RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 010125
(517 letters)
>gnl|CDD|215475 PLN02880, PLN02880, tyrosine decarboxylase.
Length = 490
Score = 700 bits (1809), Expect = 0.0
Identities = 291/493 (59%), Positives = 376/493 (76%), Gaps = 15/493 (3%)
Query: 14 SGSFTNPLDSEEFRRQGHMIIDFIADYYKNVEKYPVRSQVEPGYLQKVLPESAPNNPESM 73
+ P+D+E+ R GH ++DFIADYYK++E +PV SQV+PGYL+++LP+SAPN PE++
Sbjct: 3 GEEWLRPMDAEQLRECGHRMVDFIADYYKSIENFPVLSQVQPGYLRELLPDSAPNQPETL 62
Query: 74 ETILQDVQQHIVPGITHWQSPNYFAYFPSSGSIAGFLGEMLSSGFNIVGFNWISSPAATE 133
+ +L DVQ I+PG+THWQSPNYFAY+PS+ S+AGFLGEMLS+G NIVGF+WI+SPAATE
Sbjct: 63 DQVLDDVQAKILPGVTHWQSPNYFAYYPSNSSVAGFLGEMLSAGLNIVGFSWITSPAATE 122
Query: 134 LENIVMDWLGQMLKLPKSFLFSGNGGGVIQGTTCEAILCTLTAARDRVLNKIGRENISKL 193
LE IV+DWL ++L LP+ FL +GNGGGVIQGT EA+L L AARDRVL K+G+ + KL
Sbjct: 123 LEMIVLDWLAKLLNLPEQFLSTGNGGGVIQGTASEAVLVVLLAARDRVLRKVGKNALEKL 182
Query: 194 IVYGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDVEVGLIPLF 253
+VY SDQTH ALQKA QI GI +N R +KT S++Y L+P+ L I++D+ GLIP F
Sbjct: 183 VVYASDQTHSALQKACQIAGIHPENCRLLKTDSSTNYALAPELLSEAISTDLSSGLIPFF 242
Query: 254 LCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACICPEFRHFIDGVEGADSFS 313
LCAT+GTT+ TAVDPL L +AK G+W HVDAAYAGSACICPE+RH+IDGVE ADSF+
Sbjct: 243 LCATVGTTSSTAVDPLLELGKIAKSNGMWFHVDAAYAGSACICPEYRHYIDGVEEADSFN 302
Query: 314 LNAHKWFFATLDCCCLWVKDPRALVSSLSTNPEYLKNKATESMQVVDYKDWQITLSRRFR 373
+NAHKWF DC LWVKD AL+ SLSTNPE+LKNKA+++ VVDYKDWQI L RRFR
Sbjct: 303 MNAHKWFLTNFDCSLLWVKDRNALIQSLSTNPEFLKNKASQANSVVDYKDWQIPLGRRFR 362
Query: 374 SLKLWFVIRNYGVANLRHFLRSHVNMAKLFERLVSGDKRFEIVFPCHFAVVCFRVSPSPV 433
SLKLW V+R YGV NL+ ++R+H+ +AK FE+LV+ D RFE+V P F++VCFR+ P
Sbjct: 363 SLKLWMVLRLYGVENLQSYIRNHIKLAKEFEQLVAQDSRFEVVTPRIFSLVCFRLVP--- 419
Query: 434 LMDKLKTKYVNCLLSEEEQINEFNRELLESINASGKAYMTHAVLGGIYAIRFATGATLTE 493
+ E+ N+ N +LL+++N+SGK +++H VL G Y +RFA GA LTE
Sbjct: 420 ------------PKNNEDNGNKLNHDLLDAVNSSGKIFISHTVLSGKYVLRFAVGAPLTE 467
Query: 494 KRHVVVAWTVVQQ 506
+RHV AW V+Q
Sbjct: 468 ERHVTAAWKVLQD 480
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 609 bits (1572), Expect = 0.0
Identities = 277/496 (55%), Positives = 374/496 (75%), Gaps = 19/496 (3%)
Query: 20 PLDSEEFRRQGHMIIDFIADYYKNVEK----YPVRSQVEPGYLQKVLPESAPNNPESMET 75
P+DSE R QGH+++DFIADYYKN++ +PV SQV+PGYL+ +LP+SAP PES++
Sbjct: 53 PMDSELLREQGHIMVDFIADYYKNLQDSPQDFPVLSQVQPGYLRDMLPDSAPERPESLKE 112
Query: 76 ILQDVQQHIVPGITHWQSPNYFAYFPSSGSIAGFLGEMLSSGFNIVGFNWISSPAATELE 135
+L DV + I+PGITHWQSP+YFAY+ SS S+AGFLGEML++G ++VGF W++SPAATELE
Sbjct: 113 LLDDVSKKIMPGITHWQSPSYFAYYASSTSVAGFLGEMLNAGLSVVGFTWLTSPAATELE 172
Query: 136 NIVMDWLGQMLKLPKSFLFSGNGGGVIQGTTCEAILCTLTAARDRVLNKIGRENISKLIV 195
IV+DWL ++L+LP FL +GNGGGVIQGT CEA+L + AARDR+L K+G+ + +L+V
Sbjct: 173 IIVLDWLAKLLQLPDHFLSTGNGGGVIQGTGCEAVLVVVLAARDRILKKVGKTLLPQLVV 232
Query: 196 YGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDVEVGLIPLFLC 255
YGSDQTH + +KA I GI +N R +KT S++YG+ P+SL I+ D+ G IP F+C
Sbjct: 233 YGSDQTHSSFRKACLIGGIHEENIRLLKTDSSTNYGMPPESLEEAISHDLAKGFIPFFIC 292
Query: 256 ATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACICPEFRHFIDGVEGADSFSLN 315
AT+GTT+ AVDPL PL ++AK++GIW+HVDAAYAG+ACICPE+R FIDG+E ADSF++N
Sbjct: 293 ATVGTTSSAAVDPLVPLGNIAKKYGIWLHVDAAYAGNACICPEYRKFIDGIENADSFNMN 352
Query: 316 AHKWFFATLDCCCLWVKDPRALVSSLSTNPEYLKNKATESMQVVDYKDWQITLSRRFRSL 375
AHKW FA C LWVKD +L+ +L TNPEYL+ K ++ VV+YKDWQI+LSRRFRSL
Sbjct: 353 AHKWLFANQTCSPLWVKDRYSLIDALKTNPEYLEFKVSKKDTVVNYKDWQISLSRRFRSL 412
Query: 376 KLWFVIRNYGVANLRHFLRSHVNMAKLFERLVSGDKRFEIVFPCHFAVVCFRVSPSPVLM 435
KLW V+R YG NLR+F+R HVN+AK FE V+ D FE+V +F++VCFR++P
Sbjct: 413 KLWMVLRLYGSENLRNFIRDHVNLAKHFEDYVAQDPSFEVVTTRYFSLVCFRLAP----- 467
Query: 436 DKLKTKYVNCLLSEEEQINEFNRELLESINASGKAYMTHAVLGGIYAIRFATGATLTEKR 495
+ +E+Q NE NRELL ++N++GK +++H L G + +RFA GA LTE++
Sbjct: 468 ----------VDGDEDQCNERNRELLAAVNSTGKIFISHTALSGKFVLRFAVGAPLTEEK 517
Query: 496 HVVVAWTVVQQHLEAF 511
HV AW ++Q+H F
Sbjct: 518 HVTEAWQIIQKHASKF 533
>gnl|CDD|215836 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase
conserved domain.
Length = 373
Score = 497 bits (1282), Expect = e-175
Identities = 195/376 (51%), Positives = 251/376 (66%), Gaps = 8/376 (2%)
Query: 55 PGYLQKVLPESAPNNPESMETILQDVQQHIVPGITHWQSPNYFAYFPSSGSIAGFLGEML 114
PGYL+ +LPE+AP PE + IL D++++I+PG+T W SPN+ AYFP+ S LG+ML
Sbjct: 1 PGYLRPLLPEAAPIIPEPLLDILGDIRKNIMPGVTTWHSPNFHAYFPAGNSYPSLLGDML 60
Query: 115 SSGFNIVGFNWISSPAATELENIVMDWLGQMLKLPKSFLFSGNGGGVIQGTTCEAILCTL 174
S N GF W SSPA TELEN+VMDWL +ML LPK FL SG GGGV+QG + E+ L L
Sbjct: 61 SDAINCNGFTWESSPACTELENVVMDWLAKMLGLPKEFLGSGEGGGVLQGGSSESNLLAL 120
Query: 175 TAARDRVLNKI---GRENISKLIVYGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYG 231
AAR + + ++ G+ ++ KL+ Y SDQ H +++KAA I G++ R I T ++
Sbjct: 121 LAARTKWIRRMKAAGKPSLGKLVAYTSDQAHSSIEKAALIAGVE---LREIPTDEN--GK 175
Query: 232 LSPDSLMAQINSDVEVGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAG 291
+ L I D E GLIP F+CAT+GTT A DPL+ L D+ ++ +W+HVDAAYAG
Sbjct: 176 MRGMDLEKAIEEDKENGLIPFFVCATLGTTGSGAFDPLQELGDICNKYDLWLHVDAAYAG 235
Query: 292 SACICPEFRHFIDGVEGADSFSLNAHKWFFATLDCCCLWVKDPRALVSSLSTNPEYLKNK 351
SA ICPEFRH++ G+E ADSFS N HKW LDC LWV+D AL +L NPEYL +
Sbjct: 236 SAFICPEFRHWLFGIERADSFSFNPHKWMLVLLDCSALWVRDKGALQQALQFNPEYLGHN 295
Query: 352 ATESMQVVDYKDWQITLSRRFRSLKLWFVIRNYGVANLRHFLRSHVNMAKLFERLVSGDK 411
+S VDY DWQI LSRRFR LKLWFV+R+YGV L++ +R HV +AK FE LV D
Sbjct: 296 DKQSDVAVDYGDWQIPLSRRFRILKLWFVLRSYGVEGLQNQIRRHVELAKYFEALVRKDS 355
Query: 412 RFEIVFPCHFAVVCFR 427
RFEI +VCFR
Sbjct: 356 RFEICAERGLGLVCFR 371
>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 = 327 bits (840), Expect = e-109
Identities = 119/415 (28%), Positives = 187/415 (45%), Gaps = 73/415 (17%)
Query: 96 YFAYFPSSGSIAGFLGEMLSSGFNIVGFNWISSPAATELENIVMDWLGQMLKLPKSFLFS 155
+ A F ++ L EML+S N + F W SPAATE+E V++WL ++ LP S
Sbjct: 1 FLAGFVTTMDPPALLLEMLTSAKNAIDFTWDESPAATEMEAEVVNWLAKLFGLP-----S 55
Query: 156 GNGGGVIQGTTCEAILCTLTAARDRVLNK---IGRENISKLIVYGSDQTHCALQKAAQIV 212
+ GV E+ L L AARDR + G I KL++ SDQ H +++KAA +
Sbjct: 56 EDADGVFTSGGSESNLLALLAARDRARKRLKAGGGRGIDKLVIVCSDQAHVSVEKAAAYL 115
Query: 213 GIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDVEVGLIPLFLCATIGTTAITAVDPLKPL 272
+ V R + + + P++L A I+ D GL P+ + AT GTT A+DPL+ +
Sbjct: 116 DVKV---RLVPVDEDGR--MDPEALEAAIDEDKAEGLNPIMVVATAGTTDTGAIDPLEEI 170
Query: 273 CDVAKQFGIWVHVDAAYAGSACICPEFRHFIDGVEGADSFSLNAHKWFFATLDCCCLWVK 332
D+A+++ +W+HVDAAY G PE RH G+E DS S++ HK+ L C + V
Sbjct: 171 ADLAEKYDLWLHVDAAYGGFLLPFPEPRHLDFGIERVDSISVDPHKYGLVPLGCSAVLV- 229
Query: 333 DPRALVSSLSTNPEYLKNKATESMQVVDYKDWQITLSRRFRSLKLWFVIRNYGVANLRHF 392
R+LKLW +R +G
Sbjct: 230 ----------------------------------------RALKLWATLRRFGRDGYGEH 249
Query: 393 LRSHVNMAKLFERLVSGDKRFEIVFPCHFAVVCFRVSPSPVLMDKLKTKYVNCLLSEEEQ 452
+ V++AK L+ D FE++ + ++VCFR+ PS +
Sbjct: 250 IDRIVDLAKYLAELIRADPGFELLGEPNLSLVCFRLKPS-------------------VK 290
Query: 453 INEFNRELLESINASGKAYMTHAVLGGIYAIRFATGATLTEKRHVVVAWTVVQQH 507
++E N +L + +N G ++ LGG +RF LT + +++
Sbjct: 291 LDELNYDLSDRLNERGGWHVPATTLGGPNVLRFVVTNPLTTRDDADALLEDIERA 345
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 220 bits (563), Expect = 4e-66
Identities = 109/469 (23%), Positives = 184/469 (39%), Gaps = 39/469 (8%)
Query: 34 IDFIADYYKNVEKYPVRSQVEPGYLQKVLPESAPNNPESMETILQDVQ-QHIVPGITHWQ 92
ID + D K + P + AP E +E +L ++ I +
Sbjct: 1 IDGLIDKDMLNSKRYSGDSLSPLFGALSDSRMAPEKGEPLEEVLDELAELLIKDELYLDG 60
Query: 93 SPNYFAYFPSSGSIAGFLGEMLSSGFNIVGFNWISSPAATELENIVMDWLGQMLKLPKSF 152
P + E+L S N + SPAA ELE V++ L +L P+
Sbjct: 61 HPRANLAGFCPTRVPPVAAELLVSALNKNLGDPDESPAAAELEERVVNMLSDLLGAPEEA 120
Query: 153 LFSGNGGGVIQGTTCEAILCTLTAARDRVLNKIGRENI---SKLIVYGSDQTHCALQKAA 209
G G T EA L L AAR+R + E+ K + S+ H + +KAA
Sbjct: 121 S-----GTFTSGGT-EANLLALLAARERWRKRALAESGKPGGKPNIVCSETAHFSFEKAA 174
Query: 210 QIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDVEVGLIPLFLCATIGTTAITAVDPL 269
+ +G+ ++ + T Y + D+L I+ + I + T GTT ++D +
Sbjct: 175 RYLGLGLRRVPTVPTD----YRIDVDALEEAIDEN----TIGGVVVGTAGTTDTGSIDDI 226
Query: 270 KPLCDVAKQFGIWVHVDAAYAGSACICPEFRH-FIDGVEGADSFSLNAHKWFFATLDCCC 328
+ L D+A+++GIW+HVDAA+ G E + G+EG DS +++ HK+ A + C
Sbjct: 227 EELADIAEEYGIWLHVDAAFGGFLLPFLEPDGRWDFGLEGVDSITVDGHKYGLAPIGCGV 286
Query: 329 LWVKDPRALVSSLSTNPEYLKNKATESMQVVDYKDWQITLSRR-FRSLKLWFVIRNYGVA 387
+ +D AL L YL + I SR ++L L+ +R G
Sbjct: 287 VLFRDEEALRRILIFADYYLPGGGIPNF--------TILGSRPGRQALALYANLRRLGRE 338
Query: 388 NLRHFLRSHVNMAKLFERLVSGDKRFEIVFPCHFAVVCFRVSPSPVLMDKLKTKYVNCLL 447
R L + +A+ + FE+V +V FR+ + L
Sbjct: 339 GYRKLLDRTLELARYLAEELEKLGDFELVNEPELPIVAFRLKDD-----------EDTLA 387
Query: 448 SEEEQINEFNRELLESINASGKAYMTHAVLGGIYAIRFATGATLTEKRH 496
E+++ ++ + G A + + G ++F L R
Sbjct: 388 DLSERLDRRGWQVPAQLLPKGLAIVFGTHVTGRQGLKFIVANLLITDRE 436
>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 = 94.8 bits (236), Expect = 1e-20
Identities = 97/344 (28%), Positives = 159/344 (46%), Gaps = 48/344 (13%)
Query: 35 DFIADYYKNVEKYPVRSQVEPGYLQKVLPESAPNNPESMETILQDVQQHIVPGITHWQSP 94
F+ ++ +EK P+ S++E + +PE E + +L + H V H SP
Sbjct: 37 GFLQEHIVAIEK-PL-SEIEKDFSSAEIPEQPTFVSEHTQFLLDKLVAHSV----HTASP 90
Query: 95 NYFAYFPSSGSIAGFLGEMLSSGFNIVGFNW-----ISSPAATELENIVMDWLGQMLKLP 149
++ + S+ + F ML +V N +S A T LE V LG M L
Sbjct: 91 SFIGHMTSA--LPYF---MLPLSKLMVALNQNLVKIETSKAFTPLERQV---LGMMHHLV 142
Query: 150 --------KSFLFSGNG--GGVIQGTTCEAILCTLTAARDRVL------NKIGRENISK- 192
+ ++ S + G G T A + L AR+R+L + RE +
Sbjct: 143 YGQDDDFYRKWMHSADHSLGAFCSGGTV-ANITALWVARNRLLKADGDFKGVAREGLFAA 201
Query: 193 LIVYG--------SDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSD 244
L YG S++ H +L KAA ++GI N AIKT ++ + D+L +
Sbjct: 202 LKHYGYDGLAILVSERGHYSLGKAADVLGIGRDNLIAIKTDANNR--IDVDALRDKCAEL 259
Query: 245 VEVGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACICPEFRHFID 304
E + PL + GTT +DPL + D+A++ G HVDAA+ G+ + +RH +
Sbjct: 260 AEQNIKPLAIVGVAGTTETGNIDPLDEMADIAQELGCHFHVDAAWGGATLLSNTYRHLLK 319
Query: 305 GVEGADSFSLNAHKWFFATLDCCCLWVKDPRALVSSLSTNPEYL 348
G+E ADS +++AHK + + + KDP AL+S++ + EY+
Sbjct: 320 GIERADSVTIDAHKQLYVPMGAGMVLFKDP-ALMSAIEHHAEYI 362
>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 = 76.2 bits (188), Expect = 5e-15
Identities = 72/320 (22%), Positives = 129/320 (40%), Gaps = 44/320 (13%)
Query: 129 PAATELENIVMDWLGQMLKLPKSFLFSGNGGGVIQGTTCEAILCTLTAARDRVLNKIGRE 188
P ++E V+ LG +L LP ++ G ++ G T EA + + AA++ L + +
Sbjct: 55 PGTKKIEEEVVGSLGNLLHLPDAY------GYIVSGGT-EANIQAVRAAKN--LAREEKR 105
Query: 189 NISKLIVYGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDVEVG 248
+IV S H + +KAA+++G+++ Y + + I D +G
Sbjct: 106 T-PNIIVPES--AHFSFEKAAEMLGLEL-----RYAPLDEDYTVDVKDVEDLI-DDNTIG 156
Query: 249 LIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGS----ACICPEFRHFID 304
++ GTT + +D ++ L +A + GI++HVDAA+ G F
Sbjct: 157 IV-----GIAGTTELGQIDDIEELSKIALENGIYLHVDAAFGGFVIPFLKKGYNPPPFDF 211
Query: 305 GVEGADSFSLNAHKWFFATLDCCCLWVKDPRALVSSLSTNPEYLKNKATESMQVVDYKDW 364
+ G S +++ HK + + + + L LS + YL T Q
Sbjct: 212 SLPGVQSITIDPHKMGLSPIPAGGILFRSKSYL-KYLSVDAPYL----TVKKQAT----- 261
Query: 365 QITLSRR-FRSLKLWFVIRNYGVANLRHFLRSHVNMAKLFERLVSGDKR--FEIVFPCHF 421
IT +R + + VI+ G R + + LV K+ FE V
Sbjct: 262 -ITGTRSGASAAATYAVIKYLGREGYRKIVAECMENT---RYLVEELKKIGFEPVIEPVL 317
Query: 422 AVVCFRVSPSPVLMDKLKTK 441
+V F V + KL+ +
Sbjct: 318 NIVAFEVDDPEEVRKKLRDR 337
>gnl|CDD|235068 PRK02769, PRK02769, histidine decarboxylase; Provisional.
Length = 380
Score = 72.0 bits (177), Expect = 1e-13
Identities = 80/334 (23%), Positives = 144/334 (43%), Gaps = 68/334 (20%)
Query: 110 LGEMLSSGFNIVGFNWISSP----AATELENIVMDWLGQMLKLP--KSFLFSGNGGGVIQ 163
L S N G + S + + E VM++ ++ K+P +S+ + NGG
Sbjct: 39 LKRFFSFSINNCG-DPYSKSNYPLNSFDFERDVMNFFAELFKIPFNESWGYITNGG---- 93
Query: 164 GTTCEAILCTLTAARDRVLNKIGRENISKLIVYGSDQTHCALQKAAQIVGIDVKNFRAIK 223
E L AR+ + +Y S TH ++ K A+++ I +
Sbjct: 94 ---TEGNLYGCYLARELFPDGT---------LYYSKDTHYSVSKIARLLRIKSR-----V 136
Query: 224 TTKSSSYGLSPDSLMAQINSDVEVGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFGI-- 281
T + + D L+++I + P + A IGTT A+D +K + ++ K+ GI
Sbjct: 137 ITSLPNGEIDYDDLISKIKENKNQ---PPIIFANIGTTMTGAIDNIKEIQEILKKIGIDD 193
Query: 282 -WVHVDAAYAGSACICPEFRHFIDGV------EGADSFSLNAHKWFFATLDCCCLWVKDP 334
++H DAA +G I P F++ +G DS +++ HK+ + + C + K
Sbjct: 194 YYIHADAALSGM--ILP----FVNNPPPFSFADGIDSIAISGHKFIGSPMPCGIVLAK-- 245
Query: 335 RALVSSLSTNPEYLKNKATESMQVVDYKDWQITLSRR-FRSLKLWFVIRNYGVANLRHFL 393
+ V +S + +Y + +D I+ SR +L LW IR+ G LR +
Sbjct: 246 KKYVERISVDVDY-----------IGSRDQTISGSRNGHTALLLWAAIRSLGSKGLRQRV 294
Query: 394 RSHVNMAK-LFERL-VSGDKRFE------IVFPC 419
+ ++MA+ +RL +G + +VFPC
Sbjct: 295 QHCLDMAQYAVDRLQANGIPAWRNPNSITVVFPC 328
>gnl|CDD|237409 PRK13520, PRK13520, L-tyrosine decarboxylase; Provisional.
Length = 371
Score = 68.4 bits (168), Expect = 2e-12
Identities = 58/223 (26%), Positives = 104/223 (46%), Gaps = 31/223 (13%)
Query: 129 PAATELENIVMDWLGQMLKLPKSFLFSGNGGGVIQGTTCEAILCTLTAARDRVLNKIGRE 188
P +LE ++ LG++L LP ++ G + G T EA + + AAR+ K +
Sbjct: 55 PGTAKLEEEAVEMLGELLHLPDAY------GYITSGGT-EANIQAVRAARNLA--KAEKP 105
Query: 189 NISKLIVYGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDVEVG 248
NI +V S H + KAA ++G+++ R Y + ++ I+ + +G
Sbjct: 106 NI---VVPES--AHFSFDKAADMLGVEL---RRAPLDDD--YRVDVKAVEDLIDDNT-IG 154
Query: 249 LIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACICPEFRHFID---G 305
++ GTT + VDP+ L +A + GI++HVDAA+ G + P +
Sbjct: 155 IV-----GIAGTTELGQVDPIPELSKIALENGIFLHVDAAFGG--FVIPFLDDPPNFDFS 207
Query: 306 VEGADSFSLNAHKWFFATLDCCCLWVKDPRALVSSLSTNPEYL 348
+ G DS +++ HK A + + +D L +L+ + YL
Sbjct: 208 LPGVDSITIDPHKMGLAPIPAGGILFRDESYL-DALAVDTPYL 249
>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 = 53.5 bits (129), Expect = 2e-08
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 239 AQINSDVEVGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACICPE 298
I +++ + T TT+ + PLK + +AK++GI + VDAA AG A P
Sbjct: 81 VAILEELKAKPNVALIVITPNTTSGGVLVPLKEIRKIAKEYGILLLVDAASAGGASPAPG 140
Query: 299 FRHFIDGVEGADSFSLNAHKWF 320
GAD + + HK
Sbjct: 141 VL---IPEGGADVVTFSLHKNL 159
>gnl|CDD|166673 PLN03032, PLN03032, serine decarboxylase; Provisional.
Length = 374
Score = 50.6 bits (121), Expect = 1e-06
Identities = 58/244 (23%), Positives = 95/244 (38%), Gaps = 49/244 (20%)
Query: 185 IGRENISKLIVYGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQIN-S 243
+GRE I+Y S ++H ++ KAA++ ++ P +I+
Sbjct: 104 VGREVFPDGILYASRESHYSVFKAARMYRMEAVKV--------------PTLPSGEIDYD 149
Query: 244 DVEVGLI-----PLFLCATIGTTAITAVDPLKPLCDVAKQFGI-----WVHVDAAYAGSA 293
D+E L P L IGTT AVD L + + K+ G ++H D A G
Sbjct: 150 DLERALAKNRDKPAILNVNIGTTVKGAVDDLDRILRILKELGYTEDRFYIHCDGALFGLM 209
Query: 294 CICPEFRHFIDGVEGADSFSLNAHKWFFATLDCCCLWVKDPRALVSSLSTNPEYLKNKAT 353
+ + S S++ HK+ + C + + V +LS N EYL +
Sbjct: 210 MPFVSRAPEVTFRKPIGSVSVSGHKFLGCPMPCGVALTR--KKHVKALSQNVEYLNS--- 264
Query: 354 ESMQVVDYKDWQITLSRRFRS-LKLWFVIRNYGVANLR----------HFLRSHVNMAKL 402
+D I SR + L LW+ +R G ++ H+L+ + A L
Sbjct: 265 --------RDATIMGSRNGHAPLYLWYTLRRKGYRGIKRDVQHCMRNAHYLKDRLTEAGL 316
Query: 403 FERL 406
RL
Sbjct: 317 TCRL 320
>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 = 44.8 bits (106), Expect = 9e-05
Identities = 72/327 (22%), Positives = 127/327 (38%), Gaps = 77/327 (23%)
Query: 36 FIADYYKNVEKYP------VRSQVEPGYLQKVLPESAP-------NNPE------SMETI 76
FI D +N + Y V + G+ Q +P+ P + +M+ +
Sbjct: 8 FIGDKAENGQLYKDLLNKLVDEHL--GWRQNYMPQDKPVISPQERTSKSFTKTVNNMKDV 65
Query: 77 LQDVQQHIVPGITHWQSPN-YFAYFPSSG---SIAGFLGEMLSSGFNIVGFNWISSPAAT 132
L ++ + W S Y+ + S +I + ML +G N+ + SSPA +
Sbjct: 66 LDELSSRLRTESVPWHSAGRYWGHMNSETLMPAILAYNYAMLWNGNNVA---YESSPATS 122
Query: 133 ELE------------------NIVMD---------WLGQMLK-LP------KSFLFSGNG 158
++E +IV D W + +K LP K L +G
Sbjct: 123 QMEEEVGKEFATLMGYKNGWGHIVADGSLANLEGLWYARNIKSLPFAMKEVKPELVAGKS 182
Query: 159 GGVIQGTTCEAILCTLTAARDRVLNKI------GRENISKLIVYGSDQT-HCALQKAAQI 211
+ + I+ L +A D++ ++I +++ KL + QT H + KAA I
Sbjct: 183 DWELLNMPTKEIMDLLESAGDQI-DEIKAHSARSGKDLQKLGKWLVPQTKHYSWLKAADI 241
Query: 212 VGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDVEVGLIPLFLCATIGTTAITAVDPLKP 271
+GI + + I S+Y + + L I L + +G+T AVD +
Sbjct: 242 IGIGLD--QVIPVPVDSNYRMDINELEKIIRKLAAEKTPILGVVGVVGSTEEGAVDGIDK 299
Query: 272 LCDVAKQF---GIW--VHVDAAYAGSA 293
+ + + GI+ +HVDAAY G
Sbjct: 300 IVALRNKLMKEGIYFYLHVDAAYGGYG 326
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 39.2 bits (92), Expect = 0.004
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 10/68 (14%)
Query: 268 PLKPLCDVAKQFGIWVHVDAAYAGSACICPEFRHF-ID-GVEGADSFSLNAHKWFFATLD 325
P+K + ++A + G V VDAA A H ID G D + + HKW
Sbjct: 180 PVKEIAELAHEHGALVLVDAAQA--------AGHLPIDVQELGCDFLAFSGHKWLLGPTG 231
Query: 326 CCCLWVKD 333
L+V+
Sbjct: 232 IGVLYVRK 239
>gnl|CDD|233664 TIGR01976, am_tr_V_VC1184, cysteine desulfurase family protein,
VC1184 subfamily. This model describes a subfamily of
probable pyridoxal phosphate-dependent enzymes in the
aminotransferase class V family (pfam00266). The most
closely related characterized proteins are active as
cysteine desulfurases, selenocysteine lyases, or both;
some are involved in FeS cofactor biosynthesis and are
designated NifS. An active site Cys residue present in
those sequences, in motifs resembling GHHC or GSAC, is
not found in this family. The function of members of
this family is unknown, but seems unlike to be as an
aminotransferase [Unknown function, Enzymes of unknown
specificity].
Length = 397
Score = 35.9 bits (83), Expect = 0.041
Identities = 28/116 (24%), Positives = 44/116 (37%), Gaps = 18/116 (15%)
Query: 206 QKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDVEVGLIPLFLCATIGTTAITA 265
+AA+ G VK R ++ L PD L + ++ L T +
Sbjct: 122 LQAAERAGAKVKWARV----DEATGELHPDDLASLLSPRTR-----LVAVTAASNTLGSI 172
Query: 266 VDPLKPLCDVAKQFGIWVHVDAAYAGSACICPEFRHFIDGVE-GADSFSLNAHKWF 320
VD L + ++ G V VDA + ID GAD + +A+K+F
Sbjct: 173 VD-LAAITELVHAAGALVVVDAVHYAP-------HGLIDVQATGADFLTCSAYKFF 220
>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 = 35.8 bits (83), Expect = 0.050
Identities = 52/252 (20%), Positives = 92/252 (36%), Gaps = 55/252 (21%)
Query: 124 NWISS---PAATELENIVMDWLGQMLKLPKSFLFSGNGG-----GVIQGTTCEAILCTLT 175
N I P E+EN ++ L L+ G + EAI+
Sbjct: 68 NMIDKDEYPQTAEIENRCVNMLAD--------LWHAPAKDAEAVGTSTIGSSEAIMLGGL 119
Query: 176 AARDRVLNKI---GRENISKLIVYGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYGL 232
A + R ++ G+ +V GS+ +K A+ +++ R + Y +
Sbjct: 120 AMKWRWRKRMEAAGKPTDKPNLVMGSN-VQVCWEKFARYFDVEL---REVPMDPGR-YVI 174
Query: 233 SPDSLMAQINSDVEVGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFG------IWVHVD 286
P+ ++ ++ + +G+ +GTT + +K L D ++ I +HVD
Sbjct: 175 DPEQVVEAVDENT-IGV-----VCILGTTYTGEYEDVKALNDALDEYNAKTGWDIPIHVD 228
Query: 287 AAYAGSACICP--------EFRHFIDGVEGADSFSLNAHKWFFATLDCCCLWV--KDPRA 336
AA G I P +FR S +++ HK+ WV +D A
Sbjct: 229 AASGG--FIAPFVYPDLEWDFRL-----PRVKSINVSGHKYGLVYPGVG--WVIWRDEEA 279
Query: 337 LVSSLSTNPEYL 348
L L + YL
Sbjct: 280 LPEELIFHVNYL 291
>gnl|CDD|177904 PLN02263, PLN02263, serine decarboxylase.
Length = 470
Score = 35.6 bits (82), Expect = 0.065
Identities = 43/187 (22%), Positives = 79/187 (42%), Gaps = 45/187 (24%)
Query: 185 IGRENISKLIVYGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMA-QIN- 242
+GRE I+Y S ++H ++ KAA++ ++ D+L++ +I+
Sbjct: 171 VGREVFPDGILYASRESHYSVFKAARMYRMECVKV---------------DTLVSGEIDC 215
Query: 243 SDVEVGLI-----PLFLCATIGTTAITAVDPLKPLCDVAKQFG-----IWVHVDAAYAGS 292
+D + L+ P + IGTT AVD L + ++ G ++H D A G
Sbjct: 216 ADFKAKLLANKDKPAIINVNIGTTVKGAVDDLDLVIKTLEECGFSQDRFYIHCDGALFG- 274
Query: 293 ACICP--------EFRHFIDGVEGADSFSLNAHKWFFATLDCCCLWVKDPRALVSSLSTN 344
+ P F+ I V S++ HK+ + C + ++ LS+N
Sbjct: 275 -LMMPFVKRAPKVTFKKPIGSV------SVSGHKFVGCPMPCGVQITR--MEHINVLSSN 325
Query: 345 PEYLKNK 351
EYL ++
Sbjct: 326 VEYLASR 332
>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 = 34.5 bits (80), Expect = 0.10
Identities = 29/130 (22%), Positives = 50/130 (38%), Gaps = 24/130 (18%)
Query: 194 IVYGSDQTHCAL---QKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDVEVGLI 250
I+ + H L Q+ A+ G V R I + L D+L + ++
Sbjct: 91 ILVTEMEHHANLVPWQELAKRTGATV---RVIPVDPNGL--LDLDALEKLLTPRTKL--- 142
Query: 251 PLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACICPEFRHF-IDGVE-G 308
+ + + V+P++ + +A ++G V VDAA A H ID G
Sbjct: 143 -VAITH--VSNVTGTVNPVEEIGKLAHEYGALVVVDAAQA--------VGHRPIDVQALG 191
Query: 309 ADSFSLNAHK 318
D + + HK
Sbjct: 192 VDFLAFSGHK 201
>gnl|CDD|224029 COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase
and related enzymes [Amino acid transport and
metabolism].
Length = 386
Score = 34.5 bits (80), Expect = 0.11
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 13/63 (20%)
Query: 258 IGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYA-GSACICPEFRHFIDGVEGADSFSLNA 316
GT + P+ + ++ K+ GI HVDA A G I E G D S +A
Sbjct: 154 TGT-----IQPIAEIGEICKERGILFHVDAVQAVGKIPIDLE-------ELGVDLLSFSA 201
Query: 317 HKW 319
HK+
Sbjct: 202 HKF 204
>gnl|CDD|238510 cd01040, globin, Globins are heme proteins, which bind and
transport oxygen. This family summarizes a diverse set
of homologous protein domains, including: (1) tetrameric
vertebrate hemoglobins, which are the major protein
component of erythrocytes and transport oxygen in the
bloodstream, (2) microorganismal flavohemoglobins, which
are linked to C-terminal FAD-dependend reductase
domains, (3) homodimeric bacterial hemoglobins, such as
from Vitreoscilla, (4) plant leghemoglobins (symbiotic
hemoglobins, involved in nitrogen metabolism in plant
rhizomes), (5) plant non-symbiotic hexacoordinate
globins and hexacoordinate globins from bacteria and
animals, such as neuroglobin, (6) invertebrate
hemoglobins, which may occur in tandem-repeat
arrangements, and (7) monomeric myoglobins found in
animal muscle tissue.
Length = 140
Score = 32.4 bits (74), Expect = 0.21
Identities = 19/121 (15%), Positives = 42/121 (34%), Gaps = 34/121 (28%)
Query: 4 LTSDPELK----YNSGSFTNPLDSEEFRRQGHMIIDFIADYYKNVEKYPVRSQVEPGYLQ 59
+ PE + G S +F+ G +++ + + KN++
Sbjct: 31 FKAHPETRALFSRFGGLSAALKGSPKFKAHGKRVLNALDEAIKNLD-------------- 76
Query: 60 KVLPESAPNNPESMETILQD-VQQHIVPGITHWQSPNYFAYFPSSGSIAGFLGEMLSSGF 118
+ E+++ +L ++H G+ P +F F ++ L E+L F
Sbjct: 77 ---------DLEALKALLAKLGRKHAKRGVD----PEHFKLF--GEALLEVLAEVLGDDF 121
Query: 119 N 119
Sbjct: 122 T 122
>gnl|CDD|115288 pfam06618, DUF1148, Protein of unknown function (DUF1148). This
family consists of several Maize streak virus proteins
of unknown function.
Length = 114
Score = 32.0 bits (72), Expect = 0.24
Identities = 19/56 (33%), Positives = 28/56 (50%)
Query: 302 FIDGVEGADSFSLNAHKWFFATLDCCCLWVKDPRALVSSLSTNPEYLKNKATESMQ 357
F+ V+ AD S +KW L C +++D A + SLST L+ A S+Q
Sbjct: 58 FLLDVDMADCLSRAWNKWPGIALTWWCWYIRDRVAPIHSLSTKYHLLRGSALASLQ 113
>gnl|CDD|237836 PRK14855, nhaA, pH-dependent sodium/proton antiporter; Provisional.
Length = 423
Score = 33.3 bits (76), Expect = 0.35
Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 25/104 (24%)
Query: 48 PVRSQVEPGYLQKVLPESAPNNPESMETILQDVQQHIV--------------PGITHWQS 93
P+R + YL +L +AP PE + L+D++ + P T
Sbjct: 241 PIRRRDPLPYLASLLDAAAPGRPEVVGARLRDLEDLLERAQSPLHRLEHALHPWSTFLIL 300
Query: 94 PNYFAYFPSSGSIAG----------FLGEMLSSGFNIVGFNWIS 127
P FA F + S++G FLG +L +VG W++
Sbjct: 301 P-VFALFNAGVSVSGGGLGTVSLGVFLGLLLGKPLGVVGGAWLA 343
>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 = 32.3 bits (74), Expect = 0.54
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 10/89 (11%)
Query: 232 LSPDSLMAQINSDVEV-GLIPLFLCATIGTTAIT--AVDPLKPLCDVAKQFGIWVHVDAA 288
L+P+ L A I ++ P + T T +D LK + +AK+ G+ +H+D A
Sbjct: 108 LTPEDLEAAIRPRDDIHFPPPSLVSLENTTEGGTVYPLDELKAISALAKENGLPLHLDGA 167
Query: 289 YAGSACI---CPEFRHFIDGVEGADSFSL 314
+A + G DS S
Sbjct: 168 RLANAAAALGVALKTY----KSGVDSVSF 192
>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 = 32.1 bits (74), Expect = 0.59
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 268 PLKPLCDVAKQFGIWVHVDAAYA 290
PL L D+AK++G + VD A++
Sbjct: 150 PLPELVDLAKKYGAILFVDEAHS 172
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 32.3 bits (74), Expect = 0.59
Identities = 23/98 (23%), Positives = 43/98 (43%), Gaps = 3/98 (3%)
Query: 194 IVYGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDVEVGLIPLF 253
+ T+ + + ++ G +V + S+ + L D+L A + E + L
Sbjct: 92 AILVPAPTYPSYIRIFRLAGGEVVRYP---LYSSNDFHLDFDALEAALKEATEGNKVVLH 148
Query: 254 LCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAG 291
T + ++ L+ L D+AK+ I + VD AYAG
Sbjct: 149 TSPHNPTGTVATLEELEKLLDLAKEHNILLLVDEAYAG 186
>gnl|CDD|221822 pfam12872, OST-HTH, OST-HTH/LOTUS domain. A predicted RNA-binding
domain found in insect Oskar and vertebrate TDRD5/TDRD7
proteins that nucleate or organize structurally related
ribonucleoprotein (RNP) complexes, the polar granule and
nuage, is poorly understood. The domain adopts the
winged helix-turn- helix fold and bind RNA with a
potential specificity for dsRNA.In eukaryotes this
domain is often combined in the same polypeptide with
protein-protein- or lipid- interaction domains that
might play a role in anchoring these proteins to
specific cytoskeletal structures. Thus, proteins with
this domain might have a key role in the recognition and
localization of dsRNA, including miRNAs, rasiRNAs and
piRNAs hybridized to their targets. In other cases, this
domain is fused to ubiquitin-binding, E3 ligase and
ubiquitin-like domains indicating a previously
under-appreciated role for ubiquitination in regulating
the assembly and stability of nuage-like RNP complexes.
Both bacteria and eukaryotes encode a conserved family
of proteins that combines this predicted RNA-binding
domain with a previously uncharacterized RNAse domain
belonging to the superfamily that includes the 5'->3'
nucleases, PIN and NYN domains.
Length = 74
Score = 29.5 bits (67), Expect = 0.76
Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 9/57 (15%)
Query: 351 KATESMQVVDYKDWQITLSR---RFRSLKLWFVIRNYGVANLRHFLRSHVNMAKLFE 404
KA ES D W +LS +R L F RNYG + L L + + LFE
Sbjct: 12 KALESSS--DEDGW-ASLSELGSEYRKLFPDFDPRNYGYSKLSDLLEA---IPDLFE 62
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 32.0 bits (74), Expect = 0.83
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 5/55 (9%)
Query: 386 VANLRHFLRSHVNMAKLFERLVSGDKRFEIVFPCHFAVVCFRVSPSPVLMDKLKT 440
+ L+ L H + + L D E+ + RV+PS L+ LK
Sbjct: 1082 LERLKQVLEPHRGTSPVHLYLQDPDAEAELRLGDRW-----RVTPSDALLGDLKA 1131
>gnl|CDD|200454 cd11315, AmyAc_bac1_AmyA, Alpha amylase catalytic domain found in
bacterial Alpha-amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes Firmicutes, Proteobacteria, Actinobacteria, and
Cyanobacteria. The Alpha-amylase family comprises the
largest family of glycoside hydrolases (GH), with the
majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 352
Score = 31.5 bits (72), Expect = 0.93
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 267 DPLKPLCDVAKQFGIWVHVDA 287
D K LC A ++GI + VD
Sbjct: 68 DDFKALCAAAHKYGIKIIVDV 88
>gnl|CDD|227571 COG5246, PRP11, Splicing factor 3a, subunit 2 [RNA processing and
modification].
Length = 222
Score = 31.2 bits (70), Expect = 1.1
Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 7/79 (8%)
Query: 176 AARDRVLNKIGRENISKLIVYGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSYGLSPD 235
+ R + +GREN + Q +++ + GI R++ K GL
Sbjct: 83 SRRSEEKSSLGREN-QTTHDFRQQQKIIEAKQSLKRSGIPSYKVRSLVEPKGGRRGLG-- 139
Query: 236 SLMAQIN-SDVEVGLIPLF 253
Q+N D +P +
Sbjct: 140 ---IQVNYEDDLAEEMPQY 155
>gnl|CDD|220930 pfam10994, DUF2817, Protein of unknown function (DUF2817). This
family of proteins has no known function.
Length = 341
Score = 31.1 bits (71), Expect = 1.4
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 11/77 (14%)
Query: 193 LIVYGSDQTHCALQKAAQIVGIDVKNFRAIKTTKSSSY---GLSPDSLMAQINSDVEVGL 249
I+ AL++A + G DV +I+ S SY GL D+++ + E+
Sbjct: 226 EIICMGPDDGPALERARRWWGPDV---TSIQAGSSVSYDLTGLIIDAILELLP-QAEL-- 279
Query: 250 IPLFLCATIGTTAITAV 266
+ GT V
Sbjct: 280 --TGIVLEFGTYPPLKV 294
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 29.9 bits (68), Expect = 3.4
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 268 PLKPLCDVAKQFGIWVHVDAAYA 290
PL L ++A+++G ++VD A+A
Sbjct: 189 PLPELVELAEKYGALLYVDEAHA 211
>gnl|CDD|219946 pfam08637, NCA2, ATP synthase regulation protein NCA2. NCA2 has
been shown to be required for the regulation of ATP
synthase subunits Atp6p and Atp8p in Saccharomyces
cerevisiae.
Length = 290
Score = 29.2 bits (66), Expect = 4.9
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 32 MIIDFIADYYKN--VEKYPVRSQVEPGYLQKVL 62
M++DF+ D Y V+ + +V G L +V+
Sbjct: 80 MVVDFVVDNYPPGGVDLQQLTDKVRQGDLTEVM 112
>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 = 29.2 bits (66), Expect = 5.2
Identities = 39/196 (19%), Positives = 62/196 (31%), Gaps = 61/196 (31%)
Query: 128 SPAATELENIVMDWLGQMLKLPKSFLFSGNGGGVIQGTTCE-AILCTLTAARDRVLNKIG 186
SP ELE + +W G + LFS G ++ L D +L
Sbjct: 60 SPLHEELEEELAEWKGT----EAALLFS-------SGYLANVGVISALVGKGDLIL---- 104
Query: 187 RENISKLIVYGSDQ-THCALQKAAQIVGIDVKNFRAIKTTKSSSYGLSPDSLMAQINSDV 245
SD H +L ++ G V+ +R + L + +
Sbjct: 105 -----------SDALNHASLIDGCRLSGARVRRYRHN----------DVEHLERLLEKNR 143
Query: 246 EVGLIPLFLCATIGTTAITAVD----PLKPLCDVAKQFGIWVHVDAAYAGSACICPEFRH 301
I T + ++D PL L +A+++G W+ VD A+
Sbjct: 144 GERR------KLIVTDGVFSMDGDIAPLPQLVALAERYGAWLMVDDAHGT---------- 187
Query: 302 FIDGVEGADSFSLNAH 317
GV G D H
Sbjct: 188 ---GVLGEDGRGTLEH 200
>gnl|CDD|176217 cd08255, 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like,
2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and
other MDR family members. This subgroup of the medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family has members identified
as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A
dehydrogenase and alcohol dehydrogenases. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 277
Score = 29.2 bits (66), Expect = 5.2
Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 4/52 (7%)
Query: 247 VGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFG----IWVHVDAAYAGSAC 294
VGL+ L G + VDP ++A+ G + G
Sbjct: 109 VGLLAAQLAKAAGAREVVGVDPDAARRELAEALGPADPVAADTADEIGGRGA 160
>gnl|CDD|180565 PRK06450, PRK06450, threonine synthase; Validated.
Length = 338
Score = 29.3 bits (66), Expect = 5.3
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 428 VSPSPVLMDKLK---TKYVNCLLSEEEQINEFNREL 460
VS P L+D + ++Y C++ + +I E +EL
Sbjct: 265 VSTRPFLLDYMVKALSEYGECIVVSDNEIVEAWKEL 300
>gnl|CDD|233161 TIGR00870, trp, transient-receptor-potential calcium channel
protein. The Transient Receptor Potential Ca2+ Channel
(TRP-CC) Family (TC. 1.A.4)The TRP-CC family has also
been called the store-operated calcium channel (SOC)
family. The prototypical members include the Drosophila
retinal proteinsTRP and TRPL (Montell and Rubin, 1989;
Hardie and Minke, 1993). SOC members of the family
mediate the entry of extracellular Ca2+ into cells in
responseto depletion of intracellular Ca2+ stores
(Clapham, 1996) and agonist stimulated production of
inositol-1,4,5 trisphosphate (IP3). One member of the
TRP-CCfamily, mammalian Htrp3, has been shown to form a
tight complex with the IP3 receptor (TC #1.A.3.2.1).
This interaction is apparently required for IP3
tostimulate Ca2+ release via Htrp3. The vanilloid
receptor subtype 1 (VR1), which is the receptor for
capsaicin (the ?hot? ingredient in chili peppers) and
servesas a heat-activated ion channel in the pain
pathway (Caterina et al., 1997), is also a member of
this family. The stretch-inhibitable non-selective
cation channel(SIC) is identical to the vanilloid
receptor throughout all of its first 700 residues, but
it exhibits a different sequence in its last 100
residues. VR1 and SICtransport monovalent cations as
well as Ca2+. VR1 is about 10x more permeable to Ca2+
than to monovalent ions. Ca2+ overload probably causes
cell deathafter chronic exposure to capsaicin.
(McCleskey and Gold, 1999) [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 743
Score = 29.3 bits (66), Expect = 5.8
Identities = 11/84 (13%), Positives = 23/84 (27%), Gaps = 9/84 (10%)
Query: 330 WVKDPRALVSSLSTNPEYLKNKATESMQVVDYKDWQITLSRRFRS-LKLWFVIRNYGVAN 388
P ++ P+ + ++ D + R W
Sbjct: 643 TCPPPFNIIPG----PKSF----VGLFKRIEKHDGKKRQRWCRRVEEVNWTTWERKAETL 694
Query: 389 LRHFLRSHVNMAKLFERLVSGDKR 412
+ L M +L +R V ++R
Sbjct: 695 IEDGLHYQRVMKRLIKRYVLAEQR 718
>gnl|CDD|224919 COG2008, GLY1, Threonine aldolase [Amino acid transport and
metabolism].
Length = 342
Score = 29.2 bits (66), Expect = 5.9
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 232 LSPDSLMAQINSD----VEVGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDA 287
L+P+ + A I D L L AT G T +D L+ + V K+ G+ +H+D
Sbjct: 112 LTPEDVEAAIRPDDIHHAPTPLAVLENTATEGGTVYP-LDELEAISAVCKEHGLPLHMDG 170
Query: 288 AYAGSACI 295
A +A +
Sbjct: 171 ARLANALV 178
>gnl|CDD|214928 smart00944, Pro-kuma_activ, Pro-kumamolisin, activation domain.
This domain is found at the N-terminus of peptidases
belonging to MEROPS peptidase family S53 (sedolisin,
clan SB). The domain adopts a ferredoxin-like fold, with
an alpha+beta sandwich. Cleavage of the domain results
in activation of the peptidase.
Length = 136
Score = 28.0 bits (63), Expect = 6.2
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 67 PNNPESMETILQDVQQHIVPGITHWQSPNYFA--YFPSSGSIAGFLGEMLSSGFNIV 121
N +E ++Q+V P + SP FA + PS + L + S G ++
Sbjct: 20 QRNLAQLEQLVQEVSDPGSPNYGKFLSPEEFASLFGPSPADVNAVLAWLESHGLTVI 76
>gnl|CDD|237143 PRK12576, PRK12576, succinate dehydrogenase iron-sulfur subunit;
Provisional.
Length = 279
Score = 28.6 bits (64), Expect = 7.3
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 409 GDKRFEIV----FPCHFAVVCFRVSP---SPVLMDKLKTKYVNCLLSEEEQINEFNRELL 461
++R +I+ + C + C V P PV K KT+ + + ++ E + +
Sbjct: 194 TEERMKILIDSSWRCTYCYSCSNVCPRDIEPVTAIK-KTRSFTRVYKPKSEVAERGEKHV 252
Query: 462 ESINASG 468
E+I S
Sbjct: 253 EAIRESI 259
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 28.6 bits (65), Expect = 8.1
Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 7/69 (10%)
Query: 251 PLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACICPEFRHFIDGVE--- 307
+ + ++ + + AK+ G+ V A PE+ ++ +
Sbjct: 99 ETHSRKNLNKSREEDLENAEEAIEAAKEAGLEVEGSLEDAFGCKTDPEY--VLEVAKALE 156
Query: 308 --GADSFSL 314
GAD SL
Sbjct: 157 EAGADEISL 165
>gnl|CDD|235893 PRK06939, PRK06939, 2-amino-3-ketobutyrate coenzyme A ligase;
Provisional.
Length = 397
Score = 28.6 bits (65), Expect = 8.5
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 268 PLKPLCDVAKQFGIWVHVDAAYA 290
PL +CD+A ++ V VD ++A
Sbjct: 192 PLPEICDLADKYDALVMVDDSHA 214
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
0.322 0.136 0.415
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,485,663
Number of extensions: 2579415
Number of successful extensions: 2380
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2348
Number of HSP's successfully gapped: 52
Length of query: 517
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 416
Effective length of database: 6,457,848
Effective search space: 2686464768
Effective search space used: 2686464768
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 (21.9 bits)
S2: 61 (27.2 bits)