RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780673|ref|YP_003065086.1| pyruvate dehydrogenase subunit
beta [Candidatus Liberibacter asiaticus str. psy62]
(467 letters)
>gnl|CDD|30372 COG0022, AcoB, Pyruvate/2-oxoglutarate dehydrogenase complex,
dehydrogenase (E1) component, eukaryotic type, beta
subunit [Energy production and conversion].
Length = 324
Score = 487 bits (1255), Expect = e-138
Identities = 175/325 (53%), Positives = 227/325 (69%), Gaps = 2/325 (0%)
Query: 139 SITVREALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPITEHG 198
+T+ EA+ +A+ EEM RD+ V ++GE+V Y G ++VT+GL ++FG ERVIDTPI E G
Sbjct: 1 QMTMIEAINEAMDEEMERDERVVVLGEDVGVYGGVFRVTKGLQEKFGEERVIDTPIAESG 60
Query: 199 FAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITTSIVFRGPNGAA 258
AGI +GA+ GL+PIVE +F A DQI+N AAK RY SGGQ T IV R PNG
Sbjct: 61 IAGIAVGAALTGLRPIVEIQFADFIYPAFDQIVNQAAKIRYRSGGQFTVPIVIRTPNGGG 120
Query: 259 ARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPNPVIFLENEILYGS-SF 317
AQHSQ A ++H+PGLKVV+P T DAKGLLKAAIRDP+PVIFLE++ LY S
Sbjct: 121 IGGGAQHSQSLEALFAHIPGLKVVMPSTPYDAKGLLKAAIRDPDPVIFLEHKRLYRSFKG 180
Query: 318 EVPMVDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRP 377
EVP +D IP+G+A+I R+GSDVTI+++G + A +AA ELEK GI AE+IDLRT+ P
Sbjct: 181 EVP-EEDYTIPLGKAKIVREGSDVTIVTYGAMVHTALEAAEELEKEGISAEVIDLRTLSP 239
Query: 378 MDWQTIFESVKKTGRLVTVEEGYPQSSVGSTIANQVQRKVFDYLDAPILTITGRDVPMPY 437
+D +TI SVKKTGRLV V E +G+ IA + + FDYLDAPIL + G D P+PY
Sbjct: 240 LDKETIIASVKKTGRLVIVHEAPKTGGIGAEIAALIAEEAFDYLDAPILRVAGPDTPVPY 299
Query: 438 AANLEKLALPNVDEIIESVESICYK 462
+A LEK LPN + I+ +V+ +
Sbjct: 300 SAALEKAYLPNPERIVAAVKKVLEF 324
>gnl|CDD|35744 KOG0524, KOG0524, KOG0524, Pyruvate dehydrogenase E1, beta subunit
[Energy production and conversion].
Length = 359
Score = 472 bits (1216), Expect = e-134
Identities = 199/328 (60%), Positives = 249/328 (75%), Gaps = 3/328 (0%)
Query: 137 TSSITVREALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPITE 196
+TVREAL A+ EEM RD VF+MGEEV +Y GAYKVT+GLL +FG +RV+DTPITE
Sbjct: 32 AKEMTVREALNQAMDEEMDRDPRVFVMGEEVGQYGGAYKVTKGLLDKFGDKRVLDTPITE 91
Query: 197 HGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITTSIVFRGPNG 256
GF GI +GA+ AGL+PI EFMTFNF+MQAIDQIINSAAKT YMSGGQ IVFRGPNG
Sbjct: 92 MGFTGIAVGAAMAGLRPICEFMTFNFSMQAIDQIINSAAKTHYMSGGQQPVPIVFRGPNG 151
Query: 257 AAARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPNPVIFLENEILYGSS 316
AAA VAAQHSQ +A+WY +PGLKVV PY+A DAKGLLKAAIRD NPV+FLENE+LYG S
Sbjct: 152 AAAGVAAQHSQDFASWYGSIPGLKVVAPYSAEDAKGLLKAAIRDENPVVFLENELLYGLS 211
Query: 317 FEVP---MVDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLR 373
FE+P + D V+P+G+A+I R+G+ +TI+++ + + +AA L G+ AE+I+LR
Sbjct: 212 FEIPEEALSKDFVLPLGKAKIEREGTHITIVTYSRMVGHCLEAAETLVAKGVSAEVINLR 271
Query: 374 TIRPMDWQTIFESVKKTGRLVTVEEGYPQSSVGSTIANQVQRKVFDYLDAPILTITGRDV 433
+IRP D +TI SVKKT RLVTVEEG+PQ +G+ I Q+ FDYLDAP+ +TG DV
Sbjct: 272 SIRPFDIETIGASVKKTNRLVTVEEGWPQFGIGAEICAQIMENAFDYLDAPVQRVTGADV 331
Query: 434 PMPYAANLEKLALPNVDEIIESVESICY 461
P PYA LE A+P +I+ +V+ +C
Sbjct: 332 PTPYAKTLEDWAVPQPADIVTAVKKLCN 359
>gnl|CDD|132919 cd07036, TPP_PYR_E1-PDHc-beta_like, Pyrimidine (PYR) binding domain
of the beta subunits of the E1 components of human
pyruvate dehydrogenase complex (E1- PDHc) and related
proteins. Thiamine pyrophosphate (TPP) family,
pyrimidine (PYR) binding domain of the beta subunits of
the E1 components of: human pyruvate dehydrogenase
complex (E1- PDHc), the acetoin dehydrogenase complex
(ADC), and the branched chain alpha-keto acid
dehydrogenase/2-oxoisovalerate dehydrogenase complex
(BCADC), subfamily. The PYR domain is found in many key
metabolic enzymes which use TPP (also known as thiamine
diphosphate) as a cofactor. TPP binds in the cleft
formed by a PYR domain and a PP domain. The PYR domain,
binds the aminopyrimidine ring of TPP, the PP domain
binds the diphosphate residue. A polar interaction
between the conserved glutamate of the PYR domain and
the N1' of the TPP aminopyrimidine ring is shared by
most TPP-dependent enzymes, and participates in the
activation of TPP. The PYR and PP domains have a common
fold, but do not share strong sequence conservation. The
PP domain is not included in this sub-family. E1-PDHc is
an alpha2beta2 dimer-of-heterodimers having two active
sites lying between PYR and PP domains of separate
subunits, the PYR domains are arranged on the beta
subunit, the PP domains on the alpha subunits. PDHc
catalyzes the irreversible oxidative decarboxylation of
pyruvate to produce acetyl-CoA in the bridging step
between glycolysis and the citric acid cycle. ADC
participates in the breakdown of acetoin. BCADC
catalyzes the oxidative decarboxylation of
4-methyl-2-oxopentanoate, 3-methyl-2-oxopentanoate and
3-methyl-2-oxobutanoate during the breakdown of branched
chain amino acids.
Length = 167
Score = 311 bits (800), Expect = 2e-85
Identities = 98/167 (58%), Positives = 123/167 (73%)
Query: 144 EALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPITEHGFAGIG 203
+A+ +A+ EEM RD V ++GE+V +Y G +KVT+GLL +FG +RVIDTPI E G G+
Sbjct: 1 QAINEALDEEMERDPRVVVLGEDVGDYGGVFKVTKGLLDKFGPDRVIDTPIAEAGIVGLA 60
Query: 204 IGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITTSIVFRGPNGAAARVAA 263
+GA+ GL+PIVE M +FA+ A DQI+N AAK RYMSGGQ IV RGPNG A
Sbjct: 61 VGAAMNGLRPIVEIMFADFALPAFDQIVNEAAKLRYMSGGQFKVPIVIRGPNGGGIGGGA 120
Query: 264 QHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPNPVIFLENE 310
QHSQ AW++H+PGLKVV P T DAKGLLKAAIRD +PVIFLE++
Sbjct: 121 QHSQSLEAWFAHIPGLKVVAPSTPYDAKGLLKAAIRDDDPVIFLEHK 167
>gnl|CDD|177066 CHL00144, odpB, pyruvate dehydrogenase E1 component beta subunit;
Validated.
Length = 327
Score = 308 bits (790), Expect = 3e-84
Identities = 139/317 (43%), Positives = 206/317 (64%), Gaps = 1/317 (0%)
Query: 144 EALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPITEHGFAGIG 203
EALR+AI EEM RD VF++GE+V Y G+YKVT+GL +++G RV+DTPI E+ F G+
Sbjct: 8 EALREAIDEEMARDPRVFVIGEDVGHYGGSYKVTKGLHEKYGDLRVLDTPIAENSFTGMA 67
Query: 204 IGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITTSIVFRGPNGAAARVAA 263
IGA+ GL+PIVE M F + A +QI N+A Y SGG T IV RGP G ++ A
Sbjct: 68 IGAAMTGLRPIVEGMNMGFLLLAFNQISNNAGMLHYTSGGNFTIPIVIRGPGGVGRQLGA 127
Query: 264 QHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPNPVIFLENEILYGSSFEVPMVD 323
+HSQ +++ VPGL++V T +AKGLLK+AIR NPVIF E+ +LY E+P +
Sbjct: 128 EHSQRLESYFQSVPGLQIVACSTPYNAKGLLKSAIRSNNPVIFFEHVLLYNLKEEIPD-N 186
Query: 324 DLVIPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTI 383
+ ++P+ +A + R G+D+TI+++ + +A L + G D E+IDL +++P+D TI
Sbjct: 187 EYLLPLEKAEVVRPGNDITILTYSRMRHHVLQAVKVLVEKGYDPEIIDLISLKPLDLGTI 246
Query: 384 FESVKKTGRLVTVEEGYPQSSVGSTIANQVQRKVFDYLDAPILTITGRDVPMPYAANLEK 443
+SVKKT +++ VEE +G+ + Q+ +FD LDAPI+ ++ +DVP PY LE+
Sbjct: 247 SKSVKKTHKVLIVEECMKTGGIGAELIAQINEHLFDELDAPIVRLSSQDVPTPYNGPLEE 306
Query: 444 LALPNVDEIIESVESIC 460
+ +IIE+VE I
Sbjct: 307 ATVIQPAQIIEAVEQII 323
>gnl|CDD|35745 KOG0525, KOG0525, KOG0525, Branched chain alpha-keto acid
dehydrogenase E1, beta subunit [Energy production and
conversion].
Length = 362
Score = 241 bits (617), Expect = 2e-64
Identities = 124/324 (38%), Positives = 185/324 (57%), Gaps = 5/324 (1%)
Query: 137 TSSITVREALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPITE 196
+ + +++ A+ + D + GE+VA + G ++ T GL ++FG +RV +TP+ E
Sbjct: 38 KKKMNLYQSVNQALHIALETDPRAVVFGEDVA-FGGVFRCTTGLAEKFGKDRVFNTPLCE 96
Query: 197 HGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITT-SIVFRGPN 255
G G GIG + G I E ++ A DQI+N AAK RY SG Q + R P
Sbjct: 97 QGIVGFGIGLAAMGATAIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTIRAPW 156
Query: 256 GAAARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPNPVIFLENEILYGS 315
GA A HSQ A++ HVPG+KVVIP + AKGLL + IRDPNP IF E +ILY
Sbjct: 157 GAVGHGALYHSQSPEAFFCHVPGIKVVIPRSPRQAKGLLLSCIRDPNPCIFFEPKILYRQ 216
Query: 316 SFEVPMVDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKAA-IELEKNGIDAELIDLRT 374
+ E D +IP+ +A + R+GSD+T++++G + + A + EK GI E+IDL+T
Sbjct: 217 AVEDVPEGDYMIPLSQAEVIREGSDITLVAWGTQVHVIMEQACLAKEKLGISCEVIDLKT 276
Query: 375 IRPMDWQTIFESVKKTGRLVTVEEGYPQSSVGSTIANQVQRKVFDYLDAPILTITGRDVP 434
I P D T+ ESV+KTGRL+ E G+ IA+ VQ + F L+API + G D P
Sbjct: 277 IIPWDKDTVEESVQKTGRLLISHEAPVTGGFGAEIASTVQERCFLNLEAPISRVCGLDTP 336
Query: 435 MPYAANLEKLALPNVDEIIESVES 458
P+ E +P ++I+++++
Sbjct: 337 FPHV--FEPFYMPTKNKILDAIKK 358
>gnl|CDD|145763 pfam02779, Transket_pyr, Transketolase, pyrimidine binding domain.
This family includes transketolase enzymes, pyruvate
dehydrogenases, and branched chain alpha-keto acid
decarboxylases.
Length = 174
Score = 185 bits (471), Expect = 3e-47
Identities = 68/180 (37%), Positives = 87/180 (48%), Gaps = 10/180 (5%)
Query: 138 SSITVREALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPITEH 197
I R+A +A+AE RD V G +V G + VT+GLL G RVIDT I E
Sbjct: 1 KKIATRKASGEALAELAERDPRVVGGGADVG--GGTFTVTKGLLHPQGEGRVIDTGIAEQ 58
Query: 198 GFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQI-TTSIVFRGPNG 256
GI G + GL P VE +FA I AA Y + G++ +V R P G
Sbjct: 59 AMVGIANGMALHGLLPPVEATFGDFAN-----IRADAAIRHYAALGKLPVPFVVTRDPIG 113
Query: 257 AAARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIR--DPNPVIFLENEILYG 314
SQ A+ +PGLKVV P ++AKGLL+AAIR D +PV+F L
Sbjct: 114 VGEDGPTHQSQEDEAYLRAIPGLKVVRPSDPAEAKGLLRAAIRRDDDDPVVFRLPRQLLR 173
>gnl|CDD|145764 pfam02780, Transketolase_C, Transketolase, C-terminal domain. The
C-terminal domain of transketolase has been proposed as
a regulatory molecule binding site.
Length = 124
Score = 153 bits (388), Expect = 1e-37
Identities = 61/124 (49%), Positives = 82/124 (66%)
Query: 330 GRARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTIFESVKK 389
G+A I R+G DVTI+++G + A +AA EL GI AE+IDLRT++P+D TI ESVKK
Sbjct: 1 GKAEILREGDDVTIVAYGSMVHEALEAAEELAAEGISAEVIDLRTVKPLDEDTILESVKK 60
Query: 390 TGRLVTVEEGYPQSSVGSTIANQVQRKVFDYLDAPILTITGRDVPMPYAANLEKLALPNV 449
TGRLV VEE P+ G+ +A + + FDYLDAP+L + G D P+P++ LE L
Sbjct: 61 TGRLVVVEEAVPRGGFGAEVAAALAEEGFDYLDAPVLRVGGPDTPIPHSPALELAYLGLT 120
Query: 450 DEII 453
E I
Sbjct: 121 AEKI 124
>gnl|CDD|35777 KOG0557, KOG0557, KOG0557, Dihydrolipoamide acetyltransferase
[Energy production and conversion].
Length = 470
Score = 112 bits (282), Expect = 2e-25
Identities = 48/102 (47%), Positives = 64/102 (62%), Gaps = 3/102 (2%)
Query: 2 PILVTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILC 61
+MP+LSPTM EGNI WKK EGD + GD++ EVETDKA M+VE+ D+G L KIL
Sbjct: 38 HKTFSMPALSPTMEEGNIVSWKKKEGDKLSAGDVLLEVETDKATMDVEAQDDGYLAKILI 97
Query: 62 PNGTKNVKVNTPIAAILQEGETALDIDKMLLEKPDVAISPSS 103
G+K+V V PIA I+++ + DI L K + + S
Sbjct: 98 EEGSKDVPVGKPIAIIVEDED---DIAAFKLPKDEASSGEQS 136
>gnl|CDD|33739 COG3958, COG3958, Transketolase, C-terminal subunit [Carbohydrate
transport and metabolism].
Length = 312
Score = 112 bits (281), Expect = 3e-25
Identities = 76/281 (27%), Positives = 129/281 (45%), Gaps = 23/281 (8%)
Query: 135 APTSSITVREALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPI 194
++ ++R+ + +AE R++ D+ ++ +++ T +EF +R + I
Sbjct: 2 MAGNTESLRKVYGETLAELGRKNSDIVVLDADLSSSTK----TGYFAKEFP-DRFFNVGI 56
Query: 195 TEHGFAGIGIGASFAGLKPIVEFMTFNFAM----QAIDQIINSAAKTRYMSGGQITTSIV 250
E G G + AG KP V FA +A +QI NS A T + V
Sbjct: 57 AEQDMVGTAAGLALAGKKPFV----STFAAFLSRRAWEQIRNSIAYNNLNVKIVATHAGV 112
Query: 251 FRGPNGAAARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPNPVIFLENE 310
G +G++ + A +P + V+ P A + + +L PV
Sbjct: 113 TYGEDGSS-----HQALEDIAIMRGLPNMTVIAPADAVETRAILDQIADYKGPVYMR--- 164
Query: 311 ILYGSSFEVPM-VDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAEL 369
L V + IG+A + R GSD+TII+ G+ + A +AA L+K GI A +
Sbjct: 165 -LGRGKVPVVVDEGGYTFEIGKANVLRDGSDLTIIATGVMVAEALEAAEILKKEGISAAV 223
Query: 370 IDLRTIRPMDWQTIFESVKKTGRLVTVEEGYPQSSVGSTIA 410
I++ TI+P+D Q I ++ ++TGR+VT EE +GS +A
Sbjct: 224 INMFTIKPIDEQAILKAARETGRIVTAEEHSIIGGLGSAVA 264
>gnl|CDD|133458 cd06849, lipoyl_domain, Lipoyl domain of the dihydrolipoyl
acyltransferase component (E2) of 2-oxo acid
dehydrogenases. 2-oxo acid dehydrogenase multienzyme
complexes, like pyruvate dehydrogenase (PDH),
2-oxoglutarate dehydrogenase (OGDH) and branched-chain
2-oxo acid dehydrogenase (BCDH), contain at least three
different enzymes, 2-oxo acid dehydrogenase (E1),
dihydrolipoyl acyltransferase (E2) and dihydrolipoamide
dehydrogenase (E3) and play a key role in redox
regulation. E2, the central component of the complex,
catalyzes the transfer of the acyl group of CoA from E1
to E3 via reductive acetylation of a lipoyl group
covalently attached to a lysine residue.
Length = 74
Score = 100 bits (251), Expect = 1e-21
Identities = 35/73 (47%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 5 VTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64
+ MP L +MTEG I +W EGD +++GD++ EVETDKA +EVE+ G+L KIL G
Sbjct: 3 IKMPDLGESMTEGTIVEWLVKEGDSVEEGDVLAEVETDKATVEVEAPAAGVLAKILVEEG 62
Query: 65 TKNVKVNTPIAAI 77
V V IA I
Sbjct: 63 DT-VPVGQVIAVI 74
>gnl|CDD|31348 COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme
metabolism / Lipid metabolism].
Length = 627
Score = 91.8 bits (228), Expect = 4e-19
Identities = 63/283 (22%), Positives = 113/283 (39%), Gaps = 19/283 (6%)
Query: 187 ERVIDTPITEHGFAGIGIGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQIT 246
+R D I E G + G+KP+V + F +A DQ+I+ A
Sbjct: 358 DRFFDVGIAEQHAVTFAAGLAAEGMKPVV-AIYSTFLQRAYDQLIHDVAIQN-----LPV 411
Query: 247 TSIVFRGPNGAAARVAAQHSQCYA-AWYSHVPGLKVVIPYTASDAKGLLKAAIR-DPNPV 304
T + R G H + ++ +P + ++ P + + +L A+ D PV
Sbjct: 412 TFAIDRA--GIVGADGPTHQGLFDLSFLRCIPNMVIMAPRDEEELRQMLYTALAQDDGPV 469
Query: 305 IFLENEILYGSSFEVPMVDDLV-IPIGRARIHRQGSDVTIISFGIGMTYATKAAIELEKN 363
G+ V + +L + IG+ + ++G V I++FG + A K A +L
Sbjct: 470 AI---RYPRGNGVGVILTPELEPLEIGKGELLKEGEKVAILAFGTMLPEALKVAEKLNAY 526
Query: 364 GIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVEEGYPQSSVGSTIANQVQRKVFDYLDA 423
GI ++D R ++P+D + E K +VT+EE GS + + +
Sbjct: 527 GISVTVVDPRFVKPLDEALLLELAKSHDLVVTLEENVVDGGFGSAVLEFLAAH---GILV 583
Query: 424 PILTITGRDVPMPYAANLEKLALPNVDE--IIESVESICYKRK 464
P+L + D + + + E LA +D I + R
Sbjct: 584 PVLNLGLPDEFIDHGSPEELLAELGLDAEGIARRILEWLKARS 626
>gnl|CDD|30854 COG0508, AceF, Pyruvate/2-oxoglutarate dehydrogenase complex,
dihydrolipoamide acyltransferase (E2) component, and
related enzymes [Energy production and conversion].
Length = 404
Score = 90.8 bits (225), Expect = 7e-19
Identities = 43/84 (51%), Positives = 52/84 (61%), Gaps = 1/84 (1%)
Query: 1 MPILVTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKIL 60
M I + MP L TMTEG I +W K GD +K+GD++ EVETDKA MEV + D G+L KIL
Sbjct: 1 MAIEIKMPDLGETMTEGTIVEWLKKVGDKVKEGDVLVEVETDKATMEVPAPDAGVLAKIL 60
Query: 61 CPNGTKNVKVNTPIAAILQEGETA 84
G V V IA I +EG A
Sbjct: 61 VEEGDT-VPVGAVIARIEEEGADA 83
>gnl|CDD|132915 cd06586, TPP_enzyme_PYR, Pyrimidine (PYR) binding domain of
thiamine pyrophosphate (TPP)-dependent enzymes.
Thiamine pyrophosphate (TPP) family, pyrimidine (PYR)
binding domain; found in many key metabolic enzymes
which use TPP (also known as thiamine diphosphate) as a
cofactor. TPP binds in the cleft formed by a PYR domain
and a PP domain. The PYR domain, binds the
aminopyrimidine ring of TPP, the PP domain binds the
diphosphate residue. A polar interaction between the
conserved glutamate of the PYR domain and the N1' of the
TPP aminopyrimidine ring is shared by most TPP-dependent
enzymes, and participates in the activation of TPP. The
PYR and PP domains have a common fold, but do not share
strong sequence conservation. The PP domain is not
included in this group. Most TPP-dependent enzymes have
the PYR and PP domains on the same subunit although
these domains can be alternatively arranged in the
primary structure. In the case of 2-oxoisovalerate
dehydrogenase (2OXO), sulfopyruvate decarboxylase
(ComDE), and the E1 component of human pyruvate
dehydrogenase complex (E1- PDHc) the PYR and PP domains
appear on different subunits. TPP-dependent enzymes are
multisubunit proteins, the smallest catalytic unit being
a dimer-of-active sites. For many of these enzymes the
active sites lie between PP and PYR domains on different
subunits. However, for the homodimeric enzymes
1-deoxy-D-xylulose 5-phosphate synthase (DXS) and
Desulfovibrio africanus pyruvate:ferredoxin
oxidoreductase (PFOR), each active site lies at the
interface of the PYR and PP domains from the same
subunit.
Length = 154
Score = 75.5 bits (186), Expect = 3e-14
Identities = 40/168 (23%), Positives = 61/168 (36%), Gaps = 19/168 (11%)
Query: 148 DAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPITEHGFAGIGIGAS 207
A AE + + G E L+E G +R+IDT I E G AG G +
Sbjct: 1 AAFAEVLTAWGVRHVFGYPGDEISSLL----DALRE-GDKRIIDTVIHELGAAGAAAGYA 55
Query: 208 FAGLKPIVEFMTFNFAMQAIDQIINSAAKTRYMSGGQITTSIVFR-GPNGAAARV-AAQH 265
AG P+V + + AI+ + ++AA+ +VF G G +A+
Sbjct: 56 RAGGPPVVIVTSGTGLLNAINGLADAAAE---------HLPVVFLIGARGISAQAKQTFQ 106
Query: 266 SQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRD---PNPVIFLENE 310
S Y +P + P A G+ A PV+
Sbjct: 107 SMFDLGMYRSIPEANISSPSPAELPAGIDHAIRTAYASQGPVVVRLPR 154
>gnl|CDD|132916 cd07033, TPP_PYR_DXS_TK_like, Pyrimidine (PYR) binding domain of
1-deoxy-D-xylulose-5-phosphate synthase (DXS),
transketolase (TK), and related proteins. Thiamine
pyrophosphate (TPP) family, pyrimidine (PYR) binding
domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS),
transketolase (TK), and the beta subunits of the E1
component of the human pyruvate dehydrogenase complex
(E1- PDHc), subfamily. The PYR domain is found in many
key metabolic enzymes which use TPP (also known as
thiamine diphosphate) as a cofactor. TPP binds in the
cleft formed by a PYR domain and a PP domain. The PYR
domain, binds the aminopyrimidine ring of TPP, the PP
domain binds the diphosphate residue. A polar
interaction between the conserved glutamate of the PYR
domain and the N1' of the TPP aminopyrimidine ring is
shared by most TPP-dependent enzymes, and participates
in the activation of TPP. The PYR and PP domains have a
common fold, but do not share strong sequence
conservation. The PP domain is not included in this
sub-family. Like many TPP-dependent enzymes DXS and TK
are homodimers having a PYR and a PP domain on the same
subunit. TK has two active sites per dimer which lie
between PYR and PP domains of different subunits. For
DXS each active site is located at the interface of a
PYR and a PP domain from the same subunit. E1-PDHc is an
alpha2beta2 dimer-of-heterodimers having two active
sites but having the PYR and PP domains arranged on
separate subunits, the PYR domains on the beta subunits,
the PP domains on the alpha subunits. DXS is a
regulatory enzyme of the mevalonate-independent pathway
involved in terpenoid biosynthesis, it catalyzes a
transketolase-type condensation of pyruvate with
D-glyceraldehyde-3-phosphate to form
1-deoxy-D-xylulose-5-phosphate (DXP) and carbon dioxide.
TK catalyzes the transfer of a two-carbon unit from
ketose phosphates to aldose phosphates. In heterotrophic
organisms, TK provides a link between glycolysis and the
pentose phosphate pathway and provides precursors for
nucleotide, aromatic amino acid and vitamin
biosynthesis. TK also plays a central role in the Calvin
cycle in plants. PDHc catalyzes the irreversible
oxidative decarboxylation of pyruvate to produce
acetyl-CoA in the bridging step between glycolysis and
the citric acid cycle. This subfamily includes the beta
subunits of the E1 component of the acetoin
dehydrogenase complex (ADC) and the branched chain
alpha-keto acid dehydrogenase/2-oxoisovalerate
dehydrogenase complex (BCADC). ADC participates in the
breakdown of acetoin. BCADC catalyzes the oxidative
decarboxylation of 4-methyl-2-oxopentanoate,
3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate
during the breakdown of branched chain amino acids.
Length = 156
Score = 73.2 bits (181), Expect = 1e-13
Identities = 40/168 (23%), Positives = 66/168 (39%), Gaps = 21/168 (12%)
Query: 144 EALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQEFGCERVIDTPITEHGFAGIG 203
+A +A+ E ++D + + ++ G K ++F +R ID I E GI
Sbjct: 1 KAFGEALLELAKKDPRIVALSADLGGSTGLDK----FAKKFP-DRFIDVGIAEQNMVGIA 55
Query: 204 IGASFAGLKPIVEFMTFNFAMQAIDQIINSAAKTRY-----MSGGQITTSIVFRGPNGAA 258
G + GLKP V +F F +A DQI + A + I+ G +G
Sbjct: 56 AGLALHGLKPFVSTFSF-FLQRAYDQIRHDVALQNLPVKFVGTHAGISV-----GEDGPT 109
Query: 259 ARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRDPNPVIF 306
A +P + V+ P A++ L+AA+ PV
Sbjct: 110 -----HQGIEDIALLRAIPNMTVLRPADANETAAALEAALEYDGPVYI 152
>gnl|CDD|35743 KOG0523, KOG0523, KOG0523, Transketolase [Carbohydrate transport
and metabolism].
Length = 632
Score = 68.4 bits (167), Expect = 4e-12
Identities = 47/231 (20%), Positives = 83/231 (35%), Gaps = 29/231 (12%)
Query: 187 ERVIDTPITEHGFAGIGIGASFAGLKPIVEFMT--FNFAMQAIDQIINSAAKTRYMSGGQ 244
ER I+ I E GI G + G + F F +A DQ+ A +S
Sbjct: 362 ERFIECGIAEQNMVGIANGIACRG--RTIPFCGTFAAFFTRAFDQVRMGA-----LSQAN 414
Query: 245 I----TTSIVFRGPNGAAARVAAQHSQCYA---AWYSHVPGLKVVIPYTASDAKGLLK-A 296
+ T + G +G + A + +P + V P ++ + + A
Sbjct: 415 VIYVATHDSIGLGEDGP--------THQPIEDLAMFRSIPNMIVFRPADGNETENAVATA 466
Query: 297 AIRDPNPVIFLENEILYGSSFEVPMVDDLVIPIGRARIHRQGSDVTIISFGIGMTYATKA 356
A P I + + + I G+ + DV +I G + +A
Sbjct: 467 ANTKGTPSIRTLSR---QNLPIYNNTEIEEIGKGKYVLQEVEPDVILIGTGSEVQECLEA 523
Query: 357 AIELEKNGIDAELIDLRTIRPMDWQTIFESVKKT-GRLVTVEEGYPQSSVG 406
A L ++GI ++D T +P+D I + R+ +E+ P S+
Sbjct: 524 AELLSEDGIKVRVVDPFTWKPLDVALIRSLAQSHEYRISVLEDHVPAGSIE 574
>gnl|CDD|144088 pfam00364, Biotin_lipoyl, Biotin-requiring enzyme. This family
covers two Prosite entries, the conserved lysine
residue binds biotin in one group and lipoic acid in
the other. Note that the model may not recognize the
Glycine cleavage system H proteins.
Length = 73
Score = 68.0 bits (167), Expect = 5e-12
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 5 VTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64
+ P + ++ EG A+W GD +K G ++ EVE K ME+ + G++ +IL G
Sbjct: 3 IKSPMIGESVKEGT-AEWLVKVGDKVKAGQVLCEVEAMKMEMEIPAPVAGVVKEILVKEG 61
Query: 65 TKNVKVNTPIAAI 77
V+V P+A I
Sbjct: 62 DT-VEVGDPLAKI 73
>gnl|CDD|133456 cd06663, Biotinyl_lipoyl_domains, Biotinyl_lipoyl_domains are
present in biotin-dependent
carboxylases/decarboxylases, the dihydrolipoyl
acyltransferase component (E2) of 2-oxo acid
dehydrogenases, and the H-protein of the glycine
cleavage system (GCS). These domains transport CO2,
acyl, or methylamine, respectively, between components
of the complex/protein via a biotinyl or lipoyl group,
which is covalently attached to a highly conserved
lysine residue.
Length = 73
Score = 54.4 bits (131), Expect = 7e-08
Identities = 23/62 (37%), Positives = 38/62 (61%)
Query: 5 VTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNG 64
+ +P L+ + +G + KW K GD +K+GD++ E+E KA +VE+ G + K+L G
Sbjct: 2 ILIPDLAQHLGDGTVVKWLKKVGDKVKKGDVLAEIEAMKATSDVEAPKSGTVKKVLVKEG 61
Query: 65 TK 66
TK
Sbjct: 62 TK 63
>gnl|CDD|35779 KOG0559, KOG0559, KOG0559, Dihydrolipoamide succinyltransferase
(2-oxoglutarate dehydrogenase, E2 subunit) [Energy
production and conversion].
Length = 457
Score = 53.5 bits (128), Expect = 1e-07
Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 3 ILVTMPSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCP 62
+ V +P + ++TEG++A+W K GD + + + + E+ETDK +EV S G++ ++L
Sbjct: 73 VTVEVPPFAESITEGDLAQWLKKVGDRVNEDEAVAEIETDKTTVEVPSPASGVITELLVK 132
Query: 63 NGTKNVKVNTPIAAI 77
+G V +A I
Sbjct: 133 DGDT-VTPGQKLAKI 146
>gnl|CDD|133459 cd06850, biotinyl_domain, The biotinyl-domain or biotin carboxyl
carrier protein (BCCP) domain is present in all
biotin-dependent enzymes, such as acetyl-CoA
carboxylase, pyruvate carboxylase, propionyl-CoA
carboxylase, methylcrotonyl-CoA carboxylase,
geranyl-CoA carboxylase, oxaloacetate decarboxylase,
methylmalonyl-CoA decarboxylase, transcarboxylase and
urea amidolyase. This domain functions in transferring
CO2 from one subsite to another, allowing
carboxylation, decarboxylation, or transcarboxylation.
During this process, biotin is covalently attached to a
specific lysine.
Length = 67
Score = 39.7 bits (94), Expect = 0.002
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 17 GNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTKNVKVNTPIAA 76
G + K EGD ++ G + +E K EV + G++ +IL G V+ +
Sbjct: 8 GTVVKVLVKEGDKVEAGQPLAVLEAMKMENEVTAPVAGVVKEILVKEGD-QVEAGQLLVV 66
Query: 77 I 77
I
Sbjct: 67 I 67
>gnl|CDD|35778 KOG0558, KOG0558, KOG0558, Dihydrolipoamide transacylase
(alpha-keto acid dehydrogenase E2 subunit) [Energy
production and conversion].
Length = 474
Score = 36.2 bits (83), Expect = 0.022
Identities = 16/44 (36%), Positives = 27/44 (61%)
Query: 16 EGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKI 59
E + +W EGD ++Q D + EV++DKA + + S +G + KI
Sbjct: 78 EVTVKEWFVKEGDTVEQFDPLCEVQSDKASVTITSRYDGKVKKI 121
>gnl|CDD|33956 COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha
and beta subunits [Energy production and conversion].
Length = 640
Score = 35.7 bits (82), Expect = 0.026
Identities = 36/111 (32%), Positives = 51/111 (45%), Gaps = 14/111 (12%)
Query: 339 SDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVEE 398
+ + II+ GI Y +A LE G+D EL+ L T P+ Q I +K R++ VEE
Sbjct: 248 AKLGIIASGIAYNYVKEA---LEDLGLDDELLKLGTPYPLPEQLIENFLKGLERVLVVEE 304
Query: 399 GYPQSSVGSTIANQVQRKVFDYLDAPILTITGRD---VPMPYAANLEKLAL 446
G P I QV K Y + + G+D +PM EK+A
Sbjct: 305 GEP------FIEEQV--KALLYDAGLPVEVHGKDEGLLPMEGELTPEKIAN 347
>gnl|CDD|30857 COG0511, AccB, Biotin carboxyl carrier protein [Lipid metabolism].
Length = 140
Score = 33.1 bits (75), Expect = 0.15
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 17 GNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTKNVKVNTPIAA 76
G + K GD +K G + +E K E+E+ +G++ +IL NG V+ P+A
Sbjct: 79 GTVYKPFVEVGDTVKAGQTLAIIEAMKMENEIEAPADGVVKEILVKNGD-PVEYGDPLAV 137
Query: 77 I 77
I
Sbjct: 138 I 138
>gnl|CDD|35589 KOG0368, KOG0368, KOG0368, Acetyl-CoA carboxylase [Lipid transport
and metabolism].
Length = 2196
Score = 32.2 bits (73), Expect = 0.27
Identities = 11/55 (20%), Positives = 27/55 (49%)
Query: 8 PSLSPTMTEGNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCP 62
P++ + + G + ++ +G+ ++ G E+E K VM + + + G + I
Sbjct: 685 PTVLRSPSPGKLLQYLVEDGEHVEAGQPYAEIEVMKMVMPLVAKEPGRIQLIKQE 739
>gnl|CDD|35590 KOG0369, KOG0369, KOG0369, Pyruvate carboxylase [Energy production
and conversion].
Length = 1176
Score = 30.7 bits (69), Expect = 0.78
Identities = 14/50 (28%), Positives = 23/50 (46%)
Query: 17 GNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTK 66
G + + K EG +K+G + + K M + S G + K+ GTK
Sbjct: 1115 GTVIEIKVKEGAKVKKGQPLAVLSAMKMEMVISSPHAGTVKKVHVVQGTK 1164
>gnl|CDD|35383 KOG0161, KOG0161, KOG0161, Myosin class II heavy chain
[Cytoskeleton].
Length = 1930
Score = 30.6 bits (69), Expect = 1.1
Identities = 21/101 (20%), Positives = 38/101 (37%), Gaps = 8/101 (7%)
Query: 86 DIDKMLLEKPDVAISPSSKNTTLVF----SNEDNDKVDHQKSKNDIQDSSFAHAPTSSIT 141
DI+ LLEK V + +F S D + + ++++D F S+I
Sbjct: 255 DIETYLLEKSRVIRQAPGERNYHIFYQLLSGADPELKEELLLSDNVKDYKFLSNGESTI- 313
Query: 142 VREALRDAIAEEMRRDKDVFIMGEEVAEYQGAYKVTQGLLQ 182
D E D+ + I+G E +++ +L
Sbjct: 314 ---PGVDDAEEFQETDEAMDILGFSEEEKISIFRIVSAILH 351
>gnl|CDD|31240 COG1038, PycA, Pyruvate carboxylase [Energy production and
conversion].
Length = 1149
Score = 30.2 bits (68), Expect = 1.4
Identities = 12/50 (24%), Positives = 28/50 (56%)
Query: 17 GNIAKWKKNEGDLIKQGDIIYEVETDKAVMEVESIDEGILGKILCPNGTK 66
G + + K +GD +K+GD++ +E K + + +G + ++L +G +
Sbjct: 1088 GVVVEVKVKKGDKVKKGDVLAVIEAMKMETTISAPFDGTVKEVLVKDGDQ 1137
>gnl|CDD|29736 cd01017, AdcA, Metal binding protein AcdA. These proteins have
been shown to function in the ABC uptake of Zn2+ and
Mn2+ and in competence for genetic transformation and
adhesion. The AcdA proteins belong to the TroA
superfamily of helical backbone metal receptor proteins
that share a distinct fold and ligand binding mechanism.
They are comprised of two globular subdomains connected
by a long alpha helix and they bind their ligand in the
cleft between these domains. In addition, many of these
proteins have a low complexity region containing metal
binding histidine-rich motif (repetitive HDH sequence)..
Length = 282
Score = 29.0 bits (65), Expect = 2.8
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 3/78 (3%)
Query: 87 IDKML--LEKPDVAISPSSKNTTLVFSNEDNDKVDHQKSKND-IQDSSFAHAPTSSITVR 143
+K+L L+ + + +SK L+ + DH S + D +P +I
Sbjct: 67 AEKVLKSLQNKKLKVVEASKGIKLLKAGGAEHDHDHSHSHHHGDYDPHVWLSPVLAIQQV 126
Query: 144 EALRDAIAEEMRRDKDVF 161
E ++DA+ + +K+ +
Sbjct: 127 ENIKDALIKLDPDNKEYY 144
>gnl|CDD|30371 COG0021, TktA, Transketolase [Carbohydrate transport and
metabolism].
Length = 663
Score = 29.0 bits (65), Expect = 2.8
Identities = 31/136 (22%), Positives = 52/136 (38%), Gaps = 13/136 (9%)
Query: 276 VPGLKVVIPYTASDAKGLLKAAI--RDPNPVIFLENE---ILYGSSFEVPMVDDLVIPIG 330
+P L V+ P A++ K A+ +D + L + +L + E V+
Sbjct: 485 IPNLSVIRPADANETAAAWKYALERKDGPTALILTRQNLPVLERTDLEGVAKGAYVLKDS 544
Query: 331 RARIHRQGSDVTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTI--FESV- 387
DV +I+ G + A +AA ELE GI ++ + + + Q ESV
Sbjct: 545 GGE----DPDVILIATGSEVELAVEAAKELEAEGIKVRVVSMPSFELFEKQDEEYRESVL 600
Query: 388 -KKTGRLVTVEEGYPQ 402
V +E G
Sbjct: 601 PGAVTARVAIEAGSAL 616
>gnl|CDD|133457 cd06848, GCS_H, Glycine cleavage H-protein. Glycine cleavage
H-proteins are part of the glycine cleavage system
(GCS) found in bacteria, archea and the mitochondria of
eukaryotes. GCS is a multienzyme complex consisting of
4 different components (P-, H-, T- and L-proteins)
which catalyzes the oxidative cleavage of glycine. The
H-protein shuttles the methylamine group of glycine
from the P-protein (glycine dehydrogenase) to the
T-protein (aminomethyltransferase) via a lipoyl group,
attached to a completely conserved lysine residue.
Length = 96
Score = 28.7 bits (65), Expect = 4.0
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 24 KNEGDLIKQGDIIYEVETDKAVMEVES 50
G +K+GD VE+ KA ++ S
Sbjct: 37 PEVGTEVKKGDPFGSVESVKAASDLYS 63
>gnl|CDD|63860 cd04391, RhoGAP_ARHGAP18, RhoGAP_ARHGAP18: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
ArhGAP18-like proteins. The function of ArhGAP18 is
unknown. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude..
Length = 216
Score = 27.9 bits (62), Expect = 5.6
Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 5/78 (6%)
Query: 250 VFRGPNGAAARVAAQHSQCYAAWYSHVPGLKVVIPYTASDAKGLLKAAIRD-PNPVIFLE 308
+ R P G+A RV + A +Y V DA LLK IR+ P P++ +E
Sbjct: 43 ILRIP-GSAQRVKFLCQELEAKFYEGTFLWDQV---KQHDAASLLKLFIRELPQPLLTVE 98
Query: 309 NEILYGSSFEVPMVDDLV 326
+ S +P D +
Sbjct: 99 YLPAFYSVQGLPSKKDQL 116
>gnl|CDD|37141 KOG1930, KOG1930, KOG1930, Focal adhesion protein Tensin, contains
PTB domain [Signal transduction mechanisms,
Cytoskeleton].
Length = 483
Score = 28.1 bits (62), Expect = 5.8
Identities = 12/49 (24%), Positives = 17/49 (34%)
Query: 96 DVAISPSSKNTTLVFSNEDNDKVDHQKSKNDIQDSSFAHAPTSSITVRE 144
V P + S N V D+ +F+H+P S T E
Sbjct: 3 PVNSLPRGTPAHHMDSQRHNQSVPLPMPHRDVSLFNFSHSPRSQSTTLE 51
>gnl|CDD|38163 KOG2952, KOG2952, KOG2952, Cell cycle control protein [Cell cycle
control, cell division, chromosome partitioning,
Transcription, Signal transduction mechanisms].
Length = 351
Score = 28.0 bits (62), Expect = 6.0
Identities = 14/63 (22%), Positives = 22/63 (34%)
Query: 341 VTIISFGIGMTYATKAAIELEKNGIDAELIDLRTIRPMDWQTIFESVKKTGRLVTVEEGY 400
V + G+G+ +A+ IE+ D RT Q F+ K TV +
Sbjct: 54 VVFLPIGVGLLFASSKVIEITIRYTDCIPTGFRTNPSEYIQGHFDQTKSCTITFTVPKDM 113
Query: 401 PQS 403
Sbjct: 114 KGP 116
>gnl|CDD|144225 pfam00555, Endotoxin_M, delta endotoxin. This family contains
insecticidal toxins produced by Bacillus species of
bacteria. During spore formation the bacteria produce
crystals of this protein. When an insect ingests these
proteins they are activated by proteolytic cleavage. The
N terminus is cleaved in all of the proteins and a C
terminal extension is cleaved in some members. Once
activated the endotoxin binds to the gut epithelium and
causes cell lysis leading to death. This activated
region of the delta endotoxin is composed of three
structural domains. The N-terminal helical domain is
involved in membrane insertion and pore formation. The
second and third domains are involved in receptor
binding.
Length = 205
Score = 27.4 bits (61), Expect = 8.3
Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 1/56 (1%)
Query: 293 LLKAAIRDPNPVIFLENEILYGSSFEVPMVDDLVIPIGRARIHRQGSDVTIISFGI 348
L A IR P+ FL + +Y +S D R R G + IIS +
Sbjct: 31 LENALIRPPHLFDFLNSLTIYTNSSRNSTYDYNYWSGHRNRFSFTGGN-NIISEPL 85
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
0.316 0.134 0.378
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,451,774
Number of extensions: 292833
Number of successful extensions: 800
Number of sequences better than 10.0: 1
Number of HSP's gapped: 784
Number of HSP's successfully gapped: 45
Length of query: 467
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 370
Effective length of database: 4,167,664
Effective search space: 1542035680
Effective search space used: 1542035680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.5 bits)