVDAAYAGSALLLPEYAHLKRG----LEYVDSFAF 147
T F L+ L P C EYN HV LL + LE V +F
Sbjct: 68 TWGTVFRELKSLYPTHACYEYN---HVFP-------LLEKNCGFSEDNIPQLEDVSNFLQ 117
Query: 148 NAHKW-------LLTNHDCSAMWVKNANHLTNTFFTDRVYLKHTDAPMNTQSPD 194
+ LL++ D A H T Y++H PM T PD
Sbjct: 118 TCTGFRLRPVAGLLSSRDFLAGLAFRVFHSTQ-------YIRHPSKPMYTPEPD 164
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 28.8 bits (65), Expect = 5.0
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 12/58 (20%)
Query: 76 EDLAKGLIPCC-------LVATLG---TTGTCAFDNLEELGPICQEYNIWLHVDAAYA 123
+ L L L+ T G G A L EL + ++Y L+VD A+A
Sbjct: 156 DHLEALLEEARENGARRKLIVTEGVFSMDGDIA--PLPELVELAEKYGALLYVDEAHA 211
>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 = 28.4 bits (64), Expect = 6.4
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 5/45 (11%)
Query: 86 CLVATLGT---TGTCAFDNLEELGPICQEYNIWLHVDAAYAGSAL 127
L+ T G G A L +L + + Y WL VD A+ L
Sbjct: 148 KLIVTDGVFSMDGDIA--PLPQLVALAERYGAWLMVDDAHGTGVL 190
>gnl|CDD|163523 TIGR03811, tyr_de_CO2_Ent, tyrosine decarboxylase, Enterococcus
type. This model represents tyrosine decarboxylases in
the family of the Enterococcus faecalis enzyme Tdc.
These enzymes often are encoded next to
tyrosine/tyramine antiporter, together comprising a
system in which tyrosine decarboxylation can protect
against exposure to acid conditions. This clade differs
from the archaeal tyrosine decarboxylases associated
with methanofuran biosynthesis [Cellular processes,
Adaptations to atypical conditions].
Length = 608
Score = 28.3 bits (63), Expect = 7.1
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 12/87 (13%)
Query: 52 VPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLVATLGTTGTCAFDNLEELGPICQE 111
VPV D N + + L +++ A+ +V +G+T A D ++++ + +
Sbjct: 252 VPV-----DSNYRMDINELEKIIRKLAAEKTPILGVVGVVGSTEEGAVDGIDKIVALRNK 306
Query: 112 YN-----IWLHVDAAYAG--SALLLPE 131
+LHVDAAY G A+ L E
Sbjct: 307 LMKEGIYFYLHVDAAYGGYGRAIFLDE 333
>gnl|CDD|200432 TIGR04181, NHT_00031, aminotransferase, LLPSF_NHT_00031 family.
This clade of aminotransferases is a member of the
pfam01041 (DegT/DnrJ/EryC1/StrS) superfamily. The family
is named after the instance in Leptospira interrogans
serovar Lai, str. 56601, where it is the 31st gene in
the 91-gene lipopolysaccharide biosynthesis locus.
Members of this family are generally found within a
subcluster of seven or more genes including an
epimerase/dehydratase, four genes homologous to the
elements of the neuraminic (sialic) acid biosynthesis
cluster (NeuABCD) and a nucleotidyl transferase.
Together it is very likely that these enzymes direct the
biosynthesis of a nine-carbon sugar analogous to
CMP-neuraminic acid. These seven genes form the core of
the cassette, although they are often accompanied by
additional genes that may further modify the product
sugar.
Length = 359
Score = 28.3 bits (64), Expect = 7.3
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 18/82 (21%)
Query: 102 LEELGPICQEYNIWLHVDAAYA-GSALLLPEYAHLKRG-LEYVDSFAFNAHK-------- 151
++E+ IC E+N+ + DAA + GS Y G + F+FN +K
Sbjct: 150 MDEIMEICDEWNLPVVEDAAESLGS-----FYKGKHTGTFGDLGVFSFNGNKIITTGGGG 204
Query: 152 WLLTNHDCSAMWVKNANHLTNT 173
+LTN + K A HL+ T
Sbjct: 205 MILTNDE---ELAKRAKHLSTT 223
>gnl|CDD|199862 cd06238, M14-like_1_1, Peptidase M14-like domain; uncharacterized
subgroup. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by an N-terminal pro-region linked to the enzyme; these
proenzymes are called procarboxypeptidases. The A/B
enzymes can be further divided based on their substrate
specificity; Carboxypeptidase A-like (CPA-like) enzymes
favor hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavage.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 270
Score = 28.0 bits (63), Expect = 8.2
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 316 SFQGRPFLRFVVTSPET 332
+++GRP L V+TS E
Sbjct: 4 TYEGRPLLYAVITSAEN 20
>gnl|CDD|237314 PRK13238, tnaA, tryptophanase/L-cysteine desulfhydrase,
PLP-dependent; Provisional.
Length = 460
Score = 28.2 bits (64), Expect = 8.7
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 11/62 (17%)
Query: 101 NLEELGPICQEYNIWLHVDAA-YAGSALLL----PEYAHL------KRGLEYVDSFAFNA 149
NL + I ++Y I + +DAA +A +A + P Y + Y D +A
Sbjct: 199 NLRAVYEIAKKYGIPVVIDAARFAENAYFIKQREPGYKDKSIKEIAREMFSYADGLTMSA 258
Query: 150 HK 151
K
Sbjct: 259 KK 260
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 0.134 0.409
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,510,043
Number of extensions: 1762094
Number of successful extensions: 1408
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1388
Number of HSP's successfully gapped: 58
Length of query: 367
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 269
Effective length of database: 6,590,910
Effective search space: 1772954790
Effective search space used: 1772954790
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: 60 (26.8 bits)