RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 048438
(239 letters)
>gnl|CDD|215475 PLN02880, PLN02880, tyrosine decarboxylase.
Length = 490
Score = 313 bits (804), Expect = e-105
Identities = 136/250 (54%), Positives = 177/250 (70%), Gaps = 26/250 (10%)
Query: 1 AGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHFIDGV 60
+GLIP FLCAT+GTT+ TAVDPL L +AK G+W HVDAAYAGSACI PE+RH+IDGV
Sbjct: 236 SGLIPFFLCATVGTTSSTAVDPLLELGKIAKSNGMWFHVDAAYAGSACICPEYRHYIDGV 295
Query: 61 EGADSFSLNAHKWFFATLDCCCLW-----------ATNPEYLKNKATESKPVVDYKDWQI 109
E ADSF++NAHKWF DC LW +TNPE+LKNKA+++ VVDYKDWQI
Sbjct: 296 EEADSFNMNAHKWFLTNFDCSLLWVKDRNALIQSLSTNPEFLKNKASQANSVVDYKDWQI 355
Query: 110 TLSRSFRSLKLWFVIRNYGMENLRHFLRSHVNMARLFERLVSGDKRFEVVFPCHFAVVCF 169
L R FRSLKLW V+R YG+ENL+ ++R+H+ +A+ FE+LV+ D RFEVV P F++VCF
Sbjct: 356 PLGRRFRSLKLWMVLRLYGVENLQSYIRNHIKLAKEFEQLVAQDSRFEVVTPRIFSLVCF 415
Query: 170 RVSPLPVLMDKLKTKYENCLLSEEEQINEFNRELLESINASGKAYMTNVVLGGIYAIRFA 229
R+ P + E+ N+ N +LL+++N+SGK ++++ VL G Y +RFA
Sbjct: 416 RLVPPK---------------NNEDNGNKLNHDLLDAVNSSGKIFISHTVLSGKYVLRFA 460
Query: 230 TGATLTEERH 239
GA LTEERH
Sbjct: 461 VGAPLTEERH 470
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 282 bits (723), Expect = 6e-93
Identities = 132/249 (53%), Positives = 175/249 (70%), Gaps = 26/249 (10%)
Query: 2 GLIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHFIDGVE 61
G IP F+CAT+GTT+ AVDPL PL ++AK++GIW+HVDAAYAG+ACI PE+R FIDG+E
Sbjct: 285 GFIPFFICATVGTTSSAAVDPLVPLGNIAKKYGIWLHVDAAYAGNACICPEYRKFIDGIE 344
Query: 62 GADSFSLNAHKWFFATLDCCCLWA-----------TNPEYLKNKATESKPVVDYKDWQIT 110
ADSF++NAHKW FA C LW TNPEYL+ K ++ VV+YKDWQI+
Sbjct: 345 NADSFNMNAHKWLFANQTCSPLWVKDRYSLIDALKTNPEYLEFKVSKKDTVVNYKDWQIS 404
Query: 111 LSRSFRSLKLWFVIRNYGMENLRHFLRSHVNMARLFERLVSGDKRFEVVFPCHFAVVCFR 170
LSR FRSLKLW V+R YG ENLR+F+R HVN+A+ FE V+ D FEVV +F++VCFR
Sbjct: 405 LSRRFRSLKLWMVLRLYGSENLRNFIRDHVNLAKHFEDYVAQDPSFEVVTTRYFSLVCFR 464
Query: 171 VSPLPVLMDKLKTKYENCLLSEEEQINEFNRELLESINASGKAYMTNVVLGGIYAIRFAT 230
++P+ +E+Q NE NRELL ++N++GK ++++ L G + +RFA
Sbjct: 465 LAPVD---------------GDEDQCNERNRELLAAVNSTGKIFISHTALSGKFVLRFAV 509
Query: 231 GATLTEERH 239
GA LTEE+H
Sbjct: 510 GAPLTEEKH 518
>gnl|CDD|215836 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase
conserved domain.
Length = 373
Score = 238 bits (609), Expect = 1e-77
Identities = 95/181 (52%), Positives = 118/181 (65%), Gaps = 11/181 (6%)
Query: 1 AGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHFIDGV 60
GLIP F+CAT+GTT A DPL+ L D+ ++ +W+HVDAAYAGSA I PEFRH++ G+
Sbjct: 191 NGLIPFFVCATLGTTGSGAFDPLQELGDICNKYDLWLHVDAAYAGSAFICPEFRHWLFGI 250
Query: 61 EGADSFSLNAHKWFFATLDCCCLW-----------ATNPEYLKNKATESKPVVDYKDWQI 109
E ADSFS N HKW LDC LW NPEYL + +S VDY DWQI
Sbjct: 251 ERADSFSFNPHKWMLVLLDCSALWVRDKGALQQALQFNPEYLGHNDKQSDVAVDYGDWQI 310
Query: 110 TLSRSFRSLKLWFVIRNYGMENLRHFLRSHVNMARLFERLVSGDKRFEVVFPCHFAVVCF 169
LSR FR LKLWFV+R+YG+E L++ +R HV +A+ FE LV D RFE+ +VCF
Sbjct: 311 PLSRRFRILKLWFVLRSYGVEGLQNQIRRHVELAKYFEALVRKDSRFEICAERGLGLVCF 370
Query: 170 R 170
R
Sbjct: 371 R 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 = 196 bits (500), Expect = 1e-61
Identities = 66/239 (27%), Positives = 106/239 (44%), Gaps = 49/239 (20%)
Query: 1 AGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHFIDGV 60
GL P+ + AT GTT A+DPL+ + D+A+++ +W+HVDAAY G FPE RH G+
Sbjct: 145 EGLNPIMVVATAGTTDTGAIDPLEEIADLAEKYDLWLHVDAAYGGFLLPFPEPRHLDFGI 204
Query: 61 EGADSFSLNAHKWFFATLDCCCLWATNPEYLKNKATESKPVVDYKDWQITLSRSFRSLKL 120
E DS S++ HK+ L C + R+LKL
Sbjct: 205 ERVDSISVDPHKYGLVPLGCSAVL------------------------------VRALKL 234
Query: 121 WFVIRNYGMENLRHFLRSHVNMARLFERLVSGDKRFEVVFPCHFAVVCFRVSPLPVLMDK 180
W +R +G + + V++A+ L+ D FE++ + ++VCFR+ P
Sbjct: 235 WATLRRFGRDGYGEHIDRIVDLAKYLAELIRADPGFELLGEPNLSLVCFRLKP------- 287
Query: 181 LKTKYENCLLSEEEQINEFNRELLESINASGKAYMTNVVLGGIYAIRFATGATLTEERH 239
+++E N +L + +N G ++ LGG +RF LT
Sbjct: 288 ------------SVKLDELNYDLSDRLNERGGWHVPATTLGGPNVLRFVVTNPLTTRDD 334
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 130 bits (329), Expect = 2e-35
Identities = 57/235 (24%), Positives = 101/235 (42%), Gaps = 16/235 (6%)
Query: 10 ATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRH-FIDGVEGADSFSL 68
T GTT ++D ++ L D+A+++GIW+HVDAA+ G F E + G+EG DS ++
Sbjct: 213 GTAGTTDTGSIDDIEELADIAEEYGIWLHVDAAFGGFLLPFLEPDGRWDFGLEGVDSITV 272
Query: 69 NAHKWFFATLDCCCLWATNPEYL-KNKATESKPVVDYKDWQITL--SRS-FRSLKLWFVI 124
+ HK+ A + C + + E L + + T+ SR ++L L+ +
Sbjct: 273 DGHKYGLAPIGCGVVLFRDEEALRRILIFADYYLPGGGIPNFTILGSRPGRQALALYANL 332
Query: 125 RNYGMENLRHFLRSHVNMARLFERLVSGDKRFEVVFPCHFAVVCFRVSPLPVLMDKLKTK 184
R G E R L + +AR + FE+V +V FR+
Sbjct: 333 RRLGREGYRKLLDRTLELARYLAEELEKLGDFELVNEPELPIVAFRLKD----------- 381
Query: 185 YENCLLSEEEQINEFNRELLESINASGKAYMTNVVLGGIYAIRFATGATLTEERH 239
E+ L E+++ ++ + G A + + G ++F L +R
Sbjct: 382 DEDTLADLSERLDRRGWQVPAQLLPKGLAIVFGTHVTGRQGLKFIVANLLITDRE 436
>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 = 71.6 bits (176), Expect = 1e-14
Identities = 45/179 (25%), Positives = 77/179 (43%), Gaps = 10/179 (5%)
Query: 13 GTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIF----PEFRHFIDGVEGADSFSL 68
GTT + +D ++ L +A + GI++HVDAA+ G F F + G S ++
Sbjct: 162 GTTELGQIDDIEELSKIALENGIYLHVDAAFGGFVIPFLKKGYNPPPFDFSLPGVQSITI 221
Query: 69 NAHKWFFATLDCCCLWATNPEYLKNKATESKPVVDYKDWQITLSRS-FRSLKLWFVIRNY 127
+ HK + + + + YLK + ++ + K IT +RS + + VI+
Sbjct: 222 DPHKMGLSPIPAGGILFRSKSYLKYLSVDAPYLTVKKQATITGTRSGASAAATYAVIKYL 281
Query: 128 GMENLRHFLRSHVNMARLFERLVSGDKR--FEVVFPCHFAVVCFRVSPLPVLMDKLKTK 184
G E R + + R LV K+ FE V +V F V + KL+ +
Sbjct: 282 GREGYRKIVAECMENTR---YLVEELKKIGFEPVIEPVLNIVAFEVDDPEEVRKKLRDR 337
>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 = 68.2 bits (167), Expect = 3e-13
Identities = 27/71 (38%), Positives = 43/71 (60%)
Query: 5 PLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHFIDGVEGAD 64
PL + GTT +DPL + D+A++ G HVDAA+ G+ + +RH + G+E AD
Sbjct: 266 PLAIVGVAGTTETGNIDPLDEMADIAQELGCHFHVDAAWGGATLLSNTYRHLLKGIERAD 325
Query: 65 SFSLNAHKWFF 75
S +++AHK +
Sbjct: 326 SVTIDAHKQLY 336
>gnl|CDD|235068 PRK02769, PRK02769, histidine decarboxylase; Provisional.
Length = 380
Score = 56.2 bits (136), Expect = 3e-09
Identities = 50/173 (28%), Positives = 87/173 (50%), Gaps = 20/173 (11%)
Query: 5 PLFLCATIGTTAITAVDPLKPLCDVAKQFGI---WVHVDAAYAGSACIFPEFRHFIDGVE 61
P + A IGTT A+D +K + ++ K+ GI ++H DAA +G F +
Sbjct: 161 PPIIFANIGTTMTGAIDNIKEIQEILKKIGIDDYYIHADAALSGMILPFVNNPPPFSFAD 220
Query: 62 GADSFSLNAHKWFFATLDCCCLWATNPEYLKNKATESKPVVDY---KDWQITLSRS-FRS 117
G DS +++ HK+ + + C + +Y++ + + VDY +D I+ SR+ +
Sbjct: 221 GIDSIAISGHKFIGSPMPCGIV-LAKKKYVERISVD----VDYIGSRDQTISGSRNGHTA 275
Query: 118 LKLWFVIRNYGMENLRHFLRSHVNMAR-LFERL-VSGDKRFE------VVFPC 162
L LW IR+ G + LR ++ ++MA+ +RL +G + VVFPC
Sbjct: 276 LLLWAAIRSLGSKGLRQRVQHCLDMAQYAVDRLQANGIPAWRNPNSITVVFPC 328
>gnl|CDD|237409 PRK13520, PRK13520, L-tyrosine decarboxylase; Provisional.
Length = 371
Score = 54.9 bits (133), Expect = 8e-09
Identities = 47/179 (26%), Positives = 76/179 (42%), Gaps = 13/179 (7%)
Query: 13 GTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIF----PEFRHFIDGVEGADSFSL 68
GTT + VDP+ L +A + GI++HVDAA+ G F P F F + G DS ++
Sbjct: 160 GTTELGQVDPIPELSKIALENGIFLHVDAAFGGFVIPFLDDPPNF-DF--SLPGVDSITI 216
Query: 69 NAHKWFFATLDCCCLWATNPEYLKNKATESKPVVDYKDWQITLSRS-FRSLKLWFVIRNY 127
+ HK A + + + YL A ++ + K +T +RS + V++
Sbjct: 217 DPHKMGLAPIPAGGILFRDESYLDALAVDTPYLTSKKQATLTGTRSGAGVAATYAVMKYL 276
Query: 128 GMENLRHFLRSHVNMARLFERLVSGDKR--FEVVFPCHFAVVCFRVSPLPVLMDKLKTK 184
G E R + + R L K FE V +V F + +KL+ +
Sbjct: 277 GREGYRKVVERCMENTR---WLAEELKERGFEPVIEPVLNIVAFDDPNPDEVREKLRER 332
>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 = 52.4 bits (126), Expect = 1e-08
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 1 AGLIPLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHFIDGV 60
A + T TT+ + PLK + +AK++GI + VDAA AG A P
Sbjct: 89 AKPNVALIVITPNTTSGGVLVPLKEIRKIAKEYGILLLVDAASAGGASPAPGVL---IPE 145
Query: 61 EGADSFSLNAHKWF 74
GAD + + HK
Sbjct: 146 GGADVVTFSLHKNL 159
>gnl|CDD|166673 PLN03032, PLN03032, serine decarboxylase; Provisional.
Length = 374
Score = 39.0 bits (91), Expect = 0.001
Identities = 41/164 (25%), Positives = 67/164 (40%), Gaps = 24/164 (14%)
Query: 5 PLFLCATIGTTAITAVDPLKPLCDVAKQFGI-----WVHVDAAYAGSACIFPEFRHFIDG 59
P L IGTT AVD L + + K+ G ++H D A G F +
Sbjct: 162 PAILNVNIGTTVKGAVDDLDRILRILKELGYTEDRFYIHCDGALFGLMMPFVSRAPEVTF 221
Query: 60 VEGADSFSLNAHKWFFATLDCCCLWATNPEYLKNKATESKPVVDY---KDWQITLSRSFR 116
+ S S++ HK+ + C T +++K + V+Y +D I SR+
Sbjct: 222 RKPIGSVSVSGHKFLGCPMPCGVAL-TRKKHVKALSQN----VEYLNSRDATIMGSRNGH 276
Query: 117 S-LKLWFVIRNYGMENLR----------HFLRSHVNMARLFERL 149
+ L LW+ +R G ++ H+L+ + A L RL
Sbjct: 277 APLYLWYTLRRKGYRGIKRDVQHCMRNAHYLKDRLTEAGLTCRL 320
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 36.1 bits (84), Expect = 0.013
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 10/57 (17%)
Query: 22 PLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHF-ID-GVEGADSFSLNAHKWFFA 76
P+K + ++A + G V VDAA A H ID G D + + HKW
Sbjct: 180 PVKEIAELAHEHGALVLVDAAQA--------AGHLPIDVQELGCDFLAFSGHKWLLG 228
>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 = 33.2 bits (76), Expect = 0.100
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 9/58 (15%)
Query: 18 TAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHFIDGVE-GADSFSLNAHKWF 74
+ VD L + ++ G V VDA + ID GAD + +A+K+F
Sbjct: 171 SIVD-LAAITELVHAAGALVVVDAVHYAP-------HGLIDVQATGADFLTCSAYKFF 220
>gnl|CDD|224029 COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase
and related enzymes [Amino acid transport and
metabolism].
Length = 386
Score = 32.5 bits (75), Expect = 0.15
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 13/63 (20%)
Query: 12 IGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYA-GSACIFPEFRHFIDGVEGADSFSLNA 70
GT + P+ + ++ K+ GI HVDA A G I E G D S +A
Sbjct: 154 TGT-----IQPIAEIGEICKERGILFHVDAVQAVGKIPIDLE-------ELGVDLLSFSA 201
Query: 71 HKW 73
HK+
Sbjct: 202 HKF 204
>gnl|CDD|215366 PLN02681, PLN02681, proline dehydrogenase.
Length = 455
Score = 32.4 bits (74), Expect = 0.17
Identities = 19/86 (22%), Positives = 29/86 (33%), Gaps = 13/86 (15%)
Query: 44 AGSACIFPEFRHFIDGVEGADSFSLNAHKWFFATLDCCCLWATNPEYLKN----KATESK 99
AG A P D + H FA L + E L++ +
Sbjct: 2 AGPAATVPPAVTSTTTPASDDVLDFSDHAALFAGL-------STSELLRSLLVLQLCAIG 54
Query: 100 PVVDYKDWQITLSRS--FRSLKLWFV 123
P+VD +W +T R++ L V
Sbjct: 55 PLVDLGEWLLTSPLMVLGRAIVLALV 80
>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 = 0.20
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 22 PLKPLCDVAKQFGIWVHVDAAYA 44
PL L D+AK++G + VD A++
Sbjct: 150 PLPELVDLAKKYGAILFVDEAHS 172
>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 = 32.0 bits (73), Expect = 0.23
Identities = 21/95 (22%), Positives = 33/95 (34%), Gaps = 17/95 (17%)
Query: 9 CATIGTTAITAVDPLKPLCDVAKQFG------IWVHVDAAYAGSACIFPE------FRHF 56
+GTT + +K L D ++ I +HVDAA G F FR
Sbjct: 191 VCILGTTYTGEYEDVKALNDALDEYNAKTGWDIPIHVDAASGGFIAPFVYPDLEWDFRL- 249
Query: 57 IDGVEGADSFSLNAHKWFFATLDCCCLWATNPEYL 91
S +++ HK+ + + E L
Sbjct: 250 ----PRVKSINVSGHKYGLVYPGVGWVIWRDEEAL 280
>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 = 31.9 bits (73), Expect = 0.27
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 21 DPLKPLCDVAKQFGIWVHVDA 41
D K LC A ++GI + VD
Sbjct: 68 DDFKALCAAAHKYGIKIIVDV 88
>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 = 31.1 bits (71), Expect = 0.50
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 10/55 (18%)
Query: 20 VDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHF-IDGVE-GADSFSLNAHK 72
V+P++ + +A ++G V VDAA A H ID G D + + HK
Sbjct: 155 VNPVEEIGKLAHEYGALVVVDAAQA--------VGHRPIDVQALGVDFLAFSGHK 201
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 29.5 bits (67), Expect = 1.5
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 22 PLKPLCDVAKQFGIWVHVDAAYA 44
PL L ++A+++G ++VD A+A
Sbjct: 189 PLPELVELAEKYGALLYVDEAHA 211
>gnl|CDD|227847 COG5560, UBP12, Ubiquitin C-terminal hydrolase [Posttranslational
modification, protein turnover, chaperones].
Length = 823
Score = 29.9 bits (67), Expect = 1.5
Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 95 ATESKPVVDYKDWQITLSRSFRSLKLWFVIRNYGMENLRHFLRSHVNMARLFERLV 150
+ES P V+ L F + N G + + H SH + L ER++
Sbjct: 125 PSESAPEVESYPVVFKLHWLFSING---SLINLGHDPVPHSASSHGTLRDLSERVM 177
>gnl|CDD|216978 pfam02331, P35, Apoptosis preventing protein. This viral protein
functions to block the host apoptotic response caused by
infection by the virus. The apoptosis preventing protein
(or early 35kD protein, P35) acts by blocking caspase
protease activity.
Length = 300
Score = 29.4 bits (66), Expect = 1.6
Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 18/85 (21%)
Query: 131 NLRHFLRSHV-----NMARLFERLVSGD-KRFEVVFPC-HFAVVCFRVSPLPVLMDKLKT 183
NLR ++S + + R + S F F H++VVC LK+
Sbjct: 62 NLRDMIKSKIDEQFDQLERNYHNKRSTQMDGFHKYFKDEHYSVVCQN-------GSVLKS 114
Query: 184 KYENCLLS----EEEQINEFNRELL 204
K+E L S +++ I F + L
Sbjct: 115 KFEKILKSHDYTDKKSIEAFKKYCL 139
>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 = 2.5
Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 7/69 (10%)
Query: 5 PLFLCATIGTTAITAVDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHFIDGVE--- 61
+ + ++ + + AK+ G+ V A PE+ ++ +
Sbjct: 99 ETHSRKNLNKSREEDLENAEEAIEAAKEAGLEVEGSLEDAFGCKTDPEY--VLEVAKALE 156
Query: 62 --GADSFSL 68
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 = 3.1
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 22 PLKPLCDVAKQFGIWVHVDAAYA 44
PL +CD+A ++ V VD ++A
Sbjct: 192 PLPEICDLADKYDALVMVDDSHA 214
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 28.6 bits (64), Expect = 3.3
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 9/58 (15%)
Query: 180 KLKTKYENCLLSEEEQIN----EFN---RELLESINASGKAYMTN--VVLGGIYAIRF 228
K + NCL +++E + + N R+LL++I +G T+ V + +Y +R
Sbjct: 198 NKKEAFYNCLKNKKEDYDKKIKKINNEIRKLLKNIKCTGNMCKTDTYVDMVELYLLRV 255
>gnl|CDD|221522 pfam12309, KBP_C, KIF-1 binding protein C terminal. This family of
proteins is found in bacteria and eukaryotes. Proteins
in this family are typically between 365 and 621 amino
acids in length. There is a conserved LLP sequence
motif. KBP is a binding partner for KIF1Balpha that is a
regulator of its transport function and thus represents
a type of kinesin interacting protein.
Length = 365
Score = 28.1 bits (63), Expect = 3.9
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 132 LRHFLRSHVNMARLFERLVSGDKRFEV 158
LR L + ++ARL+ +L++ D + ++
Sbjct: 290 LRPILVAKFHIARLYSKLITADPKEKL 316
>gnl|CDD|233587 TIGR01821, 5aminolev_synth, 5-aminolevulinic acid synthase. This
model represents 5-aminolevulinic acid synthase, an
enzyme for one of two routes to the heme precursor
5-aminolevulinate. The protein is a pyridoxal
phosphate-dependent enzyme related to
2-amino-3-ketobutyrate CoA tranferase and
8-amino-7-oxononanoate synthase. This enzyme appears
restricted to the alpha Proteobacteria and mitochondrial
derivatives [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 402
Score = 28.2 bits (63), Expect = 4.0
Identities = 7/26 (26%), Positives = 17/26 (65%)
Query: 19 AVDPLKPLCDVAKQFGIWVHVDAAYA 44
+ P++ +CD+A ++G ++D +A
Sbjct: 192 DIAPIEEICDLADKYGALTYLDEVHA 217
>gnl|CDD|236299 PRK08575, PRK08575,
5-methyltetrahydropteroyltriglutamate--homocysteine
methyltransferase; Provisional.
Length = 326
Score = 28.2 bits (63), Expect = 4.0
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 173 PLPVLMDKLKTKYENCLLSEE---EQINEFNRELLESINASGKAYMTN 217
P PV + K+ + Y + +S+E + INE + E G Y T+
Sbjct: 12 PRPVKLAKVISWYNSGKISKEKLEKAINENTKRFFELAKDVGIDYTTD 59
>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 = 28.2 bits (64), Expect = 4.5
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 10/56 (17%)
Query: 19 AVDPLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHFIDGVE--GADSFSLNAHK 72
++P+K + ++A + G+ V VD A SA P +D V+ G D + + HK
Sbjct: 154 TINPVKEIGEIAHEAGVPVLVDGAQ--SAGHMP-----VD-VQDLGCDFLAFSGHK 201
>gnl|CDD|180565 PRK06450, PRK06450, threonine synthase; Validated.
Length = 338
Score = 27.8 bits (62), Expect = 5.1
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 171 VSPLPVLMDKLK---TKYENCLLSEEEQINEFNREL 203
VS P L+D + ++Y C++ + +I E +EL
Sbjct: 265 VSTRPFLLDYMVKALSEYGECIVVSDNEIVEAWKEL 300
>gnl|CDD|178298 PLN02695, PLN02695, GDP-D-mannose-3',5'-epimerase.
Length = 370
Score = 27.9 bits (62), Expect = 5.3
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 43 YAGSACIFPEFR 54
YA SACI+PEF+
Sbjct: 134 YASSACIYPEFK 145
>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 = 27.7 bits (62), Expect = 6.3
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 20 VDPLKPLCDVAKQFGIWVHVDAAYAGSACIF---PEFRHFIDGVEGADSFSL 68
+D LK + +AK+ G+ +H+D A +A + G DS S
Sbjct: 145 LDELKAISALAKENGLPLHLDGARLANAAAALGVALKTY----KSGVDSVSF 192
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 27.8 bits (63), Expect = 7.4
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 5/55 (9%)
Query: 129 MENLRHFLRSHVNMARLFERLVSGDKRFEVVFPCHFAVVCFRVSPLPVLMDKLKT 183
+E L+ L H + + L D E+ + RV+P L+ LK
Sbjct: 1082 LERLKQVLEPHRGTSPVHLYLQDPDAEAELRLGDRW-----RVTPSDALLGDLKA 1131
>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 = 27.5 bits (61), Expect = 7.5
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 6 LFLCATIGTTAITAVDPLKPLCDVAKQF---GIW--VHVDAAYAGSA 47
L + +G+T AVD + + + + GI+ +HVDAAY G
Sbjct: 280 LGVVGVVGSTEEGAVDGIDKIVALRNKLMKEGIYFYLHVDAAYGGYG 326
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 27.3 bits (61), Expect = 7.5
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 23 LKPLCDVAKQFGIWVHVDAAYAG---SACIFPEFRHFIDG 59
L+ L D+AK+ I + VD AYAG + R +
Sbjct: 164 LEKLLDLAKEHNILLLVDEAYAGFVFGSLDAVATRALLAE 203
>gnl|CDD|176245 cd08285, NADP_ADH, NADP(H)-dependent alcohol dehydrogenases. This
group is predominated by atypical alcohol
dehydrogenases; they exist as tetramers and exhibit
specificity for NADP(H) as a cofactor in the
interconversion of alcohols and aldehydes, or ketones.
Like other zinc-dependent alcohol dehydrogenases (ADH)
of the medium chain alcohol dehydrogenase/reductase
family (MDR), tetrameric ADHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains;
however, they do not have and a structural zinc in a
lobe of the catalytic domain. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 351
Score = 27.2 bits (61), Expect = 7.8
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 2 GLIPLFLCATIGT-----TAITAVDPLKPLCDVAKQFGIWVHVD 40
G+ P+ L A G I AV ++AK++G VD
Sbjct: 174 GIGPVGLMAVAGARLRGAGRIIAVGSRPNRVELAKEYGATDIVD 217
>gnl|CDD|193205 pfam12729, 4HB_MCP_1, Four helix bundle sensory module for signal
transduction. This family is a four helix bundle that
operates as a ubiquitous sensory module in prokaryotic
signal-transduction. The 4HB_MCP is always found between
two predicted transmembrane helices indicating that it
detects only extracellular signals. In many cases the
domain is associated with a cytoplasmic HAMP domain
suggesting that most proteins carrying the bundle might
share the mechanism of transmembrane signalling which is
well-characterized in E coli chemoreceptors.
Length = 181
Score = 26.8 bits (60), Expect = 8.1
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 178 MDKLKTKYENCLLSEEEQ--INEFNRELLESINASGKA 213
+DKL KYE +L+EEE+ NEF +L K
Sbjct: 91 IDKLLKKYEKTILTEEEKKLFNEFKEQLKAYRKVRNKV 128
>gnl|CDD|236931 PRK11563, PRK11563, bifunctional aldehyde dehydrogenase/enoyl-CoA
hydratase; Provisional.
Length = 675
Score = 27.5 bits (62), Expect = 8.1
Identities = 10/15 (66%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 123 VIRNYGMENLRHFLR 137
V+ NYG+ENLR FL
Sbjct: 609 VLANYGLENLR-FLT 622
>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 = 27.2 bits (61), Expect = 8.2
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 13/50 (26%)
Query: 22 PLKPLCDVAKQFGIWVHVDAAYAGSACIFPEFRHFIDGVEGADSFSLNAH 71
PL L +A+++G W+ VD A+ GV G D H
Sbjct: 164 PLPQLVALAERYGAWLMVDDAHGT-------------GVLGEDGRGTLEH 200
>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 = 27.2 bits (61), Expect = 8.8
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 19 AVDPLKPLCDVAKQFGIWVHVDAAYA 44
V+P++ + +A Q G V VD A A
Sbjct: 174 TVNPVEEIAKLAHQVGAKVLVDGAQA 199
>gnl|CDD|235655 PRK05958, PRK05958, 8-amino-7-oxononanoate synthase; Reviewed.
Length = 385
Score = 27.0 bits (61), Expect = 9.4
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 22 PLKPLCDVAKQFGIWVHVDAAYA 44
PL L +A++ G W+ VD A+
Sbjct: 186 PLAELVALARRHGAWLLVDEAHG 208
>gnl|CDD|133178 cd05046, PTK_CCK4, Pseudokinase domain of the Protein Tyrosine
Kinase, Colon Carcinoma Kinase 4. Protein Tyrosine
Kinase (PTK) family; Colon Carcinoma Kinase 4 (CCK4);
pseudokinase domain. The PTKc (catalytic domain) family,
to which this subfamily belongs, includes the catalytic
domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. CCK4,
also called protein tyrosine kinase 7 (PTK7), is an
orphan receptor tyr kinase (RTK) containing an
extracellular region with seven immunoglobulin domains,
a transmembrane segment, and an intracellular inactive
pseudokinase domain. Studies in mice reveal that CCK4 is
essential for neural development. Mouse embryos
containing a truncated CCK4 die perinatally and display
craniorachischisis, a severe form of neural tube defect.
The mechanism of action of the CCK4 pseudokinase is
still unknown. Other pseudokinases such as HER3 rely on
the activity of partner RTKs.
Length = 275
Score = 27.0 bits (60), Expect = 9.9
Identities = 16/65 (24%), Positives = 21/65 (32%), Gaps = 6/65 (9%)
Query: 139 HVNMARLFERLVSGDKRFEVVFPCHFAVVCFRVSPLPVLMDKLKTKYENCLLSEEEQINE 198
+ L E G F VF + VL+ L+ + L S E
Sbjct: 1 AFPRSNLQEITTLGRGEFGEVFLAKAKGIEEEGGETLVLVKALQKTKDENLQS------E 54
Query: 199 FNREL 203
F REL
Sbjct: 55 FRREL 59
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
0.326 0.139 0.444
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,274,992
Number of extensions: 1138878
Number of successful extensions: 1519
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1504
Number of HSP's successfully gapped: 50
Length of query: 239
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 145
Effective length of database: 6,768,326
Effective search space: 981407270
Effective search space used: 981407270
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 57 (25.6 bits)