RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4881
(423 letters)
>gnl|CDD|234139 TIGR03182, PDH_E1_alph_y, pyruvate dehydrogenase E1 component,
alpha subunit. Members of this protein family are the
alpha subunit of the E1 component of pyruvate
dehydrogenase (PDH). This model represents one branch of
a larger family that E1-alpha proteins from
2-oxoisovalerate dehydrogenase, acetoin dehydrogenase,
another PDH clade, etc [Energy metabolism, Pyruvate
dehydrogenase].
Length = 315
Score = 310 bits (797), Expect = e-104
Identities = 107/202 (52%), Positives = 139/202 (68%), Gaps = 4/202 (1%)
Query: 197 VPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENNGYGMG 256
VPL G+A A KY G V +GDGAANQGQ +E +N+A LW +P IFV ENN Y MG
Sbjct: 116 VPLATGLAFANKYRGNDNVTACFFGDGAANQGQFYESFNMAALWKLPVIFVIENNLYAMG 175
Query: 257 TSSERASASVDYYTRGD--YIPGIWVDGMDILAVREAARFAVNHCRSDKGPILLETATYR 314
T+ ER+S+ D Y RG+ IPG VDGMD+LAVREAA+ AV RS KGPILLE TYR
Sbjct: 176 TAVERSSSVTDLYKRGESFGIPGERVDGMDVLAVREAAKEAVERARSGKGPILLEMKTYR 235
Query: 315 YSGHSMSDPGTSYRTRDEIQEVRQTRDPISSLKDKILNASLVTPEELKKIDTEVKAEIDA 374
+ GHSMSDP YR+++E++E R RDPI LK +++ + + EELK+ID EV+AE++
Sbjct: 236 FRGHSMSDPA-KYRSKEEVEEWR-KRDPIEKLKARLIEQGIASEEELKEIDKEVRAEVEE 293
Query: 375 VIKKARADPEVGLDELTGDIYA 396
++ A PE ++EL D+YA
Sbjct: 294 AVEFAENSPEPPVEELYTDVYA 315
>gnl|CDD|215152 PLN02269, PLN02269, Pyruvate dehydrogenase E1 component subunit
alpha.
Length = 362
Score = 303 bits (779), Expect = e-100
Identities = 116/213 (54%), Positives = 145/213 (68%), Gaps = 1/213 (0%)
Query: 196 TVPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENNGYGM 255
VPLG G+A A KY+ + V FALYGDGAANQGQ+FE NIA LW++P IFVCENN YGM
Sbjct: 143 QVPLGAGLAFAQKYNKEENVAFALYGDGAANQGQLFEALNIAALWDLPVIFVCENNHYGM 202
Query: 256 GTSSERASASVDYYTRGDYIPGIWVDGMDILAVREAARFAVNHCRSDKGPILLETATYRY 315
GT+ RA+ S YY RGDY+PG+ VDGMD+LAV++A +FA H S GPI+LE TYRY
Sbjct: 203 GTAEWRAAKSPAYYKRGDYVPGLKVDGMDVLAVKQACKFAKEHALS-NGPIVLEMDTYRY 261
Query: 316 SGHSMSDPGTSYRTRDEIQEVRQTRDPISSLKDKILNASLVTPEELKKIDTEVKAEIDAV 375
GHSMSDPG++YRTRDEI VRQ RDPI ++ +L L T ELK I+ E++ E+D
Sbjct: 262 HGHSMSDPGSTYRTRDEISGVRQERDPIERVRKLLLAHELATEAELKDIEKEIRKEVDDA 321
Query: 376 IKKARADPEVGLDELTGDIYAVPLETDIRGTTP 408
+ KA+ P EL ++Y L + G
Sbjct: 322 VAKAKESPMPDPSELFTNVYVKGLGVESYGADR 354
>gnl|CDD|201386 pfam00676, E1_dh, Dehydrogenase E1 component. This family uses
thiamine pyrophosphate as a cofactor. This family
includes pyruvate dehydrogenase, 2-oxoglutarate
dehydrogenase and 2-oxoisovalerate dehydrogenase.
Length = 303
Score = 293 bits (751), Expect = 3e-97
Identities = 107/194 (55%), Positives = 135/194 (69%), Gaps = 2/194 (1%)
Query: 197 VPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENNGYGMG 256
VPLG GIALAAKY G K V L+GDGA NQGQ FE N A LW +P IFVCENN Y +
Sbjct: 110 VPLGAGIALAAKYRGKKEVAITLFGDGATNQGQFFEALNFAALWKLPVIFVCENNQYAIS 169
Query: 257 TSSERASASVDYYT--RGDYIPGIWVDGMDILAVREAARFAVNHCRSDKGPILLETATYR 314
T +ER+SAS Y RG IPGI VDGMD LAV +A +FA R+ GP L+E TYR
Sbjct: 170 TPAERSSASTTYADRARGYGIPGIRVDGMDPLAVYQAVKFAAERARTGNGPTLIELVTYR 229
Query: 315 YSGHSMSDPGTSYRTRDEIQEVRQTRDPISSLKDKILNASLVTPEELKKIDTEVKAEIDA 374
Y GHSMSD ++YRTR+E++EVR+ +DPI LK +++ +V+ EELK+I+ EV+ EI+
Sbjct: 230 YGGHSMSDDPSTYRTREEVEEVRKKKDPIKRLKKHLVSRGVVSEEELKEIEKEVRKEIEE 289
Query: 375 VIKKARADPEVGLD 388
+KKA +DPE +
Sbjct: 290 AVKKAESDPEPNPE 303
>gnl|CDD|238958 cd02000, TPP_E1_PDC_ADC_BCADC, Thiamine pyrophosphate (TPP) family,
E1 of PDC_ADC_BCADC subfamily, TPP-binding module;
composed of proteins similar to the E1 components of the
human pyruvate dehydrogenase complex (PDC), the acetoin
dehydrogenase complex (ADC) and the branched chain
alpha-keto acid dehydrogenase/2-oxoisovalerate
dehydrogenase complex (BCADC). PDC 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 while BCADC participates in
the breakdown of branched chain amino acids. BCADC
catalyzes the oxidative decarboxylation of
4-methyl-2-oxopentanoate, 3-methyl-2-oxopentanoate and
3-methyl-2-oxobutanoate (branched chain 2-oxo acids
derived from the transamination of leucine, valine and
isoleucine).
Length = 293
Score = 277 bits (712), Expect = 1e-91
Identities = 87/185 (47%), Positives = 113/185 (61%), Gaps = 3/185 (1%)
Query: 197 VPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENNGYGMG 256
VPL G ALA KY G V +GDGA N+G E N A LW +P IFVCENNGY +
Sbjct: 110 VPLAAGAALALKYRGEDRVAVCFFGDGATNEGDFHEALNFAALWKLPVIFVCENNGYAIS 169
Query: 257 TSSERASASVDYYTRGD--YIPGIWVDGMDILAVREAARFAVNHCRSDKGPILLETATYR 314
T + R +A R IPGI VDG D+LAV EAA+ AV R+ GP L+E TYR
Sbjct: 170 TPTSRQTAGTSIADRAAAYGIPGIRVDGNDVLAVYEAAKEAVERARAGGGPTLIEAVTYR 229
Query: 315 YSGHSMSDPGTSYRTRDEIQEVRQTRDPISSLKDKILNASLVTPEELKKIDTEVKAEIDA 374
GHS SD + YRT++E++E + RDPI L+ ++ A ++T EEL I+ EVKAE++
Sbjct: 230 LGGHSTSDDPSRYRTKEEVEE-WKKRDPILRLRKYLIEAGILTEEELAAIEAEVKAEVEE 288
Query: 375 VIKKA 379
++ A
Sbjct: 289 AVEFA 293
>gnl|CDD|223997 COG1071, AcoA, Pyruvate/2-oxoglutarate dehydrogenase complex,
dehydrogenase (E1) component, eukaryotic type, alpha
subunit [Energy production and conversion].
Length = 358
Score = 257 bits (658), Expect = 2e-82
Identities = 91/203 (44%), Positives = 125/203 (61%), Gaps = 4/203 (1%)
Query: 197 VPLGVGIALAAKYSGTK-GVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENNGYGM 255
+PL G ALA KY GTK GV A +GDGA NQG E N A +W +P +FV ENN Y +
Sbjct: 142 IPLAAGAALALKYRGTKDGVAVAFFGDGATNQGDFHEALNFAAVWKLPVVFVIENNQYAI 201
Query: 256 GTSSERASASVDYYTRGD--YIPGIWVDGMDILAVREAARFAVNHCRSDKGPILLETATY 313
R +A+ R IPG+ VDG D+LAV EAA+ AV R+ +GP L+E TY
Sbjct: 202 SVPRSRQTAAEIIAARAAAYGIPGVRVDGNDVLAVYEAAKEAVERARAGEGPTLIEAVTY 261
Query: 314 RYSGHSMSDPGTSYRTRDEIQEVRQTRDPISSLKDKILNASLVTPEELKKIDTEVKAEID 373
RY GHS SD + YR+++E++E + RDPI L+ ++ A +++ EEL+ I+ E KAE+D
Sbjct: 262 RYGGHSTSDDPSKYRSKEEVEEWK-KRDPIVRLRKYLIEAGILSEEELEAIEAEAKAEVD 320
Query: 374 AVIKKARADPEVGLDELTGDIYA 396
++ A A P + EL D+YA
Sbjct: 321 EAVEFAEASPYPDVSELFEDVYA 343
>gnl|CDD|213783 TIGR03181, PDH_E1_alph_x, pyruvate dehydrogenase E1 component,
alpha subunit. Members of this protein family are the
alpha subunit of the E1 component of pyruvate
dehydrogenase (PDH). This model represents one branch of
a larger family that E1-alpha proteins from
2-oxoisovalerate dehydrogenase, acetoin dehydrogenase,
another PDH clade, etc [Energy metabolism, Pyruvate
dehydrogenase].
Length = 341
Score = 181 bits (462), Expect = 1e-53
Identities = 64/204 (31%), Positives = 104/204 (50%), Gaps = 3/204 (1%)
Query: 197 VPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENNGYGMG 256
G+A A K G V +GDG ++G +E N A ++ P +F +NN + +
Sbjct: 128 YLHAAGVAYALKLRGEDNVAVTYFGDGGTSEGDFYEALNFAGVFKAPVVFFVQNNQWAIS 187
Query: 257 TSSERASASVDYYTRG-DY-IPGIWVDGMDILAVREAARFAVNHCRSDKGPILLETATYR 314
+ +A+ + Y IPG+ VDG D+LAV + AV RS GP L+E TYR
Sbjct: 188 VPRSKQTAAPTLAQKAIAYGIPGVQVDGNDVLAVYAVTKEAVERARSGGGPTLIEAVTYR 247
Query: 315 YSGHSMSDPGTSYRTRDEIQEVRQTRDPISSLKDKILNASLVTPEELKKIDTEVKAEIDA 374
H+ +D T YRT++E +E R+ +DPI L+ + L E+ + ++ E +AE+
Sbjct: 248 LGPHTTADDPTRYRTKEEEEEWRK-KDPILRLRKYLERKGLWDEEQEEALEEEAEAEVAE 306
Query: 375 VIKKARADPEVGLDELTGDIYAVP 398
+ +A A P +D++ +YA
Sbjct: 307 AVAEALALPPPPVDDIFDHVYAEL 330
>gnl|CDD|177069 CHL00149, odpA, pyruvate dehydrogenase E1 component alpha subunit;
Reviewed.
Length = 341
Score = 167 bits (424), Expect = 4e-48
Identities = 77/184 (41%), Positives = 112/184 (60%), Gaps = 6/184 (3%)
Query: 215 VCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENNGYGMGTSSERASASVDYYTRGDY 274
CF +GDG N GQ FE N+A LW +P IFV ENN + +G + R+++ + + + +
Sbjct: 161 ACF--FGDGTTNNGQFFECLNMAVLWKLPIIFVVENNQWAIGMAHHRSTSIPEIHKKAEA 218
Query: 275 --IPGIWVDGMDILAVREAARFAVNHCRSDKGPILLETATYRYSGHSMSDPGTSYRTRDE 332
+PGI VDGMD+LAVRE A+ AV R GP L+E TYR+ GHS++DP R++ E
Sbjct: 219 FGLPGIEVDGMDVLAVREVAKEAVERARQGDGPTLIEALTYRFRGHSLADP-DELRSKQE 277
Query: 333 IQEVRQTRDPISSLKDKILNASLVTPEELKKIDTEVKAEIDAVIKKARADPEVGLDELTG 392
+E RDPI LK I++ L + +EL KI EVK EI+ ++ A + PE + +L
Sbjct: 278 -KEAWVARDPIKKLKSYIIDNELASQKELNKIQREVKIEIEQAVQFAISSPEPNISDLKK 336
Query: 393 DIYA 396
++A
Sbjct: 337 YLFA 340
>gnl|CDD|215213 PLN02374, PLN02374, pyruvate dehydrogenase (acetyl-transferring).
Length = 433
Score = 158 bits (402), Expect = 3e-44
Identities = 76/216 (35%), Positives = 120/216 (55%), Gaps = 21/216 (9%)
Query: 197 VPLGVGIALAAKY-------SGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCE 249
+P+ G A ++KY V A +GDG N GQ FE N+A LW +P +FV E
Sbjct: 200 IPVATGAAFSSKYRREVLKEESCDDVTLAFFGDGTCNNGQFFECLNMAALWKLPIVFVVE 259
Query: 250 NNGYGMGTSSERASASVDYYTRGDY--IPGIWVDGMDILAVREAARFAVNHCRSDKGPIL 307
NN + +G S RA++ + + +G +PG+ VDGMD+L VRE A+ A+ R +GP L
Sbjct: 260 NNLWAIGMSHLRATSDPEIWKKGPAFGMPGVHVDGMDVLKVREVAKEAIERARRGEGPTL 319
Query: 308 LETATYRYSGHSMSDPGTSYRTRDEIQEVRQ-----TRDPISSLKDKILNASLVTPEELK 362
+E TYR+ GHS++DP DE+++ + RDPI++LK ++ L T ELK
Sbjct: 320 VECETYRFRGHSLADP-------DELRDPAEKAHYAARDPIAALKKYLIENGLATEAELK 372
Query: 363 KIDTEVKAEIDAVIKKARADPEVGLDELTGDIYAVP 398
I+ ++ ++ ++ A A P +L +++A P
Sbjct: 373 AIEKKIDEVVEDAVEFADASPLPPRSQLLENVFADP 408
>gnl|CDD|197836 smart00704, ZnF_CDGSH, CDGSH-type zinc finger. Function unknown.
Length = 38
Score = 50.0 bits (120), Expect = 1e-08
Identities = 15/23 (65%), Positives = 19/23 (82%)
Query: 80 AICRCWKSKKFPFCDNSHKYHNK 102
A+CRC +SK FP+CD SHK HN+
Sbjct: 15 ALCRCGRSKNFPYCDGSHKKHNE 37
>gnl|CDD|220203 pfam09360, zf-CDGSH, Iron-binding zinc finger CDGSH type. The
CDGSH-type zinc finger domain binds iron rather than
zinc as a redox-active pH-labile 2Fe-2S cluster. The
conserved sequence
C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining
feature of this family. The domain is oriented towards
the cytoplasm and is tethered to the mitochondrial
membrane by a more N-terminal domain found in higher
vertebrates, MitoNEET_N, pfam10660. The domain forms a
uniquely folded homo-dimer and spans the outer
mitochondrial membrane, orienting the iron-binding
residues towards the cytoplasm.
Length = 34
Score = 49.1 bits (118), Expect = 2e-08
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 69 RFTIDTGIHTEAICRCWKSKKFPFCDNSHK 98
+ ++ + A+CRC +SK PFCD SHK
Sbjct: 7 KVELEKKTY--ALCRCGRSKNQPFCDGSHK 34
>gnl|CDD|223641 COG0567, SucA, 2-oxoglutarate dehydrogenase complex, dehydrogenase
(E1) component, and related enzymes [Energy production
and conversion].
Length = 906
Score = 51.1 bits (123), Expect = 8e-07
Identities = 49/237 (20%), Positives = 89/237 (37%), Gaps = 44/237 (18%)
Query: 218 ALYGDGA-ANQGQVFEVYNIAKL--------WNIPCIFVCENNGYGMGTSSERASASVDY 268
++GD A A QG V E N+++L W+I + N T+S + S Y
Sbjct: 330 LIHGDAAFAGQGVVAETLNLSRLDGYSVGGTWHI--VI----NNQIGFTTSPADARSTPY 383
Query: 269 YT---RGDYIPGIWVDGMDILAVREAARFAVNHCRSDKGPILLETATYRYSGHS-MSDPG 324
T + P V+ D AV A A+ + K ++++ YR GH+ +P
Sbjct: 384 CTDVAKMIEAPIFHVNADDPEAVLFAPALALEYRNGFKKDVVIDLVCYRRHGHNEGDEPS 443
Query: 325 TS----YRTRDEIQEVRQTRDPISSLKDKILNASLVTPEELKKIDTEVKAEIDA---VIK 377
+ Y Q++++ DK++ +++ EE ++ + + +D V+K
Sbjct: 444 VTQPLMY------QKIKKHPTVRKLYADKLIAEGVISEEEADELVNDYRDALDQGFEVVK 497
Query: 378 KARAD-------PEVGLDELTGDIYAVPLETDIRGTTPFNSYP-----HKRVGKAIN 422
+ + L VP +T + P H RV K +
Sbjct: 498 EYKEMDWLEGDWSGYLNAGLRHVDTGVPKKTLKELGKKLCTIPEGFEVHPRVKKILE 554
>gnl|CDD|161785 TIGR00239, 2oxo_dh_E1, 2-oxoglutarate dehydrogenase, E1 component.
The 2-oxoglutarate dehydrogenase complex consists of
this thiamine pyrophosphate-binding subunit (E1),
dihydrolipoamide succinyltransferase (E2), and lipoamide
dehydrogenase (E3). The E1 ortholog from Corynebacterium
glutamicum is unusual in having an N-terminal extension
that resembles the dihydrolipoamide succinyltransferase
(E2) component of 2-oxoglutarate dehydrogenase [Energy
metabolism, TCA cycle].
Length = 929
Score = 46.4 bits (110), Expect = 2e-05
Identities = 44/179 (24%), Positives = 78/179 (43%), Gaps = 19/179 (10%)
Query: 212 TKGVCFALYGDGA-ANQGQVFEVYNIAKLWNIP---CIFVCENNGYGMGTSSERASASVD 267
TK + ++GD A A QG V E N++KL I + NN G T+ + S
Sbjct: 342 TKVLAILIHGDAAFAGQGVVQETLNMSKLRGYSVGGTIHIIINNQIGFTTNP-LDARSTP 400
Query: 268 YYT---RGDYIPGIWVDGMDILAVREAARFAVNHCRSDKGPILLETATYRYSGHSMSD-P 323
Y + + P V+ D AV A R AV + + K + ++ YR GH+ +D P
Sbjct: 401 YCSDLAKMIQAPIFHVNADDPEAVAFATRLAVEYRNTFKRDVFIDLVGYRRHGHNEADEP 460
Query: 324 GTS----YRTRDEIQEVRQTRDPISSLKDKILNASLVTPEELKKIDTEVKAEIDAVIKK 378
+ Y Q++++ P DK+++ + T E++ ++ + ++A
Sbjct: 461 SATQPLMY------QKIKKHPTPRKVYADKLVSEGVATEEDVTEMVNLYRDALEAADCV 513
>gnl|CDD|226468 COG3959, COG3959, Transketolase, N-terminal subunit [Carbohydrate
transport and metabolism].
Length = 243
Score = 44.6 bits (106), Expect = 3e-05
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 198 PLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIA---KLWNIPCIFVCENNGYG 254
+ VG+AL AK G+ + + GDG ++GQV+E A KL N+ V N
Sbjct: 126 SVAVGMALGAKLKGSPYRVYVILGDGELDEGQVWEAAMTAAHYKLDNL-IAIVDRNKLQL 184
Query: 255 MGTSSE 260
G + E
Sbjct: 185 DGETEE 190
>gnl|CDD|238318 cd00568, TPP_enzymes, Thiamine pyrophosphate (TPP) enzyme family,
TPP-binding module; found in many key metabolic enzymes
which use TPP (also known as thiamine diphosphate) as a
cofactor. These enzymes include, among others, the E1
components of the pyruvate, the acetoin and the branched
chain alpha-keto acid dehydrogenase complexes.
Length = 168
Score = 41.1 bits (97), Expect = 3e-04
Identities = 32/121 (26%), Positives = 41/121 (33%), Gaps = 15/121 (12%)
Query: 197 VPLGVGIALAAKYSGTKGVCFALYGDGAAN-QGQVFEVYNIAKLWNIPCIFVC-ENNGYG 254
+P +G ALAA VC A GDG GQ A + +P I V N GYG
Sbjct: 52 LPAAIGAALAAP--DRPVVCIA--GDGGFMMTGQELAT---AVRYGLPVIVVVFNNGGYG 104
Query: 255 MGTSSERASASVDYYTRGDYIPGI--WVDGMDILAVR----EAARFAVNHCRSDKGPILL 308
+ A P + VR E A+ + GP L+
Sbjct: 105 TIRMHQEAFYGGRVSGTDLSNPDFAALAEAYGAKGVRVEDPEDLEAALAEALAAGGPALI 164
Query: 309 E 309
E
Sbjct: 165 E 165
>gnl|CDD|238974 cd02016, TPP_E1_OGDC_like, Thiamine pyrophosphate (TPP) family, E1
of OGDC-like subfamily, TPP-binding module; composed of
proteins similar to the E1 component of the
2-oxoglutarate dehydrogenase multienzyme complex (OGDC).
OGDC catalyzes the oxidative decarboxylation of
2-oxoglutarate to succinyl-CoA and carbon dioxide, a key
reaction of the tricarboxylic acid cycle.
Length = 265
Score = 41.7 bits (99), Expect = 3e-04
Identities = 39/140 (27%), Positives = 60/140 (42%), Gaps = 19/140 (13%)
Query: 198 PLGVGIALAAKYS-----GTKGVCFALYGDGA-ANQGQVFEVYNIAKLWNIP------CI 245
P+ +G A + K + ++GD A A QG V+E N L N+P I
Sbjct: 120 PVVMGKTRAKQDYRGDGERDKVLPILIHGDAAFAGQGVVYETLN---LSNLPGYTTGGTI 176
Query: 246 FVCENNGYGMGTSSERASASVDYYT---RGDYIPGIWVDGMDILAVREAARFAVNHCRSD 302
+ NN G T + +S Y T + P V+G D AV A R A+ + +
Sbjct: 177 HIVVNNQIGFTTDPRDSRSS-PYCTDVAKMIGAPIFHVNGDDPEAVVRATRLALEYRQKF 235
Query: 303 KGPILLETATYRYSGHSMSD 322
K ++++ YR GH+ D
Sbjct: 236 KKDVVIDLVCYRRHGHNELD 255
>gnl|CDD|238970 cd02012, TPP_TK, Thiamine pyrophosphate (TPP) family, Transketolase
(TK) subfamily, TPP-binding module; 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. In addition, the enzyme plays a central
role in the Calvin cycle in plants. Typically, TKs are
homodimers. They require TPP and divalent cations, such
as magnesium ions, for activity.
Length = 255
Score = 41.3 bits (98), Expect = 4e-04
Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 11/102 (10%)
Query: 197 VPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIA---KLWNIPCIFVCENNGY 253
+ + VG+ALA K G + L GDG +G V+E + A KL N+ I ++N
Sbjct: 111 LSVAVGMALAEKLLGFDYRVYVLLGDGELQEGSVWEAASFAGHYKLDNLIAIV--DSNRI 168
Query: 254 GMGTSSERASASVDYYTR----GDYIPGIWVDGMDILAVREA 291
+ ++ + D + G + I VDG D+ + A
Sbjct: 169 QIDGPTDDILFTEDLAKKFEAFGWNV--IEVDGHDVEEILAA 208
>gnl|CDD|238960 cd02002, TPP_BFDC, Thiamine pyrophosphate (TPP) family, BFDC
subfamily, TPP-binding module; composed of proteins
similar to Pseudomonas putida benzoylformate
decarboxylase (BFDC). P. putida BFDC plays a role in the
mandelate pathway, catalyzing the conversion of
benzoylformate to benzaldehyde and carbon dioxide. This
enzyme is dependent on TPP and a divalent metal cation
as cofactors.
Length = 178
Score = 36.4 bits (85), Expect = 0.010
Identities = 22/63 (34%), Positives = 24/63 (38%), Gaps = 17/63 (26%)
Query: 198 PLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLW-----NIPCIFVCENN- 251
P VG ALA K V GDG+ Y I LW +P V NN
Sbjct: 56 PAAVGAALAN--PDRKVVAII--GDGSFM-------YTIQALWTAARYGLPVTVVILNNR 104
Query: 252 GYG 254
GYG
Sbjct: 105 GYG 107
>gnl|CDD|225904 COG3369, COG3369, Zinc finger domain containing protein
(CDGSH-type) [Function unknown].
Length = 78
Score = 33.6 bits (77), Expect = 0.024
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 80 AICRCWKSKKFPFCDNSHK 98
A+CRC S+ PFCD +HK
Sbjct: 32 ALCRCGHSENKPFCDGTHK 50
>gnl|CDD|238963 cd02005, TPP_PDC_IPDC, Thiamine pyrophosphate (TPP) family,
PDC_IPDC subfamily, TPP-binding module; composed of
proteins similar to pyruvate decarboxylase (PDC) and
indolepyruvate decarboxylase (IPDC). PDC, a key enzyme
in alcoholic fermentation, catalyzes the conversion of
pyruvate to acetaldehyde and CO2. It is able to utilize
other 2-oxo acids as substrates. In plants and various
plant-associated bacteria, IPDC plays a role in the
indole-3-pyruvic acid (IPA) pathway, a
tryptophan-dependent biosynthetic route to
indole-3-acetaldehyde (IAA). IPDC catalyzes the
decarboxylation of IPA to IAA. Both PDC and IPDC depend
on TPP and Mg2+ as cofactors.
Length = 183
Score = 33.7 bits (78), Expect = 0.099
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 9/67 (13%)
Query: 196 TVPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENNGYGM 255
+VP +G ALAA L GDG+ Q V E+ + + P IF+ N+GY +
Sbjct: 55 SVPAALGAALAAPDRRV----ILLVGDGSF-QMTVQELSTMIRYGLNPIIFLINNDGYTI 109
Query: 256 GTSSERA 262
ERA
Sbjct: 110 ----ERA 112
>gnl|CDD|224076 COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme
metabolism / Lipid metabolism].
Length = 627
Score = 33.7 bits (78), Expect = 0.20
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 1/57 (1%)
Query: 197 VPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYN-IAKLWNIPCIFVCENNG 252
+ +G+A A G A+ GDGA G FE N I + +N
Sbjct: 121 ISAALGMAKARDLKGEDRNVVAVIGDGALTGGMAFEALNNAGADLKSNLIVILNDNE 177
>gnl|CDD|129308 TIGR00204, dxs, 1-deoxy-D-xylulose-5-phosphate synthase. DXP
synthase is a thiamine diphosphate-dependent enzyme
related to transketolase and the pyruvate dehydrogenase
E1-beta subunit. By an acyloin condensation of pyruvate
with glyceraldehyde 3-phosphate, it produces
1-deoxy-D-xylulose 5-phosphate, a precursor of thiamine
diphosphate (TPP), pyridoxal phosphate, and the
isoprenoid building block isopentenyl diphosphate (IPP)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other, Biosynthesis of cofactors, prosthetic
groups, and carriers, Pyridoxine, Biosynthesis of
cofactors, prosthetic groups, and carriers, Thiamine].
Length = 617
Score = 33.6 bits (77), Expect = 0.23
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 196 TVPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYN 235
++ G+GIA+AA+ G + GDGA G FE N
Sbjct: 116 SISAGLGIAVAAEKKGADRKTVCVIGDGAITAGMAFEALN 155
>gnl|CDD|238965 cd02007, TPP_DXS, Thiamine pyrophosphate (TPP) family, DXS
subfamily, TPP-binding module;
1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a
regulatory enzyme of the mevalonate-independent pathway
involved in terpenoid biosynthesis. Terpeniods are plant
natural products with important pharmaceutical activity.
DXS catalyzes a transketolase-type condensation of
pyruvate with D-glyceraldehyde-3-phosphate to form
1-deoxy-D-xylulose-5-phosphate (DXP) and carbon dioxide.
The formation of DXP leads to the formation of the
terpene precursor IPP (isopentyl diphosphate) and to the
formation of thiamine (vitamin B1) and pyridoxal
(vitamin B6).
Length = 195
Score = 31.4 bits (72), Expect = 0.54
Identities = 34/119 (28%), Positives = 51/119 (42%), Gaps = 11/119 (9%)
Query: 196 TVPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENNGYGM 255
++ +G+A+A G K A+ GDGA G FE N A I + +N M
Sbjct: 80 SISAALGMAVARDLKGKKRKVIAVIGDGALTGGMAFEALNNAGYLKSNMIVILNDN--EM 137
Query: 256 GTSSERASASVDYYTR-G-DYIPGIWVDGMDILAVREAARFAVNHCRSDKGPILLETAT 312
+ S + + G YI G VDG +I A+ + + + KGP+LL T
Sbjct: 138 -SISPNVGTPGNLFEELGFRYI-GP-VDGHNIEALIK----VLKEVKDLKGPVLLHVVT 189
>gnl|CDD|178194 PLN02582, PLN02582, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 677
Score = 32.2 bits (73), Expect = 0.59
Identities = 18/56 (32%), Positives = 27/56 (48%)
Query: 196 TVPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENN 251
T+ G+G+A+ G K A+ GDGA GQ +E N A + I + +N
Sbjct: 149 TISAGLGMAVGRDLKGKKNNVVAVIGDGAMTAGQAYEAMNNAGYLDSDMIVILNDN 204
>gnl|CDD|177878 PLN02234, PLN02234, 1-deoxy-D-xylulose-5-phosphate synthase.
Length = 641
Score = 32.0 bits (72), Expect = 0.66
Identities = 16/56 (28%), Positives = 26/56 (46%)
Query: 196 TVPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENN 251
T+ G+G+A+ G ++ GDGA GQ +E N A + I + +N
Sbjct: 182 TLSAGLGMAVGRDLKGMNNSVVSVIGDGAMTAGQAYEAMNNAGYLHSNMIVILNDN 237
>gnl|CDD|220103 pfam09074, Mer2, Mer2. Mer2 (Rec107) forms part of a complex that
is required for meiotic double strand DNA break
formation. Mer2 increases in abundance and is
phosphorylated during the prophase phase of cell
division. Blocking double strand break formation results
in delayed dephosphorylation and dissociation of Mer2
from the chromosome.
Length = 190
Score = 29.9 bits (67), Expect = 1.6
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 10/76 (13%)
Query: 122 VLDKYTLPTPNRSITYPTPSTMSDSQVDKAID----------KYVKENEYSQDSDENMTN 171
+ +K N + PS + D+ D + K + +QDS ENM+N
Sbjct: 104 LSEKVKTINGNSMMGQVPPSEVERINSDEPFDIIKSFEARQLENNKSVDATQDSVENMSN 163
Query: 172 QLVTVTNQLVTVTNQL 187
QL + L++V+ QL
Sbjct: 164 QLESKKYVLLSVSRQL 179
>gnl|CDD|181008 PRK07509, PRK07509, enoyl-CoA hydratase; Provisional.
Length = 262
Score = 30.2 bits (69), Expect = 1.8
Identities = 12/48 (25%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 339 TRDPIS-SLKDKILNASLVTPEELKKIDTEVKAEIDAVIKKARADPEV 385
D +S +++D I + L P+++ +D + E+ A IK+ + D +
Sbjct: 1 MMDRVSVTIEDGIADVRLNRPDKMNALDFAMFEELIATIKRLKKDRGI 48
>gnl|CDD|185269 PRK15371, PRK15371, effector protein YopJ; Provisional.
Length = 287
Score = 30.1 bits (68), Expect = 2.0
Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 14/93 (15%)
Query: 102 KFHKDNVGPLIIDGNTF-PDYVLDKYTLPTPNRSITYPTPSTMSDSQVDKAIDKYVKENE 160
K H+DN+ ++ DG P LD Y LP + +Q K +++Y+ N
Sbjct: 192 KLHEDNIKGILCDGENPLPHDKLDPY-LP----------VTFYKHTQGKKRLNEYLNTNP 240
Query: 161 YSQDSDENMTNQLVT--VTNQLVTVTNQLVTVT 191
+ + N + + N L V + ++V+
Sbjct: 241 QAVGTVVNKKGETLVERFDNNLSIVDGKELSVS 273
>gnl|CDD|146915 pfam04513, Baculo_PEP_C, Baculovirus polyhedron envelope protein,
PEP, C terminus. Polyhedra are large crystalline
occlusion bodies containing nucleopolyhedrovirus
virions, and surrounded by an electron-dense structure
called the polyhedron envelope or polyhedron calyx. The
polyhedron envelope (associated) protein PEP is thought
to be an integral part of the polyhedron envelope. PEP
is concentrated at the surface of polyhedra, and is
thought to be important for the proper formation of the
periphery of polyhedra. It is thought that PEP may
stabilise polyhedra and protect them from fusion or
aggregation.
Length = 140
Score = 28.9 bits (65), Expect = 2.4
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 168 NMTNQLVTVTNQLVTVTNQLVTVTNQLVT 196
N NQ + +TN L + Q V + QL T
Sbjct: 10 NGGNQFLELTNVLNAIRLQNVQIAAQLTT 38
>gnl|CDD|217223 pfam02775, TPP_enzyme_C, Thiamine pyrophosphate enzyme, C-terminal
TPP binding domain.
Length = 151
Score = 29.1 bits (66), Expect = 2.5
Identities = 20/64 (31%), Positives = 25/64 (39%), Gaps = 17/64 (26%)
Query: 200 GVGIALAAK--YSGTKGVCFALYGDGAANQGQVFEVYNIAKLW-----NIPCIFVCENNG 252
G+ A+ AK V A GDG N+ +L N+P V NNG
Sbjct: 33 GLPAAIGAKLARPDRPVVAIA--GDGGFQ-------MNLQELATAVRYNLPITVVVLNNG 83
Query: 253 -YGM 255
YGM
Sbjct: 84 GYGM 87
>gnl|CDD|218079 pfam04420, CHD5, CHD5-like protein. Members of this family are
probably coiled-coil proteins that are similar to the
CHD5 (Congenital heart disease 5) protein. In
Saccharomyces cerevisiae this protein localises to the
ER and is thought to play a homeostatic role.
Length = 161
Score = 29.2 bits (66), Expect = 2.8
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 14/62 (22%)
Query: 330 RDEIQEVRQTRDPISS---------LKDKI--LNASLVTPEELKKIDTEVKAEIDAVIKK 378
R EI E+++ + IS+ L K+ L L E+LKK T K++ V+KK
Sbjct: 46 RKEILELKRELNSISAQDEFAKWAKLNRKLDKLTDEL---EKLKKELTAQKSKFKWVLKK 102
Query: 379 AR 380
R
Sbjct: 103 LR 104
>gnl|CDD|217224 pfam02776, TPP_enzyme_N, Thiamine pyrophosphate enzyme, N-terminal
TPP binding domain.
Length = 172
Score = 28.7 bits (65), Expect = 3.3
Identities = 24/141 (17%), Positives = 37/141 (26%), Gaps = 40/141 (28%)
Query: 186 QLVTVTNQLVTVPLGVGIALA-AKYSGTKGVCFALYGDGAANQ-GQVFEVYNIAKLWNIP 243
+ V ++ A A+ +G GV G GA N + A + IP
Sbjct: 41 RYVLTRHEQG----AGFAADGYARATGKPGVVLVTSGPGATNALTGLAN----AYVDGIP 92
Query: 244 CIFVCENNGYGMGTSSERASASVDYYTRGDYIPGIWVDGMDILA--------VREAARF- 294
+ + S V G +D + + V
Sbjct: 93 VLVI---------------SGQVPTSDLGRGGLQEELDQLALFRPVTKWAERVTSPDEIP 137
Query: 295 -----AVNHCRSD-KGPILLE 309
A S GP+ LE
Sbjct: 138 EALDRAFRAALSGRPGPVYLE 158
>gnl|CDD|181601 PRK08978, PRK08978, acetolactate synthase 2 catalytic subunit;
Reviewed.
Length = 548
Score = 29.5 bits (67), Expect = 3.6
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 202 GIALAA----KYSGTKGVCFALYGDGAAN 226
G A+AA + +G GVC A G GA N
Sbjct: 49 GAAMAAIGYARATGKVGVCIATSGPGATN 77
>gnl|CDD|235718 PRK06154, PRK06154, hypothetical protein; Provisional.
Length = 565
Score = 29.4 bits (66), Expect = 3.9
Identities = 33/128 (25%), Positives = 49/128 (38%), Gaps = 24/128 (18%)
Query: 200 GVGIALAAKYSGTKGVCFALYGDGAANQ-GQVFEVYNIAKLWNIPCIFVCENNGYGMGTS 258
G+G+A+ AK + + L+GD A G FE A IP + + NN G
Sbjct: 436 GLGLAMGAKLARPDALVINLWGDAAFGMTGMDFET---AVRERIPILTILLNNFSMGGYD 492
Query: 259 SERASASVDYYTR---GDYIP-----GIWVD-----GMDILAVREAARFAVNHCRSDKG- 304
++ Y GDY G + + M + A+ A R + +G
Sbjct: 493 KVMPVSTTKYRATDISGDYAAIARALGGYGERVEDPEMLVPALLRALR------KVKEGT 546
Query: 305 PILLETAT 312
P LLE T
Sbjct: 547 PALLEVIT 554
>gnl|CDD|226470 COG3961, COG3961, Pyruvate decarboxylase and related thiamine
pyrophosphate-requiring enzymes [Carbohydrate transport
and metabolism / Coenzyme metabolism / General function
prediction only].
Length = 557
Score = 29.6 bits (67), Expect = 4.0
Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 11/68 (16%)
Query: 196 TVPLGVGIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNI-PCIFVCENNGYG 254
T+P +G ALAA GDG+ Q V E+ + + W + P IFV N+GY
Sbjct: 416 TLPAALGAALAAPDRRV----ILFIGDGSL-QLTVQEISTMIR-WGLKPIIFVLNNDGY- 468
Query: 255 MGTSSERA 262
+ ERA
Sbjct: 469 ---TIERA 473
>gnl|CDD|227482 COG5153, CVT17, Putative lipase essential for disintegration of
autophagic bodies inside the vacuole [Intracellular
trafficking and secretion / Lipid metabolism].
Length = 425
Score = 29.2 bits (65), Expect = 4.2
Identities = 22/82 (26%), Positives = 32/82 (39%), Gaps = 5/82 (6%)
Query: 255 MGTSSERASASVDYYTRGDYIPGIWVDGMDILAVR-EAARFAVNHCRSDKGPILLETATY 313
+G SS R D+ + Y G+ + L R E ++ D P+LL+T Y
Sbjct: 29 VGKSSSRMDQKSDFRLKSIYRHGVGAN--HRLHQRLEVTPEVISAATEDMLPLLLQTPIY 86
Query: 314 RYSGHSMSDPGTSYR--TRDEI 333
G SYR + EI
Sbjct: 87 GTYGELRRVQLASYRFKSVLEI 108
>gnl|CDD|148614 pfam07106, TBPIP, Tat binding protein 1(TBP-1)-interacting protein
(TBPIP). This family consists of several eukaryotic
TBP-1 interacting protein (TBPIP) sequences. TBP-1 has
been demonstrated to interact with the human
immunodeficiency virus type 1 (HIV-1) viral protein Tat,
then modulate the essential replication process of HIV.
In addition, TBP-1 has been shown to be a component of
the 26S proteasome, a basic multiprotein complex that
degrades ubiquitinated proteins in an ATP-dependent
fashion. Human TBPIP interacts with human TBP-1 then
modulates the inhibitory action of human TBP-1 on
HIV-Tat-mediated transactivation.
Length = 169
Score = 28.0 bits (63), Expect = 5.6
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 6/51 (11%)
Query: 330 RDEIQEVRQTRDPISSLKDKI--LNASLVTPEELKKIDTEVKAEIDAVIKK 378
R+E+Q ++Q S+L+ ++ L + L T EEL++ E+K E+ + +K
Sbjct: 85 REEVQLLKQD---CSTLEIELKSLTSDL-TTEELQEEIQELKKEVREIEEK 131
>gnl|CDD|205913 pfam13739, DUF4163, Domain of unknown function (DUF4163). The
structure of this domain is and alpha-beta-two layer
sandwich, identified from a Fervidobacterium nodosum
Rt17-B1 like protein. The function is not known except
that it is found in association with Heat-shock cognate
70kd protein 44kd ATPase, pfam11738.
Length = 101
Score = 27.3 bits (61), Expect = 5.6
Identities = 10/53 (18%), Positives = 21/53 (39%), Gaps = 6/53 (11%)
Query: 125 KYTLPTPNRSITYPTPSTMSDSQVDKAIDKYVKE------NEYSQDSDENMTN 171
I+YP S + + ++ K I+ ++K NE +++ E
Sbjct: 8 SKKNEYYEYDISYPVFSGLKNKELQKKINDFIKNKILKFINELEKEAKEAKKK 60
>gnl|CDD|147958 pfam06081, DUF939, Bacterial protein of unknown function (DUF939).
This family consists of several hypothetical bacterial
proteins of unknown function.
Length = 141
Score = 27.9 bits (63), Expect = 5.7
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 173 LVTVTNQLVTVTNQLVTVTNQLVTVPLGVGIAL 205
VTV + +V+ + N+ + + +G+G+AL
Sbjct: 103 SVTVLHIMVSKSISFFLFLNEFLLIMIGIGVAL 135
>gnl|CDD|131325 TIGR02272, gentisate_1_2, gentisate 1,2-dioxygenase. This family
consists of gentisate 1,2-dioxygenases. This
ring-opening enzyme acts in salicylate degradation that
goes via gentisate rather than via catechol. It converts
gentisate to maleylpyruvate. Some putative gentisate
1,2-dioxygenases are excluded by a relatively high
trusted cutoff score because they are too closely
related to known examples of 1-hydroxy-2-naphthoate
dioxygenase. Therefore some homologs may be bona fide
gentisate 1,2-dioxygenases even if they score below the
given cutoffs.
Length = 335
Score = 28.6 bits (64), Expect = 6.2
Identities = 36/141 (25%), Positives = 55/141 (39%), Gaps = 41/141 (29%)
Query: 246 FVCENNGYGMGTSSERASASVDYYTRGDYI----------------PGIWVDGMDILAVR 289
F+ E G ER + GD+I P IW+DG+DI V+
Sbjct: 106 FIVEGKGAFTAVDGERTTMHP-----GDFIITPSWTWHDHGNPGDEPMIWLDGLDIPLVQ 160
Query: 290 E-AARFAVNHCRSDKGPILLETATY--RYSGHSM----------SDPGTSY---RTRDEI 333
FA + D+ P+ RY GH+M S P +Y R+R+ +
Sbjct: 161 LFDCSFAEGY-PEDQQPVTRPEGDSLARY-GHNMLPVRHKRSDRSSPIFNYPYERSREAL 218
Query: 334 QEVRQTR--DPISSLKDKILN 352
++ +T DP LK + +N
Sbjct: 219 DDLTRTGEWDPWHGLKLRYVN 239
>gnl|CDD|236551 PRK09533, PRK09533, bifunctional transaldolase/phosoglucose
isomerase; Validated.
Length = 948
Score = 28.8 bits (65), Expect = 6.3
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 363 KIDTEVKAEIDAVIKKARADPE-VGLDELTGDI 394
+ID+ V +D I A E L+ L G +
Sbjct: 206 RIDSAVDKRLDEKIAAANDPAEKAALEALKGKV 238
>gnl|CDD|153377 cd07365, MhpB_like, Subunit B of the Class III Extradiol
ring-cleavage dioxygenase, 2,3-dihydroxyphenylpropionate
1,2-dioxygenase (MhpB), which catalyzes the oxidization
and subsequent ring-opening of
2,3-dihydroxyphenylpropionate.
2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB)
catalyzes the oxidization and subsequent ring-opening of
2,3-dihydroxyphenylpropionate, yielding the product
2-hydroxy-6-oxo-nona-2,4-diene 1,9-dicarboxylate. It is
an essential enzyme in the beta-phenylpropionic
degradation pathway, in which beta-phenylpropionic is
first hydrolyzed to produce
2,3-dihydroxyphenylpropionate. The enzyme is a member of
the class III extradiol dioxygenase family, a group of
enzymes which use a non-heme Fe(II) to cleave aromatic
rings between a hydroxylated carbon and an adjacent
non-hydroxylated carbon. LigAB-like class III enzymes
are usually composed of two subunits, designated A and
B, which form a tetramer composed of two copies of each
subunit. This model represents the catalytic subunit, B.
MhpB is likely to be a tetramer.
Length = 310
Score = 28.4 bits (64), Expect = 6.3
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 5/26 (19%)
Query: 365 DTEVKAEIDAVIKKARA-----DPEV 385
EV AE+DA ARA DPE+
Sbjct: 20 APEVVAEVDAAFAAARAFVAAFDPEL 45
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 28.5 bits (65), Expect = 6.4
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 360 ELKKIDTEVKAEIDAVIKKARADPEVGLDELTGD 393
ELK + E +I+ ++K+A D E GL EL +
Sbjct: 147 ELKPLSEE---DIEQLLKRALEDKERGLVELDDE 177
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 28.4 bits (64), Expect = 8.2
Identities = 13/46 (28%), Positives = 21/46 (45%)
Query: 355 LVTPEELKKIDTEVKAEIDAVIKKARADPEVGLDELTGDIYAVPLE 400
+ E+L++I+ V E K A GLD+L ++ LE
Sbjct: 292 IADEEKLEEIEASVLEEGGEEPLKISATKGCGLDKLREEVRKTALE 337
>gnl|CDD|226627 COG4147, DhlC, Predicted symporter [General function prediction
only].
Length = 529
Score = 28.5 bits (64), Expect = 8.5
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 258 SSERASASVDYYTRGDYIPGIWVDGMDI 285
+S+R ++ DYY G I G +G+ I
Sbjct: 26 ASKRTRSATDYYVAGGRITGFQ-NGLAI 52
>gnl|CDD|224378 COG1461, COG1461, Predicted kinase related to dihydroxyacetone
kinase [General function prediction only].
Length = 542
Score = 28.4 bits (64), Expect = 8.6
Identities = 25/103 (24%), Positives = 39/103 (37%), Gaps = 9/103 (8%)
Query: 167 ENMTNQLVTVTNQLVTVTNQLVTVTNQLVTVPLGVGIA-LAAKYSGTKGVCFALYGDGAA 225
ENM Q V + + T +V V G GIA L G + G
Sbjct: 302 ENMREQHEEVLEKEGENKLKKETKDRGIVAVADGEGIADLFKSL----GADVVIEGGQTM 357
Query: 226 NQGQVFEVYNIAKLWNIPCIFVCENNG-YGMGTSSERASASVD 267
N ++ + N +F+ NN M ++E+A+ +VD
Sbjct: 358 NP-STDDIVEAIESVNAKNVFILPNNKNIIM--AAEQAAEAVD 397
>gnl|CDD|183601 PRK12571, PRK12571, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 641
Score = 28.2 bits (63), Expect = 9.7
Identities = 27/133 (20%), Positives = 40/133 (30%), Gaps = 14/133 (10%)
Query: 202 GIALAAKYSGTKGVCFALYGDGAANQGQVFEVYNIAKLWNIPCIFVCENNGY-------G 254
G A A G A+ GDG+ G +E N A + I + +N
Sbjct: 130 GFAKARALGQPDGDVVAVIGDGSLTAGMAYEALNNAGAADRRLIVILNDNEMSIAPPVGA 189
Query: 255 MGTSSERASASVDYYTRGDYIPGIWVDGMDILAVREAARFAVNHCRS-DKGPILLETATY 313
+ +S + G+ +R+ AR A G L E +
Sbjct: 190 LAAYLSTLRSSDPFARLRAIAKGVEERLPG--PLRDGARRARELVTGMIGGGTLFEELGF 247
Query: 314 RY----SGHSMSD 322
Y GH M
Sbjct: 248 TYVGPIDGHDMEA 260
>gnl|CDD|187617 cd05359, ChcA_like_SDR_c, 1-cyclohexenylcarbonyl_coenzyme
A_reductase (ChcA)_like, classical (c) SDRs. This
subgroup contains classical SDR proteins, including
members identified as 1-cyclohexenylcarbonyl coenzyme A
reductase. ChcA of Streptomyces collinus is implicated
in the final reduction step of shikimic acid to
ansatrienin. ChcA shows sequence similarity to the SDR
family of NAD-binding proteins, but it lacks the
conserved Tyr of the characteristic catalytic site. This
subgroup also contains the NADH-dependent
enoyl-[acyl-carrier-protein(ACP)] reductase FabL from
Bacillus subtilis. This enzyme participates in bacterial
fatty acid synthesis, in type II fatty-acid synthases
and catalyzes the last step in each elongation cycle.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 242
Score = 27.7 bits (62), Expect = 9.7
Identities = 12/59 (20%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 350 ILNASLVTPEELKKIDTEVKAE---IDAVIKKARADPEVGLDELTGDIYAVPLETDIRG 405
++ A + P++++++ VK +D ++ A A L ELT + + T+++
Sbjct: 52 VVRADVSQPQDVEEMFAAVKERFGRLDVLVSNAAAGAFRPLSELTPAHWDAKMNTNLKA 110
>gnl|CDD|227950 COG5663, COG5663, Uncharacterized conserved protein [Function
unknown].
Length = 194
Score = 27.5 bits (61), Expect = 9.9
Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 15/58 (25%)
Query: 10 VICLDLLTFIPTCYPVEDTTEKVFGPLDYE-----NIPSEEFWGTEPRRLINKYYSKH 62
I D TF P P + + P DY+ NI +EEFW K+ +
Sbjct: 16 TITDDP-TFAPYLNPAFEKSLSEADPTDYDLHKILNITTEEFW---------KWMEQT 63
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
0.317 0.135 0.407
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,478,449
Number of extensions: 2074307
Number of successful extensions: 2253
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2232
Number of HSP's successfully gapped: 64
Length of query: 423
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 323
Effective length of database: 6,502,202
Effective search space: 2100211246
Effective search space used: 2100211246
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 (21.7 bits)
S2: 60 (26.9 bits)