RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15126
(300 letters)
>gnl|CDD|240128 cd04824, eu_ALAD_PBGS_cysteine_rich, Porphobilinogen synthase
(PBGS), which is also called delta-aminolevulinic acid
dehydratase (ALAD), catalyzes the condensation of two
5-aminolevulinic acid (ALA) molecules to form the
pyrrole porphobilinogen (PBG), which is the second step
in the biosynthesis of tetrapyrroles, such as heme,
vitamin B12 and chlorophyll. This reaction involves the
formation of a Schiff base link between the substrate
and the enzyme. PBGSs are metalloenzymes, some of which
have a second, allosteric metal binding site, beside the
metal ion binding site in their active site. Although
PBGS is a family of homologous enzymes, its metal ion
utilization at catalytic site varies between zinc and
magnesium and/or potassium. PBGS can be classified into
two groups based on differences in their active site
metal binding site. The eukaryotic PBGSs represented by
this model, which contain a cysteine-rich zinc binding
motif (DXCXCX(Y/F)X3G(H/Q)CG), require zinc for their
activity, they do not contain an additional allosteric
metal binding site and do not bind magnesium.
Length = 320
Score = 362 bits (930), Expect = e-126
Identities = 147/292 (50%), Positives = 185/292 (63%), Gaps = 52/292 (17%)
Query: 5 DETASFADTPDNPLFQVIPMIRKQFPSLTIACDVCLCGYTSHGHCAIFNEDGSIHYEKTL 64
D + S AD D P+ Q I +IR++FP L IACDVCLC YTSHGHC I EDG+I+ E ++
Sbjct: 81 DRSGSAADDEDGPVIQAIKLIREEFPELLIACDVCLCEYTSHGHCGILYEDGTINNEASV 140
Query: 65 KRLADISKAFSDAGAHIVAPSDMMDNRIHAIKQSLFTSRQSSTTGLLSYSAKFCSAFYGP 124
KRLA+++ A++ AGAHIVAPSDMMD R+ AIKQ+L + + ++SYSAKF S YGP
Sbjct: 141 KRLAEVALAYAKAGAHIVAPSDMMDGRVRAIKQALIQAGLGNKVSVMSYSAKFASCLYGP 200
Query: 125 FREAAGSAPTFGDRSCYQLPCGSKGLAIRAAVCLCGYTSHGHCAIFNEDGSIHYEKTLKR 184
FR+AA SAP+FGDR CYQLP G++GLA+RA
Sbjct: 201 FRDAACSAPSFGDRRCYQLPPGARGLALRAVE---------------------------- 232
Query: 185 LADISKAFSDAVYVPNHNTDRFQARDVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFV 244
RDVS+GAD +MVKP PYLDI+ E K +HP PL V
Sbjct: 233 ------------------------RDVSEGADMIMVKPGTPYLDIVREAKDKHPDLPLAV 268
Query: 245 YQVSGEYAMLAFAAQAGALDLKRALMETLTCLRRGGADVIISYYTPRVLEWL 296
Y VSGEYAML AA+AGA DLKRA++E +T RR GAD+II+Y+TP +L+WL
Sbjct: 269 YHVSGEYAMLHAAAEAGAFDLKRAVLEAMTGFRRAGADIIITYFTPELLDWL 320
>gnl|CDD|214968 smart01004, ALAD, Delta-aminolevulinic acid dehydratase. This
entry represents porphobilinogen (PBG) synthase (PBGS,
or 5-aminoaevulinic acid dehydratase, or ALAD, ), which
functions during the second stage of tetrapyrrole
biosynthesis. This enzyme catalyses a Knorr-type
condensation reaction between two molecules of ALA to
generate porphobilinogen, the pyrrolic building block
used in later steps. The structure of the enzyme is
based on a TIM barrel topology made up of eight
identical subunits, where each subunit binds to a metal
ion that is essential for activity, usually zinc (in
yeast, mammals and certain bacteria) or magnesium (in
plants and other bacteria). A lysine has been implicated
in the catalytic mechanism. The lack of PBGS enzyme
causes a rare porphyric disorder known as ALAD
porphyria, which appears to involve conformational
changes in the enzyme.
Length = 321
Score = 346 bits (890), Expect = e-120
Identities = 123/299 (41%), Positives = 166/299 (55%), Gaps = 62/299 (20%)
Query: 2 DLRDETASFADTPDNPLFQVIPMIRKQFPSLTIACDVCLCGYTSHGHCAIFNEDGSIHYE 61
+ +DE S A PD + + I I+K FP L + DVCLC YTSHGHC I +EDG + +
Sbjct: 81 EKKDEDGSEAYNPDGLVQRAIRAIKKAFPDLVVITDVCLCEYTSHGHCGILDEDGYVDND 140
Query: 62 KTLKRLADISKAFSDAGAHIVAPSDMMDNRIHAIKQSL----FTSRQSSTTGLLSYSAKF 117
+TL+ LA + + ++AGA IVAPSDMMD R+ AI+++L FT ++SYSAK+
Sbjct: 141 ETLEVLAKQALSQAEAGADIVAPSDMMDGRVGAIREALDAAGFTD-----VPIMSYSAKY 195
Query: 118 CSAFYGPFREAAGSAPTFGDRSCYQLPCGSKGLAIRAAVCLCGYTSHGHCAIFNEDGSIH 177
SAFYGPFR+AAGSAP FGDR YQ+ ++ A+R
Sbjct: 196 ASAFYGPFRDAAGSAPQFGDRKTYQMDPANRREALREV---------------------- 233
Query: 178 YEKTLKRLADISKAFSDAVYVPNHNTDRFQARDVSQGADFLMVKPALPYLDIISEVKSRH 237
A D+++GAD +MVKPALPYLDII VK
Sbjct: 234 ------------------------------ALDIAEGADMVMVKPALPYLDIIRRVKDEF 263
Query: 238 PAYPLFVYQVSGEYAMLAFAAQAGALDLKRALMETLTCLRRGGADVIISYYTPRVLEWL 296
P+ YQVSGEYAM+ AAQ G +D +R ++E+L ++R GAD+II+Y+ WL
Sbjct: 264 D-LPVAAYQVSGEYAMIKAAAQNGWIDEERVVLESLLSIKRAGADLIITYFAKEAARWL 321
>gnl|CDD|215945 pfam00490, ALAD, Delta-aminolevulinic acid dehydratase.
Length = 322
Score = 341 bits (877), Expect = e-118
Identities = 126/299 (42%), Positives = 166/299 (55%), Gaps = 63/299 (21%)
Query: 2 DLRDETASFADTPDNPLFQVIPMIRKQFPSLTIACDVCLCGYTSHGHCAIFNEDGSIHYE 61
+L+DE S A PD + + I I++ FP L + DVCLC YTSHGHC I EDG + +
Sbjct: 83 ELKDEDGSEAYNPDGLVQRAIRAIKEAFPDLVVITDVCLCEYTSHGHCGIL-EDGEVDND 141
Query: 62 KTLKRLADISKAFSDAGAHIVAPSDMMDNRIHAIKQSL----FTSRQSSTTGLLSYSAKF 117
+TL+ LA + + ++AGA IVAPSDMMD R+ AI+++L FT ++SYSAK+
Sbjct: 142 ETLELLAKQALSHAEAGADIVAPSDMMDGRVGAIREALDEAGFT-----DVPIMSYSAKY 196
Query: 118 CSAFYGPFREAAGSAPTFGDRSCYQLPCGSKGLAIRAAVCLCGYTSHGHCAIFNEDGSIH 177
SAFYGPFR+AAGSAP FGDR YQ+ ++ A+R
Sbjct: 197 ASAFYGPFRDAAGSAPAFGDRKTYQMDPANRREALREV---------------------- 234
Query: 178 YEKTLKRLADISKAFSDAVYVPNHNTDRFQARDVSQGADFLMVKPALPYLDIISEVKSRH 237
A D+ +GAD +MVKPALPYLDII VK R
Sbjct: 235 ------------------------------ALDIEEGADMVMVKPALPYLDIIRRVKDRF 264
Query: 238 PAYPLFVYQVSGEYAMLAFAAQAGALDLKRALMETLTCLRRGGADVIISYYTPRVLEWL 296
P+ YQVSGEYAM+ AAQ G LD KR ++E+L ++R GAD+II+Y+ WL
Sbjct: 265 D-LPVAAYQVSGEYAMIKAAAQNGWLDEKRVVLESLLSIKRAGADLIITYFAKEAARWL 322
>gnl|CDD|223191 COG0113, HemB, Delta-aminolevulinic acid dehydratase [Coenzyme
metabolism].
Length = 330
Score = 318 bits (817), Expect = e-109
Identities = 121/303 (39%), Positives = 166/303 (54%), Gaps = 62/303 (20%)
Query: 1 MDLRDETASFADTPDNPLFQVIPMIRKQFPSLTIACDVCLCGYTSHGHCAIFNEDGSIHY 60
+DET S A PD + + + I++ FP L + DVCLC YT HGHC I ++ G +
Sbjct: 86 DSKKDETGSEAYDPDGIVQRAVRAIKEAFPELVVITDVCLCEYTDHGHCGILDDGGYVDN 145
Query: 61 EKTLKRLADISKAFSDAGAHIVAPSDMMDNRIHAIKQSL----FTSRQSSTTGLLSYSAK 116
++TL+ LA + + ++AGA IVAPSDMMD R+ AI+++L F ++SYSAK
Sbjct: 146 DETLEILAKQAVSQAEAGADIVAPSDMMDGRVGAIREALDEAGFID-----VPIMSYSAK 200
Query: 117 FCSAFYGPFREAAGSAPTFGDRSCYQLPCGSKGLAIRAAVCLCGYTSHGHCAIFNEDGSI 176
+ SAFYGPFR+AAGSAP FGDR YQ+ ++ A+R
Sbjct: 201 YASAFYGPFRDAAGSAPKFGDRKTYQMDPANRREALREI--------------------- 239
Query: 177 HYEKTLKRLADISKAFSDAVYVPNHNTDRFQARDVSQGADFLMVKPALPYLDIISEVKSR 236
D+ +GAD LMVKPALPYLDII VK
Sbjct: 240 -------------------------------ELDIEEGADILMVKPALPYLDIIRRVKEE 268
Query: 237 HPAYPLFVYQVSGEYAMLAFAAQAGALDLKRALMETLTCLRRGGADVIISYYTPRVLEWL 296
P+ YQVSGEYAM+ AAQ G +D ++ ++E+LT ++R GAD+II+Y+ V EWL
Sbjct: 269 FNL-PVAAYQVSGEYAMIKAAAQNGWIDEEKVVLESLTSIKRAGADLIITYFAKEVAEWL 327
Query: 297 RED 299
+E
Sbjct: 328 KEG 330
>gnl|CDD|238226 cd00384, ALAD_PBGS, Porphobilinogen synthase (PBGS), which is also
called delta-aminolevulinic acid dehydratase (ALAD),
catalyzes the condensation of two 5-aminolevulinic acid
(ALA) molecules to form the pyrrole porphobilinogen
(PBG), which is the second step in the biosynthesis of
tetrapyrroles, such as heme, vitamin B12 and
chlorophyll. This reaction involves the formation of a
Schiff base link between the substrate and the enzyme.
PBGSs are metalloenzymes, some of which have a second,
allosteric metal binding site, beside the metal ion
binding site in their active site. Although PBGS is a
family of homologous enzymes, its metal ion utilization
at catalytic site varies between zinc and magnesium
and/or potassium. PBGS can be classified into two groups
based on differences in their active site metal binding
site. They either contain a cysteine-rich zinc binding
site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an
aspartate-rich magnesium binding site (consensus
DXALDX(Y/F)X3G(H/Q)DG). The cysteine-rich zinc binding
site appears more common. Most members represented by
this model also have a second allosteric magnesium
binding site (consensus RX~164DX~65EXXXD, missing in a
eukaryotic subfamily with cysteine-rich zinc binding
site).
Length = 314
Score = 307 bits (790), Expect = e-105
Identities = 115/297 (38%), Positives = 160/297 (53%), Gaps = 63/297 (21%)
Query: 4 RDETASFADTPDNPLFQVIPMIRKQFPSLTIACDVCLCGYTSHGHCAIFNEDGSIHYEKT 63
+DE S A PD + + I I++ P L + DVCLC YT HGHC I +D + + T
Sbjct: 77 KDEIGSEAYDPDGIVQRAIRAIKEAVPELVVITDVCLCEYTDHGHCGIL-KDDYVDNDAT 135
Query: 64 LKRLADISKAFSDAGAHIVAPSDMMDNRIHAIKQSL----FTSRQSSTTGLLSYSAKFCS 119
L+ LA I+ + ++AGA IVAPSDMMD R+ AI+++L F+ ++SYSAK+ S
Sbjct: 136 LELLAKIAVSHAEAGADIVAPSDMMDGRVAAIREALDEAGFSD-----VPIMSYSAKYAS 190
Query: 120 AFYGPFREAAGSAPTFGDRSCYQLPCGSKGLAIRAAVCLCGYTSHGHCAIFNEDGSIHYE 179
AFYGPFR+AA SAP+FGDR YQ+ ++ A+R
Sbjct: 191 AFYGPFRDAADSAPSFGDRKTYQMDPANRREALREV------------------------ 226
Query: 180 KTLKRLADISKAFSDAVYVPNHNTDRFQARDVSQGADFLMVKPALPYLDIISEVKSRHPA 239
D+ +GAD LMVKPAL YLDII +V+ R
Sbjct: 227 ----------------------------ELDIEEGADILMVKPALAYLDIIRDVRERFD- 257
Query: 240 YPLFVYQVSGEYAMLAFAAQAGALDLKRALMETLTCLRRGGADVIISYYTPRVLEWL 296
P+ Y VSGEYAM+ AA+ G +D +R ++E+LT ++R GAD+II+Y+ WL
Sbjct: 258 LPVAAYNVSGEYAMIKAAAKNGWIDEERVVLESLTSIKRAGADLIITYFAKDAARWL 314
>gnl|CDD|236450 PRK09283, PRK09283, delta-aminolevulinic acid dehydratase;
Validated.
Length = 323
Score = 186 bits (476), Expect = 2e-57
Identities = 75/146 (51%), Positives = 98/146 (67%), Gaps = 10/146 (6%)
Query: 2 DLRDETASFADTPDNPLFQVIPMIRKQFPSLTIACDVCLCGYTSHGHCAIFNEDGSIHYE 61
+L+DE S A PD + + I I+K FP L + DVCL YTSHGHC I EDG + +
Sbjct: 83 ELKDEDGSEAYNPDGLVQRAIRAIKKAFPELGVITDVCLDEYTSHGHCGIL-EDGYVDND 141
Query: 62 KTLKRLADISKAFSDAGAHIVAPSDMMDNRIHAIKQSL----FTSRQSSTTGLLSYSAKF 117
+TL+ LA + + ++AGA IVAPSDMMD R+ AI+++L FT ++SYSAK+
Sbjct: 142 ETLELLAKQALSQAEAGADIVAPSDMMDGRVGAIREALDEAGFTD-----VPIMSYSAKY 196
Query: 118 CSAFYGPFREAAGSAPTFGDRSCYQL 143
SAFYGPFR+AAGSAP FGDR YQ+
Sbjct: 197 ASAFYGPFRDAAGSAPQFGDRKTYQM 222
Score = 154 bits (391), Expect = 1e-44
Identities = 46/90 (51%), Positives = 61/90 (67%), Gaps = 1/90 (1%)
Query: 208 ARDVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQVSGEYAMLAFAAQAGALDLKR 267
A D+ +GAD +MVKPALPYLDII VK P+ YQVSGEYAM+ AAQ G +D +R
Sbjct: 235 ALDIEEGADMVMVKPALPYLDIIRRVKDEFN-LPVAAYQVSGEYAMIKAAAQNGWIDEER 293
Query: 268 ALMETLTCLRRGGADVIISYYTPRVLEWLR 297
++E+L ++R GAD I++Y+ WLR
Sbjct: 294 VVLESLLSIKRAGADGILTYFAKDAARWLR 323
Score = 46.6 bits (112), Expect = 6e-06
Identities = 18/34 (52%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 156 VCLCGYTSHGHCAIFNEDGSIHYEKTLKRLADIS 189
VCL YTSHGHC I EDG + ++TL+ LA +
Sbjct: 119 VCLDEYTSHGHCGIL-EDGYVDNDETLELLAKQA 151
>gnl|CDD|240127 cd04823, ALAD_PBGS_aspartate_rich, Porphobilinogen synthase (PBGS),
which is also called delta-aminolevulinic acid
dehydratase (ALAD), catalyzes the condensation of two
5-aminolevulinic acid (ALA) molecules to form the
pyrrole porphobilinogen (PBG), which is the second step
in the biosynthesis of tetrapyrroles, such as heme,
vitamin B12 and chlorophyll. This reaction involves the
formation of a Schiff base link between the substrate
and the enzyme. PBGSs are metalloenzymes, some of which
have a second, allosteric metal binding site, beside the
metal ion binding site in their active site. Although
PBGS is a family of homologous enzymes, its metal ion
utilization at catalytic site varies between zinc and
magnesium and/or potassium. PBGS can be classified into
two groups based on differences in their active site
metal binding site. All of PBGS_aspartate_rich contain
an aspartate rich metal binding site with the general
sequence DXALDX(Y/F)X3G(H/Q)DG. They also contain an
allosteric magnesium binding sequence RX~164DX~65EXXXD
and are activated by magnesium and/or potassium, but not
by zinc. PBGSs_aspartate_rich are found in some
bacterial species and photosynthetic organisms such as
vascular plants, mosses and algae, but not in archaea.
Length = 320
Score = 150 bits (381), Expect = 2e-43
Identities = 69/146 (47%), Positives = 91/146 (62%), Gaps = 10/146 (6%)
Query: 2 DLRDETASFADTPDNPLFQVIPMIRKQFPSLTIACDVCLCGYTSHGHCAIFNEDGSIHYE 61
+L+ E S A PDN + + I I++ FP L I DV L YTSHGH I DG I +
Sbjct: 80 ELKSEDGSEAYNPDNLVCRAIRAIKEAFPELGIITDVALDPYTSHGHDGIV-RDGGILND 138
Query: 62 KTLKRLADISKAFSDAGAHIVAPSDMMDNRIHAIKQSL----FTSRQSSTTGLLSYSAKF 117
+T++ L + ++AGA IVAPSDMMD RI AI+++L FT +LSY+AK+
Sbjct: 139 ETVEVLCKQALVQAEAGADIVAPSDMMDGRIGAIREALDAEGFT-----NVSILSYAAKY 193
Query: 118 CSAFYGPFREAAGSAPTFGDRSCYQL 143
SAFYGPFR+A GSAP GD+ YQ+
Sbjct: 194 ASAFYGPFRDALGSAPRKGDKKTYQM 219
Score = 141 bits (357), Expect = 8e-40
Identities = 47/90 (52%), Positives = 60/90 (66%), Gaps = 1/90 (1%)
Query: 208 ARDVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQVSGEYAMLAFAAQAGALDLKR 267
A D+++GAD +MVKP +PYLDII VK P F YQVSGEYAML AAQ G LD +
Sbjct: 232 ALDIAEGADMVMVKPGMPYLDIIRRVKDEFGV-PTFAYQVSGEYAMLKAAAQNGWLDEDK 290
Query: 268 ALMETLTCLRRGGADVIISYYTPRVLEWLR 297
++E+L +R GAD I++Y+ EWLR
Sbjct: 291 VMLESLLAFKRAGADGILTYFAKEAAEWLR 320
>gnl|CDD|172020 PRK13384, PRK13384, delta-aminolevulinic acid dehydratase;
Provisional.
Length = 322
Score = 117 bits (295), Expect = 6e-31
Identities = 45/86 (52%), Positives = 59/86 (68%), Gaps = 1/86 (1%)
Query: 210 DVSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQVSGEYAMLAFAAQAGALDLKRAL 269
D ++GAD LMVKP PYLD++S ++ PL YQV GEYAM+ FAA AGALD + +
Sbjct: 238 DEAEGADILMVKPGTPYLDVLSRLRQETH-LPLAAYQVGGEYAMIKFAALAGALDERAVV 296
Query: 270 METLTCLRRGGADVIISYYTPRVLEW 295
ETL L+R GAD+I+SYY + +W
Sbjct: 297 TETLGGLKRAGADLIVSYYAKQYAQW 322
Score = 109 bits (275), Expect = 5e-28
Identities = 50/135 (37%), Positives = 77/135 (57%), Gaps = 5/135 (3%)
Query: 11 ADT--PDNPLFQVIPMIRKQFPSLTIACDVCLCGYTSHGHCAIFNEDGSIHYEKTLKRLA 68
+DT + L +++ I+ P + + D+C C YT HGHC + + D + + T++ L
Sbjct: 92 SDTWDDNGLLARMVRTIKAAVPEMMVIPDICFCEYTDHGHCGVLHND-EVDNDATVENLV 150
Query: 69 DISKAFSDAGAHIVAPSDMMDNRIHAIKQSLFTSRQSSTTGLLSYSAKFCSAFYGPFREA 128
S + AGA ++APS MMD ++ AI+Q L + +L++SAKF S+FYGPFR A
Sbjct: 151 KQSVTAAKAGADMLAPSAMMDGQVKAIRQGLDAAGFEHVA-ILAHSAKFASSFYGPFRAA 209
Query: 129 AGSAPTFGDRSCYQL 143
+ GDR YQL
Sbjct: 210 VDCELS-GDRKSYQL 223
Score = 31.2 bits (71), Expect = 0.53
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 156 VCLCGYTSHGHCAIFNEDGSIHYEKTLKRL 185
+C C YT HGHC + + D + + T++ L
Sbjct: 121 ICFCEYTDHGHCGVLHND-EVDNDATVENL 149
>gnl|CDD|215237 PLN02433, PLN02433, uroporphyrinogen decarboxylase.
Length = 345
Score = 33.8 bits (78), Expect = 0.085
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 223 ALPYLD-IISEVKSRHPAYPLFVYQVSGEYAMLAFAAQAGA 262
+ PYL+ I+ EVK+RHP PL +Y +G +L A G
Sbjct: 215 SKPYLEKIVDEVKARHPDVPLILY-ANGSGGLLERLAGTGV 254
>gnl|CDD|233585 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model
represents NtrC, a DNA-binding response regulator that
is phosphorylated by NtrB and interacts with sigma-54.
NtrC usually controls the expression of glutamine
synthase, GlnA, and may be called GlnL, GlnG, etc
[Central intermediary metabolism, Nitrogen metabolism,
Regulatory functions, DNA interactions, Signal
transduction, Two-component systems].
Length = 463
Score = 29.7 bits (67), Expect = 2.3
Identities = 27/102 (26%), Positives = 41/102 (40%), Gaps = 15/102 (14%)
Query: 169 IFNEDGSIHY--EKTLKRLADISKAFSDAVYVPNHNTDRFQARDVSQG----ADFLMVKP 222
+ ++D SI + EK L R + F +A V +A Q D M P
Sbjct: 3 VVDDDRSIRWVLEKALSRAGYEVRTFGNAASV-------LRALARGQPDLLITDVRM--P 53
Query: 223 ALPYLDIISEVKSRHPAYPLFVYQVSGEYAMLAFAAQAGALD 264
LD++ ++K RHP P+ V + A Q GA +
Sbjct: 54 GEDGLDLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFE 95
>gnl|CDD|240345 PTZ00287, PTZ00287, 6-phosphofructokinase; Provisional.
Length = 1419
Score = 29.2 bits (65), Expect = 3.7
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 164 HGHCAIFNEDGS-IHYEKTLKRLADISKAFSDAVYV--PNHNTDRFQARDVSQGADFLMV 220
HGH A N+D S + YE+ K + KA + + NH D +D + FL
Sbjct: 96 HGHSASLNDDLSPLQYERI-KYQPTLPKALASEYQILEENHGDDFINKKDYEEVKRFLKN 154
Query: 221 KPALPYLDI 229
LP L++
Sbjct: 155 LHNLPILNV 163
>gnl|CDD|238368 cd00717, URO-D, Uroporphyrinogen decarboxylase (URO-D) is a dimeric
cytosolic enzyme that decarboxylates the four acetate
side chains of uroporphyrinogen III (uro-III) to create
coproporphyrinogen III, without requiring any prosthetic
groups or cofactors. This reaction is located at the
branching point of the tetrapyrrole biosynthetic
pathway, leading to the biosynthesis of heme,
chlorophyll or bacteriochlorophyll. URO-D deficiency is
responsible for the human genetic diseases familial
porphyria cutanea tarda (fPCT) and hepatoerythropoietic
porphyria (HEP).
Length = 335
Score = 28.6 bits (65), Expect = 4.2
Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 223 ALPYL-DIISEVKSRHPAYPLFVYQVSGEYAMLAFAAQAGA 262
LPYL II EVK R P P+ ++ G +L AQ GA
Sbjct: 213 VLPYLKRIIEEVKKRLPGVPVILF-AKGAGGLLEDLAQLGA 252
>gnl|CDD|184349 PRK13824, PRK13824, replication initiation protein RepC;
Provisional.
Length = 404
Score = 28.7 bits (65), Expect = 4.7
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 248 SGEYAMLAFAAQAGALDLKRALMETLTCLRR 278
+ E+ LA A L+R L E LT RR
Sbjct: 148 AEEFEALAEQVAAERKALRR-LRERLTLCRR 177
>gnl|CDD|131498 TIGR02445, fadA, fatty oxidation complex, beta subunit FadA. This
subunit of the FadBA complex has acetyl-CoA
C-acyltransferase (EC 2.3.1.16) activity, and is also
known as beta-ketothiolase and fatty oxidation complex,
beta subunit. This protein is almost always located
adjacent to FadB (TIGR02437). The FadBA complex is the
major complex active for beta-oxidation of fatty acids
in E. coli [Fatty acid and phospholipid metabolism,
Degradation].
Length = 385
Score = 28.4 bits (63), Expect = 5.3
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 42 GYTSHGHCAIFNEDGSIHYEKTLKRLADISKAFSDAGAHIVA 83
G+ + G F+ D I E T++ LA + AF + A
Sbjct: 192 GHDADGFLKQFDYDEVIRPETTVESLAALRPAFDPKNGTVTA 233
>gnl|CDD|238543 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 .
Length = 235
Score = 27.9 bits (63), Expect = 5.5
Identities = 17/45 (37%), Positives = 20/45 (44%), Gaps = 6/45 (13%)
Query: 181 TLKRLADISKAFSDAVYVPNHNTDRFQARDVSQGADFLMVKPALP 225
TLKRLAD F+ AV + N T R + G KPA
Sbjct: 151 TLKRLAD---EFNVAVVITNQVTARPDGAAMFGGDP---KKPAGG 189
>gnl|CDD|179749 PRK04147, PRK04147, N-acetylneuraminate lyase; Provisional.
Length = 293
Score = 28.0 bits (63), Expect = 6.0
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 170 FNEDGSIHYEKTLKRLAD--ISKAFSDAVYV 198
F+EDG I E+ L+RL I K D +YV
Sbjct: 15 FDEDGQID-EQGLRRLVRFNIEKQGIDGLYV 44
>gnl|CDD|173975 cd08210, RLP_RrRLP, Ribulose bisphosphate carboxylase like proteins
(RLPs) similar to R.rubrum RLP. RLP from Rhodospirillum
rubrum plays a role in an uncharacterized sulfur salvage
pathway and has been shown to catalyze a novel
isomerization reaction that converts
5-methylthio-d-ribulose 1-phosphate to a 3:1 mixture of
1-methylthioxylulose 5-phosphate and
1-methylthioribulose 5-phosphate.
Length = 364
Score = 28.0 bits (63), Expect = 7.3
Identities = 22/96 (22%), Positives = 32/96 (33%), Gaps = 12/96 (12%)
Query: 195 AVYVPNHNTDRFQARD-----VSQGADFLMVKPALPYLDIISEVKSRHPAYPLFVYQVSG 249
+Y PN Q + GA +++ P L LD E+ P+ +
Sbjct: 194 TLYAPNVTGPPTQLLERARFAKEAGAGGVLIAPGLTGLDTFRELAEDFDFLPILAHP--- 250
Query: 250 EYAMLAFAAQAGALDLKRALMETLTCLRRGGADVII 285
A +G L TL R GAD +I
Sbjct: 251 --AFAGAFVSSGDGISHALLFGTLF--RLAGADAVI 282
>gnl|CDD|239426 cd03310, CIMS_like, CIMS - Cobalamine-independent methonine
synthase, or MetE. Many members have been characterized
as 5-methyltetrahydropteroyltriglutamate-homocysteine
methyltransferases, EC:2.1.1.14, mostly from bacteria
and plants. This enzyme catalyses the last step in the
production of methionine by transferring a methyl group
from 5-methyltetrahydrofolate to L-homocysteine without
using an intermediate methyl carrier. The active enzyme
has a dual (beta-alpha)8-barrel structure, and this
model covers both the N-and C-terminal barrel, and some
single-barrel sequences, mostly from Archaea. It is
assumed that the homologous N-terminal barrel has
evolved from the C-terminus via gene duplication and has
subsequently lost binding sites, and it seems as if the
two barrels forming the active enzyme may sometimes
reside on different polypeptides. The C-terminal domain
incorporates the Zinc ion, which binds and activates
homocysteine. Side chains from both barrels contribute
to the binding of the folate substrate.
Length = 321
Score = 27.8 bits (62), Expect = 7.4
Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 3/53 (5%)
Query: 225 PYLDIISEVKSRHPAYPLFVYQVSG--EYAMLAFAAQAGALDLKRALMETLTC 275
LD + EV + V+G A+LAF G D L ++L
Sbjct: 100 LELDYLEEVAEAYKEALKVKVVVTGPLTLALLAFLP-NGEPDAYEDLAKSLAE 151
>gnl|CDD|234308 TIGR03682, arCOG04112, diphthamide biosynthesis enzyme Dph2.
Members of this family are the archaeal protein Dph2,
members of the universal archaeal protein family
designated arCOG04112. The chemical function of this
protein is analogous to the radical SAM family
(pfam04055), although the sequence is not homologous.
The chemistry involves [4Fe-4S]-aided formation of a
3-amino-3-carboxypropyl radical rather than the
canonical 5'-deoxyadenosyl radical of the radical SAM
family.
Length = 308
Score = 27.6 bits (62), Expect = 8.3
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 265 LKRALMETLTCLRRGGADVIIS 286
LKR E L G +VIIS
Sbjct: 13 LKRRAFEIAQKLEEKGYEVIIS 34
>gnl|CDD|234277 TIGR03604, TOMM_cyclo_SagD, thiazole/oxazole-forming peptide
maturase, SagD family component. Members of this
protein family include enzymes related to SagD,
previously referred to as a scaffold or docking protein
involved in the biosynthesis of streptolysin S in
Streptococcus pyogenes from the protoxin polypeptide
(product of the sagA gene). Newer evidence describes an
enzymatic activity, an ATP-dependent cyclodehydration
reaction, previously ascribed to the SagC component.
This protein family serves as a marker for widely
distributed prokaryotic systems for making a general
class of heterocycle-containing bacteriocins.
Length = 377
Score = 27.3 bits (61), Expect = 9.8
Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 8/45 (17%)
Query: 232 EVKSRHPAYPLFVYQVSGEYAMLAFAAQAGALDLKRALMETLTCL 276
K+ A PL V +A L++ALME L
Sbjct: 193 LAKNPDDALPLLVVGAGAHL----DPERA----LRKALMEAAQML 229
>gnl|CDD|215801 pfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein.
Length = 682
Score = 27.7 bits (62), Expect = 9.9
Identities = 12/33 (36%), Positives = 14/33 (42%)
Query: 134 TFGDRSCYQLPCGSKGLAIRAAVCLCGYTSHGH 166
G S QL + GL I AA+ L H H
Sbjct: 116 AIGITSNLQLYQTAIGLLILAALMLFAGWFHYH 148
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
0.323 0.136 0.416
Gapped
Lambda K H
0.267 0.0905 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,351,252
Number of extensions: 1434115
Number of successful extensions: 1484
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1463
Number of HSP's successfully gapped: 45
Length of query: 300
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 204
Effective length of database: 6,679,618
Effective search space: 1362642072
Effective search space used: 1362642072
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.2 bits)