RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781020|ref|YP_003065433.1| isopentenyl pyrophosphate
isomerase [Candidatus Liberibacter asiaticus str. psy62]
(337 letters)
>gnl|CDD|73373 cd02811, IDI-2_FMN, Isopentenyl-diphosphate:dimethylallyl
diphosphate isomerase type 2 (IDI-2) FMN-binding domain.
Two types of IDIs have been characterized at present.
The long known IDI-1 is only dependent on divalent
metals for activity, whereas IDI-2 requires a metal, FMN
and NADPH. IDI-2 catalyzes the interconversion of
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP) in the mevalonate pathway..
Length = 326
Score = 393 bits (1011), Expect = e-110
Identities = 150/326 (46%), Positives = 211/326 (64%), Gaps = 5/326 (1%)
Query: 5 RKIDHINIVCKDPGIDRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSM 64
RK +H+ + ++ FDD L+H ALPE+ D++D S EFLGK+LS PLLIS+M
Sbjct: 1 RKDEHLELCLEENVESGGSTGFDDVRLVHNALPELDLDDIDLSTEFLGKRLSAPLLISAM 60
Query: 65 TGGNNKMIERINRNLAIAAEKTKVAMAVGSQRVMFSDHNAIKSFEL-RQYAPHTVLISNL 123
TGG+ K + INRNLA AAE+ +AM VGSQR D +SF + R+ P+ LI+NL
Sbjct: 61 TGGSEK-AKEINRNLAEAAEELGIAMGVGSQRAALEDPELAESFTVVREAPPNGPLIANL 119
Query: 124 GAVQLNYDFGVQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTNFADLSSKIALLSSAMD 183
GAVQLN +GV++A +AV ++ AD L +HLNPLQE +QP G+ +F +I L A+
Sbjct: 120 GAVQLN-GYGVEEARRAVEMIEADALAIHLNPLQEAVQPEGDRDFRGWLERIEELVKALS 178
Query: 184 VPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRGGTSWSRIESHR--DLESDIGIVFQDW 241
VP+++KEVG G+S + +G++ D+AG GGTSW+R+E++R D + + F DW
Sbjct: 179 VPVIVKEVGFGISRETAKRLADAGVKAIDVAGAGGTSWARVENYRAKDSDQRLAEYFADW 238
Query: 242 GIPTPLSLEMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFLKPAMDSSDAV 301
GIPT SL R + IASGG+RNG+DI K++ LGA L G+A PFLK A++ +AV
Sbjct: 239 GIPTAASLLEVRSALPDLPLIASGGIRNGLDIAKALALGADLVGMAGPFLKAALEGEEAV 298
Query: 302 VAAIESLRKEFIVSMFLLGTKRVQEL 327
+ IE + +E +MFL G K + EL
Sbjct: 299 IETIEQIIEELRTAMFLTGAKNLAEL 324
>gnl|CDD|31495 COG1304, LldD, L-lactate dehydrogenase (FMN-dependent) and related
alpha-hydroxy acid dehydrogenases [Energy production and
conversion].
Length = 360
Score = 230 bits (587), Expect = 6e-61
Identities = 120/340 (35%), Positives = 170/340 (50%), Gaps = 26/340 (7%)
Query: 5 RKIDHINIVCKDPGID--RNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLIS 62
K H + + RN++ F+D L R LPE+ D++D S FLG+KLS P++I+
Sbjct: 13 PKAFHYIDGGAEDEVTLRRNREAFEDIALRPRVLPEV--DDIDLSTTFLGQKLSAPIIIA 70
Query: 63 SMTGGN--NKMIERINRNLAIAAEKTKVAMAVGSQRVMFSDHNAIKSFEL-----RQYAP 115
MTGG + E IN LA AA + + VGSQR+ + A F+L R++AP
Sbjct: 71 PMTGGGLAHPEGEVINAKLAAAAGEPFILSTVGSQRI--EEVAAAPPFQLYFSKDREFAP 128
Query: 116 HTV-LISNLGAVQLNY----DFGVQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTNFAD 170
+ V +N GA QL G ++ AV+ + A L +HLN LQE QP G+ +
Sbjct: 129 NLVDRAANAGAKQLVLTVDSPVGGERERDAVNGISAPALAIHLNVLQEATQPEGDRDGKG 188
Query: 171 LSSKIALLSSAMDVPLLLKEVGCGLSSMDIELGLKSGIRY-FDIAGRGGTSWSRIESHRD 229
IA SA+ VP++ KE G G+S + GI D AG GGT IE
Sbjct: 189 GLDSIAEYVSALSVPVISKEDGAGISKEWAGPLVLKGILAPEDAAGAGGTGADGIEVSNH 248
Query: 230 LESDIGIVFQDWGIPTPLSL-EMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLAS 288
G DWGI T SL E+ + + IA GG+R+G+D+ K++ LGA G+
Sbjct: 249 -----GGRQLDWGISTADSLPEIVEAVGDRIEVIADGGIRSGLDVAKALALGADAVGIGR 303
Query: 289 PFLKPAMDS-SDAVVAAIESLRKEFIVSMFLLGTKRVQEL 327
PFL V +E +RKE ++M L G K ++EL
Sbjct: 304 PFLYGLAAGGEAGVERVLEIIRKELKIAMALTGAKNIEEL 343
>gnl|CDD|144604 pfam01070, FMN_dh, FMN-dependent dehydrogenase.
Length = 301
Score = 87.9 bits (219), Expect = 3e-18
Identities = 78/313 (24%), Positives = 119/313 (38%), Gaps = 46/313 (14%)
Query: 20 DRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSMTGGNNKMIERINRNL 79
RN+ FD L R L ++S + D S LG++LS P I+ G L
Sbjct: 23 RRNRAAFDRIRLRPRVLRDVS--DRDTSTTLLGQRLSLPFGIAPT-GMQGLAHPDGELAL 79
Query: 80 AIAAEKTKVAMAVGSQRVMFSDHNAIKSFE-LRQYAPHTVL--ISNLGAVQLNYDFGVQK 136
A AA + + + A S E + A + + +L D +++
Sbjct: 80 ARAAAAAGIPFVLST--------VASTSLEEVAAAAGGPLWFQLYVPKDRELTEDL-LER 130
Query: 137 AHQAVHVLGADGLFLHLNPLQEIIQPNGNTNFADLSSKIALLSSAMDVPLLLKEVGCGLS 196
A A G L L ++ + N D +A L PL+LK + LS
Sbjct: 131 AEAA----GYKALVLTVDTPVLGNRERDLRNGDD----LAWLRDQWKGPLVLKGI---LS 179
Query: 197 SMDIELGLKSGIRYFDIAGRGGTSWSRIESHRDLESDIGIVFQDWGIPTPLSL-EMARPY 255
D + +++G+ ++ GG R L D T +L E+
Sbjct: 180 PEDAKRAVEAGVDGIVVSNHGG---------RQL---------DGAPATIDALPEIVAAV 221
Query: 256 CNEAQFIASGGLRNGVDILKSIILGASLGGLASPFLKP-AMDSSDAVVAAIESLRKEFIV 314
+ GG+R G D+LK++ LGA L PFL A V A+E LR E
Sbjct: 222 GGRIPVLVDGGIRRGTDVLKALALGADAVLLGRPFLYGLAAGGEAGVAHALEILRDELER 281
Query: 315 SMFLLGTKRVQEL 327
+M LLG + +L
Sbjct: 282 TMALLGCTSIADL 294
>gnl|CDD|73371 cd02809, alpha_hydroxyacid_oxid_FMN, Family of homologous
FMN-dependent alpha-hydroxyacid oxidizing enzymes. This
family occurs in both prokaryotes and eukaryotes.
Members of this family include flavocytochrome b2
(FCB2), glycolate oxidase (GOX), lactate monooxygenase
(LMO), mandelate dehydrogenase (MDH), and long chain
hydroxyacid oxidase (LCHAO). In green plants, glycolate
oxidase is one of the key enzymes in photorespiration
where it oxidizes glycolate to glyoxylate. LMO catalyzes
the oxidation of L-lactate to acetate and carbon
dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate.
It is an enzyme in the mandelate pathway that occurs in
several strains of Pseudomonas which converts
(R)-mandelate to benzoate..
Length = 299
Score = 64.7 bits (158), Expect = 3e-11
Identities = 74/318 (23%), Positives = 114/318 (35%), Gaps = 62/318 (19%)
Query: 21 RNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSMTGGNNKMIERINRNLA 80
RN+ FD L R L ++S + D S LG+KL+ P I+ TG A
Sbjct: 31 RNRAAFDRIRLRPRVLRDVS--KRDTSTTLLGQKLAMPFGIAP-TGLQGLAHPDGELATA 87
Query: 81 IAAEKTKVAMAVGSQRVMFSDHNAIKSFELRQYAPHTVLISNLGAVQLNYDFG------- 133
AA + + + + S E + A QL Y
Sbjct: 88 RAAAAAGIPFTLSTV--------STTSLE--EVAAAA---PGPRWFQL-YVPRDREITED 133
Query: 134 -VQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTNFADLSSKIALLSSAMDVPLLLKEVG 192
+++A A G L L + + + D +A L S PL+LK +
Sbjct: 134 LLRRAEAA----GYKALVLTV----DTPVLGRRLTWDD----LAWLRSQWKGPLILKGI- 180
Query: 193 CGLSSMDIELGLKSGIRYFDIAGRGGTSWSRIESHRDLESDIGIVFQDWGIPTPLSL--E 250
L+ D + +G ++ GG R L+ G P + E
Sbjct: 181 --LTPEDALRAVDAGADGIVVSNHGG---------RQLD----------GAPATIDALPE 219
Query: 251 MARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFLKP-AMDSSDAVVAAIESLR 309
+ + + GG+R G D+LK++ LGA + PFL A V +E LR
Sbjct: 220 IVAAVGGRIEVLLDGGIRRGTDVLKALALGADAVLIGRPFLYGLAAGGEAGVAHVLEILR 279
Query: 310 KEFIVSMFLLGTKRVQEL 327
E +M LLG + +L
Sbjct: 280 DELERAMALLGCASLADL 297
>gnl|CDD|73376 cd02922, FCB2_FMN, Flavocytochrome b2 (FCB2) FMN-binding domain.
FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a
respiratory enzyme located in the intermembrane space of
fungal mitochondria which catalyzes the oxidation of
L-lactate to pyruvate. FCB2 also participates in a short
electron-transport chain involving cytochrome c and
cytochrome oxidase which ultimately directs the reducing
equivalents gained from L-lactate oxidation to oxygen,
yielding one molecule of ATP for every L-lactate
molecule consumed. FCB2 is composed of 2 domains: a
C-terminal flavin-binding domain, which includes the
active site for lacate oxidation, and an N-terminal
b2-cytochrome domain, required for efficient cytochrome
c reduction. FCB2 is a homotetramer and contains two
noncovalently bound cofactors, FMN and heme per
subunit..
Length = 344
Score = 63.7 bits (155), Expect = 7e-11
Identities = 83/351 (23%), Positives = 124/351 (35%), Gaps = 80/351 (22%)
Query: 20 DRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLIS--SMTGGNNKMIERINR 77
N + F R L ++ +VD S LG K+S P IS ++ + E
Sbjct: 30 RENLEAFQRIRFRPRVLRDVE--KVDTSTTILGHKVSLPFFISPAALAKLAHPDGEL--- 84
Query: 78 NLAIAAEKTKVAMAVGSQRVMFSDHNAIKSFE--LRQYAPHTVL---------------- 119
NLA AA K + + + NA S E + P L
Sbjct: 85 NLARAAGKHGILQMIST--------NASCSLEEIVDARPPDQPLFFQLYVNKDRTKTEEL 136
Query: 120 ---ISNLG--AVQLNYDFGV---------QKAHQAVHVLGADGLFLHLNPLQEIIQPNGN 165
LG A+ L D V KA +AV A +
Sbjct: 137 LKRAEKLGAKAIFLTVDAPVLGKRERDERLKAEEAVSDGPAGKK--TKAKGGGAGRAMSG 194
Query: 166 TNFADLS-SKIALLSSAMDVPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRGGTSWSRI 224
L+ I L +P++LK V D L + G+ ++ GG
Sbjct: 195 FIDPTLTWDDIKWLRKHTKLPIVLKGVQTV---EDAVLAAEYGVDGIVLSNHGG------ 245
Query: 225 ESHRDLESDIGIVFQDWGIPTPLS--LEMARPYC----NEAQFIASGGLRNGVDILKSII 278
R L+ P P+ LE+ R +C ++ + GG+R G D+LK++
Sbjct: 246 ---RQLD----------TAPAPIEVLLEI-RKHCPEVFDKIEVYVDGGVRRGTDVLKALC 291
Query: 279 LGASLGGLASPFL-KPAMDSSDAVVAAIESLRKEFIVSMFLLGTKRVQELY 328
LGA GL PFL + + V AI+ L+ E +M LLG + +L
Sbjct: 292 LGAKAVGLGRPFLYALSAYGEEGVEKAIQILKDEIETTMRLLGVTSLDQLG 342
>gnl|CDD|35758 KOG0538, KOG0538, KOG0538, Glycolate oxidase [Energy production and
conversion].
Length = 363
Score = 59.1 bits (143), Expect = 2e-09
Identities = 73/348 (20%), Positives = 127/348 (36%), Gaps = 59/348 (16%)
Query: 20 DRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSMTGGNNKMIE-RINRN 78
D N F R L ++S ++D S LG+K+S P++I+ KM
Sbjct: 34 DENINAFRRILFRPRILRDVS--KIDTSTTVLGQKISAPIMIAPT--AMQKMAHPDGELA 89
Query: 79 LAIAAEKTKVAMAVGS------QRVMFSDHNAIKSFELRQYAPHTVLIS--------NLG 124
A AA+ M + S + + + I+ F+L Y +
Sbjct: 90 TARAAQAAGTIMILSSWATCSVEDIASAAPPGIRWFQLYVYKDRDITEQLVKRAEKAGFK 149
Query: 125 AVQLNYD---FGVQKAHQAVHVLGADGLFLH--LNPLQEIIQPNGNTNFADLSSK----- 174
A+ L D G +++ L L ++ G++ A S
Sbjct: 150 ALVLTVDTPRLGRRESDIKNKFSLPKNLTLKNFEGLKLTEVEEAGDSGLAAYVSSQIDPS 209
Query: 175 -----IALLSSAMDVPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRGGTSWSRIESHRD 229
I L S +P+++K V L+ D +++G+ ++ GG R
Sbjct: 210 LSWKDIKWLRSITKLPIVVKGV---LTGEDARKAVEAGVAGIIVSNHGG---------RQ 257
Query: 230 LESDIGIVFQDWGIPTPLSL--EMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLA 287
L+ +P + E+ + GG+R G D+LK++ LGA +
Sbjct: 258 LD----------YVPATIEALPEVVKAVEGRIPVFLDGGVRRGTDVLKALALGAKGVFIG 307
Query: 288 SPFL-KPAMDSSDAVVAAIESLRKEFIVSMFLLGTKRVQELYLNTALI 334
P + A V ++ LR EF ++M L G + V+E+ N L
Sbjct: 308 RPIVWGLAAKGEAGVKKVLDILRDEFELTMALSGCRSVKEITRNHVLT 355
>gnl|CDD|73383 cd03332, LMO_FMN, L-Lactate 2-monooxygenase (LMO) FMN-binding
domain. LMO is a FMN-containing enzyme that catalyzes
the conversion of L-lactate and oxygen to acetate,
carbon dioxide, and water. LMO is a member of the family
of alpha-hydroxy acid oxidases. It is thought to be a
homooctamer with two- and four- fold axes in the center
of the octamer..
Length = 383
Score = 48.7 bits (116), Expect = 2e-06
Identities = 74/352 (21%), Positives = 122/352 (34%), Gaps = 66/352 (18%)
Query: 19 IDRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLL------ISSMTGGNNKMI 72
N+ F W ++ R L E D SVE G+ L+ PLL
Sbjct: 50 ARANRDAFSRWRIVPRML--RGVTERDLSVELFGRTLAAPLLLAPIGVQELFHPDAELAT 107
Query: 73 ERINRNLAI------AAEKT--KVAMAVGSQRVMF-----SDHNAIKSFELR-QYAPHTV 118
R L + A+ + VA A G F D + +S R + A + V
Sbjct: 108 ARAAAELGVPYILSTASSSSIEDVAAAAGDAPRWFQLYWPKDDDLTESLLRRAEKAGYRV 167
Query: 119 LISNLGAVQLNY-----DFGV--QKAHQAVHVLGADGLFLHL--NPLQEIIQPNGNTN-- 167
L+ L L + D G + +D +F P+ E +
Sbjct: 168 LVVTLDTWSLGWRPRDLDLGYLPFLRGIGIANYFSDPVFRKKLAEPVGEDPEAPPPMEAA 227
Query: 168 ---FADLSS-------KIALLSSAMDVPLLLKEVGCGLSSMDIELGLKSGIRYFDIAGRG 217
F + S +A L D+P++LK + L D +++G+ ++ G
Sbjct: 228 VARFVSVFSGPSLTWEDLAFLREWTDLPIVLKGI---LHPDDARRAVEAGVDGVVVSNHG 284
Query: 218 GTSWSRIESHRDLESDIGIVFQDWGIPTPLSL-EMARPYCNEAQFIASGGLRNGVDILKS 276
G D I +L E+ + + G+R G DI+K+
Sbjct: 285 GRQ------------------VDGSIAALDALPEIVEAVGDRLTVLFDSGVRTGADIMKA 326
Query: 277 IILGASLGGLASPFLKP-AMDSSDAVVAAIESLRKEFIVSMFLLGTKRVQEL 327
+ LGA + P+ A+ D V + +L E ++M L G + + EL
Sbjct: 327 LALGAKAVLIGRPYAYGLALGGEDGVEHVLRNLLAELDLTMGLAGIRSIAEL 378
>gnl|CDD|73370 cd02808, GltS_FMN, Glutamate synthase (GltS) FMN-binding domain.
GltS is a complex iron-sulfur flavoprotein that
catalyzes the reductive synthesis of L-glutamate from
2-oxoglutarate and L-glutamine via intramolecular
channelling of ammonia, a reaction in the plant, yeast
and bacterial pathway for ammonia assimilation. It is a
multifunctional enzyme that functions through three
distinct active centers, carrying out L-glutamine
hydrolysis, conversion of 2-oxoglutarate into
L-glutamate, and electron uptake from an electron
donor..
Length = 392
Score = 45.6 bits (108), Expect = 2e-05
Identities = 68/308 (22%), Positives = 108/308 (35%), Gaps = 40/308 (12%)
Query: 8 DHINIVCKDPGIDRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGK--KLSFPLLISSMT 65
N + G R+ F H P+ D+ K KL P IS+M+
Sbjct: 27 RAGNSRGRPFGTLRDLLEFGAQLAKHPLEPDEEVDDRVTIGPNAEKPLKLDSPFNISAMS 86
Query: 66 GGNNKMIERINRNLAIAAEKTKVAMAVGSQRVMFSDHNAIKSFELRQYAP-----HTVLI 120
G + + LAI A A G + + ++Q A +
Sbjct: 87 FG--ALSKEAKEALAIGAALAGTASNTG-EGGELPEEREGGGDIIKQVASGRFGVRPEYL 143
Query: 121 SNLGAVQLNYDFGVQKAHQAVHVLGAD-----GLFLHLNPLQEIIQPNGNTNF---ADLS 172
+ A+++ G + H+ G + P ++I P + + DL+
Sbjct: 144 NKADAIEIKIGQGAKPGEGG-HLPGEKVTEEIAKIRGIPPGVDLISPPPHHDIYSIEDLA 202
Query: 173 SKIALLSSAMD-VPLLLKEVGCGLSSMDIELGLKSG-IRYFDIAGR-GGTSWSRIESHRD 229
I L A P+ +K + G DI G+ + + I G GGT + + D
Sbjct: 203 QLIEDLREATGGKPIGVK-LVAGHGEGDIAAGVAAAGADFITIDGAEGGTGAAPLTF-ID 260
Query: 230 LESDIGIVFQDWGIPTPLSLEMARPYCNEA------QFIASGGLRNGVDILKSIILGASL 283
G+PT L L A + IASGGLR G D+ K++ LGA
Sbjct: 261 ----------HVGLPTELGLARAHQALVKNGLRDRVSLIASGGLRTGADVAKALALGADA 310
Query: 284 GGLASPFL 291
G+ + L
Sbjct: 311 VGIGTAAL 318
>gnl|CDD|30418 COG0069, GltB, Glutamate synthase domain 2 [Amino acid transport
and metabolism].
Length = 485
Score = 39.9 bits (93), Expect = 0.001
Identities = 35/134 (26%), Positives = 49/134 (36%), Gaps = 19/134 (14%)
Query: 166 TNFADLSSKIALLSSAMDVPLLLKEVGCGLSSMDIELG-LKSGIRYFDIAG-RGGTSWSR 223
+ DL+ I L A + ++ I G K+G I G GGT S
Sbjct: 285 YSIEDLAQLIKDLKEANPWAKISVKLVAEHGVGTIAAGVAKAGADVITIDGADGGTGASP 344
Query: 224 IESHRDLESDIGIVFQDWGIPTPLSL----EMARPYC--NEAQFIASGGLRNGVDILKSI 277
+ S GIP L L + ++ + IA GGLR G D+ K+
Sbjct: 345 LTSIDH-----------AGIPWELGLAETHQTLVLNGLRDKVKLIADGGLRTGADVAKAA 393
Query: 278 ILGASLGGLASPFL 291
LGA G + L
Sbjct: 394 ALGADAVGFGTAAL 407
>gnl|CDD|73399 cd04737, LOX_like_FMN, L-Lactate oxidase (LOX) FMN-binding domain.
LOX is a member of the family of FMN-containing
alpha-hydroxyacid oxidases and catalyzes the oxidation
of l-lactate using molecular oxygen to generate pyruvate
and H2O2. This family occurs in both prokaryotes and
eukaryotes. Members of this family include
flavocytochrome b2 (FCB2), glycolate oxidase (GOX),
lactate monooxygenase (LMO), mandelate dehydrogenase
(MDH), and long chain hydroxyacid oxidase (LCHAO)..
Length = 351
Score = 39.9 bits (93), Expect = 0.001
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 262 IASGGLRNGVDILKSIILGASLGGLASPFLKP-AMDSSDAVVAAIESLRKEFIVSMFLLG 320
I G+R G + K++ GA + P L A+ + V + +E L KE + M L G
Sbjct: 280 IFDSGVRRGEHVFKALASGADAVAVGRPVLYGLALGGAQGVASVLEHLNKELKIVMQLAG 339
Query: 321 TKRVQEL 327
T+ ++++
Sbjct: 340 TRTIEDV 346
Score = 30.7 bits (69), Expect = 0.68
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 22 NKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSM 64
N + F+ ++ R L + + D S E LG KL P++++ +
Sbjct: 40 NTRAFNHKQIVPRVLQGV--ESPDTSTELLGIKLKTPIIMAPI 80
>gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase.
This family represents a region of the glutamate
synthase protein. This region is expressed as a separate
subunit in the glutamate synthase alpha subunit from
archaebacteria, or part of a large multidomain enzyme in
other organisms. The aligned region of these proteins
contains a putative FMN binding site and Fe-S cluster.
Length = 367
Score = 39.2 bits (92), Expect = 0.001
Identities = 34/117 (29%), Positives = 46/117 (39%), Gaps = 13/117 (11%)
Query: 170 DLSSKIALLSSA-MDVPLLLKEVGCGLSSMDIELGL-KSGIRYFDIAG-RGGTSWSRIES 226
DL+ I L P+ +K + G I G+ K+G I G GGT S S
Sbjct: 188 DLAQLIYDLKEINPKAPISVK-LVSGHGVGTIAAGVAKAGADIILIDGHDGGTGASPKTS 246
Query: 227 --HRDLESDIGIVFQDWGIPTPLSLEMARPYCNEAQFIASGGLRNGVDILKSIILGA 281
H L ++ + L R + IA GGLR G D+ K+ LGA
Sbjct: 247 IKHAGLPWELALAEVH----QTLVENGLR---DRVSLIADGGLRTGADVAKAAALGA 296
>gnl|CDD|73398 cd04736, MDH_FMN, Mandelate dehydrogenase (MDH)-like FMN-binding
domain. MDH is part of a widespread family of
homologous FMN-dependent a-hydroxy acid oxidizing
enzymes that oxidizes (S)-mandelate to phenylglyoxalate.
MDH is an enzyme in the mandelate pathway that occurs in
several strains of Pseudomonas which converts
(R)-mandelate to benzoate. This family occurs in both
prokaryotes and eukaryotes. Members of this family
include flavocytochrome b2 (FCB2), glycolate oxidase
(GOX), lactate monooxygenase (LMO), mandelate
dehydrogenase (MDH), and long chain hydroxyacid oxidase
(LCHAO)..
Length = 361
Score = 36.9 bits (85), Expect = 0.008
Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 3/81 (3%)
Query: 18 GIDRNKKFFDDWHLIHRALPEISFDEVDPSVEFLGKKLSFPLLISSMTGGNNKMIERINR 77
G+ N+ FD W I R L ++S + D S GK S PL+I+ TG N +
Sbjct: 28 GLRHNRDAFDRWRFIPRRLVDVS--KRDISASLFGKVWSAPLVIAP-TGLNGAFWPNGDL 84
Query: 78 NLAIAAEKTKVAMAVGSQRVM 98
LA AA K + + + M
Sbjct: 85 ALARAAAKAGIPFVLSTASNM 105
>gnl|CDD|144171 pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain. This
family is involved in biosynthesis of guanosine
nucleotide. Members of this family contain a TIM barrel
structure. In the inosine monophosphate dehydrogenases 2
CBS domains pfam00571 are inserted in the TIM barrel.
This family is a member of the common phosphate binding
site TIM barrel family.
Length = 467
Score = 32.2 bits (74), Expect = 0.18
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 262 IASGGLRNGVDILKSIILGAS---LGGL 286
IA GG+R DI K++ GAS LG L
Sbjct: 330 IADGGIRYSGDIAKALAAGASAVMLGSL 357
>gnl|CDD|72988 cd03229, ABC_Class3, This class is comprised of all BPD (Binding
Protein Dependent) systems that are largely represented
in archaea and eubacteria and are primarily involved in
scavenging solutes from the environment. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins..
Length = 178
Score = 30.5 bits (69), Expect = 0.61
Identities = 23/105 (21%), Positives = 44/105 (41%), Gaps = 11/105 (10%)
Query: 217 GGTSWSRIE-SHRDLESDIGIVFQDWGIPTPLSLEMARPYCNEAQFIASGGLRNGVDILK 275
G + +E L IG+VFQD+ + L++ SGG + V + +
Sbjct: 60 DGEDLTDLEDELPPLRRRIGMVFQDFALFPHLTVL------ENIALGLSGGQQQRVALAR 113
Query: 276 SIILGASLGGLASPF--LKPAMDSSDAVVAAIESLRKEFIVSMFL 318
++ + + L P L P V A ++SL+ + +++ L
Sbjct: 114 ALAMDPDVLLLDEPTSALDPITRRE--VRALLKSLQAQLGITVVL 156
>gnl|CDD|73364 cd00381, IMPDH, IMPDH: The catalytic domain of the inosine
monophosphate dehydrogenase. IMPDH catalyzes the
NAD-dependent oxidation of inosine 5'-monophosphate
(IMP) to xanthosine 5' monophosphate (XMP). It is a
rate-limiting step in the de novo synthesis of the
guanine nucleotides. There is often a CBS domain
inserted in the middle of this domain, which is proposed
to play a regulatory role. IMPDH is a key enzyme in the
regulation of cell proliferation and differentiation. It
has been identified as an attractive target for
developing chemotherapeutic agents..
Length = 325
Score = 30.5 bits (69), Expect = 0.74
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 262 IASGGLRNGVDILKSIILGASLGGLASPF 290
IA GG+R DI+K++ GA L S
Sbjct: 201 IADGGIRTSGDIVKALAAGADAVMLGSLL 229
>gnl|CDD|32253 COG2070, COG2070, Dioxygenases related to 2-nitropropane
dioxygenase [General function prediction only].
Length = 336
Score = 30.3 bits (68), Expect = 0.81
Identities = 11/40 (27%), Positives = 19/40 (47%)
Query: 252 ARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFL 291
+ IA+GG+ +G I ++ LGA + + FL
Sbjct: 178 VVDAVDGIPVIAAGGIADGRGIAAALALGADGVQMGTRFL 217
>gnl|CDD|73401 cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like
proteins. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
This subgroup has the conserved FMN binding site, but
lacks some catalytic residues and may therefore be
inactive..
Length = 325
Score = 30.2 bits (68), Expect = 0.95
Identities = 14/50 (28%), Positives = 27/50 (54%)
Query: 258 EAQFIASGGLRNGVDILKSIILGASLGGLASPFLKPAMDSSDAVVAAIES 307
+A ASGG+ + D++K ++ GA + S L+ D ++A +E+
Sbjct: 237 KASLAASGGVHDAEDVVKYLLAGADVVMTTSALLRHGPDYIGTLLAGLEA 286
>gnl|CDD|176716 cd09014, BphC-JF8_C_like, C-terminal, catalytic, domain of
BphC_JF8, (2,3-dihydroxybiphenyl 1,2-dioxygenase) from
Bacillus sp. JF8 and similar proteins.
2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes
the extradiol ring cleavage reaction of
2,3-dihydroxybiphenyl, a key step in the
polychlorinated biphenyls (PCBs) degradation pathway
(bph pathway). BphC belongs to the type I extradiol
dioxygenase family, which requires a metal ion in the
active site in its catalytic mechanism. Polychlorinated
biphenyl degrading bacteria demonstrate a multiplicity
of BphCs. This subfamily of BphC is represented by the
enzyme purified from the thermophilic biphenyl and
naphthalene degrader, Bacillus sp. JF8. The members in
this family of BphC enzymes may use either Mn(II) or
Fe(II) as cofactors. The enzyme purified from Bacillus
sp. JF8 is Mn(II)-dependent, however, the enzyme from
Rhodococcus jostii RHAI has Fe(II) bound to it.
BphC_JF8 is thermostable and its optimum activity is at
85 degrees C. The enzymes in this family have an
internal duplication. This family represents the
C-terminal repeat.
Length = 166
Score = 28.8 bits (65), Expect = 2.0
Identities = 9/27 (33%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 2 VNDRKIDHINIVCKDPGIDRNKKFFDD 28
V R++DH+N++ D D N+ F ++
Sbjct: 2 VGVRRLDHVNLLASDV--DANRDFMEE 26
>gnl|CDD|73372 cd02810, DHOD_DHPD_FMN, Dihydroorotate dehydrogenase (DHOD) and
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding
domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
DHPD catalyzes the first step in pyrimidine degradation:
the NADPH-dependent reduction of uracil and thymine to
the corresponding 5,6-dihydropyrimidines. DHPD contains
two FAD, two FMN and eight [4Fe-4S] clusters, arranged
in two electron transfer chains that pass its
homodimeric interface twice. Two of the Fe-S clusters
show a hitherto unobserved coordination involving a
glutamine residue..
Length = 289
Score = 28.7 bits (64), Expect = 2.1
Identities = 38/191 (19%), Positives = 74/191 (38%), Gaps = 19/191 (9%)
Query: 109 ELRQYAPHTVLISNLGAVQLN-YDFGVQKAHQAVHVLGADGLFLHLNPLQEIIQPNGNTN 167
+ ++ P LI+++G Y +K +A GA L L+L+ +
Sbjct: 91 KAKKEFPGQPLIASVGGSSKEDYVELARKIERA----GAKALELNLSCPNVGGGRQLGQD 146
Query: 168 FADLSSKIALLSSAMDVPLLLKEVGCGLSSMDIELGLKS----GIRYF----DIAGRGGT 219
+++ + + +A+D+PLL+K + DI K+ G I+GR
Sbjct: 147 PEAVANLLKAVKAAVDIPLLVK-LSPYFDLEDIVELAKAAERAGADGLTAINTISGRVVD 205
Query: 220 SWSRIESHRDLESDIGIVFQDWGIPTPLSL--EMARPYCNEAQFIASGGLRNGVDILKSI 277
+ + + P L +A + I GG+ +G D+L+ +
Sbjct: 206 LKTVGPGPKRGTGGLS---GAPIRPLALRWVARLAARLQLDIPIIGVGGIDSGEDVLEML 262
Query: 278 ILGASLGGLAS 288
+ GAS +A+
Sbjct: 263 MAGASAVQVAT 273
>gnl|CDD|153133 cd01583, IPMI, 3-isopropylmalate dehydratase catalyzes the
isomerization between 2-isopropylmalate and
3-isopropylmalate. Aconatase-like catalytic domain of
3-isopropylmalate dehydratase and related
uncharacterized proteins. 3-isopropylmalate dehydratase
catalyzes the isomerization between 2-isopropylmalate
and 3-isopropylmalate, via the formation of
2-isopropylmaleate 3-isopropylmalate. IPMI is involved
in fungal and bacterial leucine biosynthesis and is also
found in eukaryotes.
Length = 382
Score = 27.9 bits (63), Expect = 4.3
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 195 LSSMDIELGLKSGIRYFD------IAGRGGTSWSRIESHRDLESDIGIVFQ 239
L +M IE G K+GI D + GRG W ++S D E D +
Sbjct: 183 LCNMAIEAGAKAGIVAPDETTFEYLKGRGKAYWKELKSDEDAEYDKVVEID 233
>gnl|CDD|176555 cd08616, PI-PLCXD1c, Catalytic domain of
phosphatidylinositol-specific phospholipase C, X domain
containing 1. This subfamily corresponds to the
catalytic domain present in a group of
phosphatidylinositol-specific phospholipase C X domain
containing 1 (PI-PLCXD1), 2 (PI-PLCXD2) and 3
(PI-PLCXD3), which are bacterial
phosphatidylinositol-specific phospholipase C (PI-PLC,
EC 4.6.1.13) sequence homologs found in vertebrates. The
typical eukaryotic phosphoinositide-specific
phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain
organization that consists of a PLC catalytic core
domain, and various regulatory domains. The catalytic
core domain is assembled from two highly conserved X-
and Y-regions split by a divergent linker sequence. In
contrast, members in this group contain a single
TIM-barrel type catalytic domain, X domain, and are more
closely related to bacterial PI-PLCs, which participate
in Ca2+-independent PI metabolism, hydrolyzing the
membrane lipid phosphatidylinositol (PI) to produce
phosphorylated myo-inositol and diacylglycerol (DAG).
Although the biological function of eukaryotic PI-PLCXDs
still remains unclear, it may distinct from that of
typical eukaryotic PI-PLCs.
Length = 290
Score = 27.6 bits (62), Expect = 4.5
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 10/41 (24%)
Query: 197 SMDIELGLKSGIRYFDIAGRGGTSWSRIESHRDLESDIGIV 237
S+ I L++GIRYFD+ RI + + ++D+ V
Sbjct: 61 SLTITEQLEAGIRYFDL---------RI-ATKPKDNDLYFV 91
>gnl|CDD|176528 cd08586, PI-PLCc_BcPLC_like, Catalytic domain of Bacillus cereus
phosphatidylinositol-specific phospholipases C and
similar proteins. This subfamily corresponds to the
catalytic domain present in Bacillus cereus
phosphatidylinositol-specific phospholipase C (PI-PLC,
EC 4.6.1.13) and its sequence homologs found in bacteria
and eukaryota. Bacterial PI-PLCs participate in
Ca2+-independent PI metabolism, hydrolyzing the membrane
lipid phosphatidylinositol (PI) to produce
phosphorylated myo-inositol and diacylglycerol (DAG).
Although their precise physiological function remains
unclear, bacterial PI-PLCs may function as virulence
factors in some pathogenic bacteria. Bacterial PI-PLCs
contain a single TIM-barrel type catalytic domain. Their
catalytic mechanism is based on general base and acid
catalysis utilizing two well conserved histidines, and
consists of two steps, a phosphotransfer and a
phosphodiesterase reaction. This family also includes
some uncharacterized eukaryotic homologs, which contains
a single TIM-barrel type catalytic domain, X domain.
They are similar to bacterial PI-PLCs, and distinct from
typical eukaryotic PI-PLCs, which have a multidomain
organization that consists of a PLC catalytic core
domain, and various regulatory domains, and strictly
require Ca2+ for their catalytic activities. The
prototype of this family is Bacillus cereus PI-PLC,
which has a moderate thermal stability and is active as
a monomer.
Length = 279
Score = 27.6 bits (62), Expect = 5.4
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 197 SMDIELGLKSGIRYFDI 213
I L +GIR+ DI
Sbjct: 36 DWSIAEQLNAGIRFLDI 52
>gnl|CDD|30516 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 27.1 bits (60), Expect = 6.8
Identities = 11/43 (25%), Positives = 20/43 (46%)
Query: 250 EMARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLASPFLK 292
E+ + + I GG+ G D L+ I+ GAS + + +
Sbjct: 233 ELYKRLGGDIPIIGVGGIETGEDALEFILAGASAVQVGTALIY 275
>gnl|CDD|176529 cd08587, PI-PLCXDc_like, Catalytic domain of
phosphatidylinositol-specific phospholipase C X domain
containing and similar proteins. This family
corresponds to the catalytic domain present in
phosphatidylinositol-specific phospholipase C X domain
containing proteins (PI-PLCXD) which are bacterial
phosphatidylinositol-specific phospholipase C (PI-PLC,
EC 4.6.1.13) sequence homologs mainly found in
eukaryota. The typical eukaryotic
phosphoinositide-specific phospholipase C (PI-PLC, EC
3.1.4.11) have a multidomain organization that consists
of a PLC catalytic core domain, and various regulatory
domains. The catalytic core domain is assembled from two
highly conserved X- and Y-regions split by a divergent
linker sequence. In contrast, eukaryotic PI-PLCXDs and
their bacterial homologs contain a single TIM-barrel
type catalytic domain, X domain, which is more closely
related to that of bacterial PI-PLCs. Although the
biological function of eukaryotic PI-PLCXDs still
remains unclear, it may be distinct from that of typical
eukaryotic PI-PLCs.
Length = 288
Score = 26.9 bits (60), Expect = 7.3
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 9/31 (29%)
Query: 204 LKSGIRYFDIAGRGGTSWSRIESHRDLESDI 234
L++GIRYFD+ R+ D E+ +
Sbjct: 61 LEAGIRYFDL---------RVAYKPDSENKL 82
>gnl|CDD|30622 COG0274, DeoC, Deoxyribose-phosphate aldolase [Nucleotide transport
and metabolism].
Length = 228
Score = 26.7 bits (59), Expect = 8.4
Identities = 12/38 (31%), Positives = 15/38 (39%)
Query: 251 MARPYCNEAQFIASGGLRNGVDILKSIILGASLGGLAS 288
M ASGG+R D I GA+ G +S
Sbjct: 176 MKETVGGRVGVKASGGIRTAEDAKAMIEAGATRIGTSS 213
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.321 0.138 0.400
Gapped
Lambda K H
0.267 0.0731 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,063,342
Number of extensions: 217808
Number of successful extensions: 538
Number of sequences better than 10.0: 1
Number of HSP's gapped: 520
Number of HSP's successfully gapped: 39
Length of query: 337
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 243
Effective length of database: 4,232,491
Effective search space: 1028495313
Effective search space used: 1028495313
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.1 bits)