Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate PfGW456L13_4146 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= CharProtDB::CH_003230 (714 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4146 Length = 714 Score = 386 bits (992), Expect = e-111 Identities = 268/724 (37%), Positives = 371/724 (51%), Gaps = 31/724 (4%) Query: 3 MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAK 61 M+ A D I V+TID+PG+ NT+ A + + + +L +K+ + GV+ SAK Sbjct: 1 MSEAIRYEKDQDQIVVLTIDMPGQSANTMNAVYREAMADCVTRLVADKDSIAGVIITSAK 60 Query: 62 PDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGLE 118 F AG D+N + Q A+A L ++ AL V+AAI+GA LGGG E Sbjct: 61 K-TFFAGGDLNELIKVGKPQ-AKAFYDMVLSLKGQLRALETLGKPVVAAINGAALGGGWE 118 Query: 119 LALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQ 178 + LACH RV D P LGLPEV LGLLPG GG R+ R++G+ AL +L GK++R Q Sbjct: 119 ICLACHHRVALDHPSVQLGLPEVTLGLLPGGGGVVRMVRMLGLEKALPYLLEGKKVRPPQ 178 Query: 179 ALKLGLVDDVVP-HSILLEAAVELAKKERPSSRPLPVRERILAGPLGR----ALLFKMVG 233 AL+ GL+D + H LL A + + V+ + G A + + Sbjct: 179 ALQAGLIDALATDHEDLLAKARTWILANPAAVQRWDVKGYQIPGGTPSNPKVAQMLAIAP 238 Query: 234 KKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAST 293 KTQG PA E+IL G + E R F EL S+ L F+ Sbjct: 239 SILRSKTQGTMPAPEKILCAAVEGAQVDFDTANLIETRYFTELTTGQVSKNLIGTFWFQL 298 Query: 294 DVKKDPGSDAP---PAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALK 350 + GS P VG+LG G+MG GIA+V+A AGI V +KDIN Sbjct: 299 NEINAGGSRPQGFAPYVTRKVGVLGAGMMGAGIAFVSA-SAGIDVVLKDINLAAAQKGKA 357 Query: 351 YSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEV 410 +S L+ KV R + +RD L+ I + A DLIIEAVFE+ +LK ++ Sbjct: 358 HSAALLDKKVARGQISIEQRDTVLSRIQTSESDADLAGCDLIIEAVFEDRDLKAKVSLAA 417 Query: 411 EQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTI 470 ++ A + ASNTS+LPI +A + IGLHFFSPVEKMPLVEII A TS +T+ Sbjct: 418 QKVVGADAVIASNTSTLPISGLACAVPDQSKFIGLHFFSPVEKMPLVEIIKGANTSDETL 477 Query: 471 ATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPV 530 A + KTPIVV D GF+ +R+ + NE I ML +G I+ K G PV Sbjct: 478 ARGFDYVLQIKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVSAAMIETEARKAGMPV 537 Query: 531 GPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPA-NVVSSILND-DRKGRKNGRGFY 584 GP+ + DEV + I L+A PA V+ +LN+ R G+ G GFY Sbjct: 538 GPLAISDEVSLSLMNHIRLQTAKDLQAEGKPLTEHPAFTVIDLLLNEFKRPGKAGGGGFY 597 Query: 585 LYGQKGRKSKKQVDPAIYPLIGT---QGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRS 641 Y G+K ++P + T + G+IS V +R + + E VRCV+E V+ S Sbjct: 598 EYPAGGQKH-------LWPELKTRFEKADGQISPKDVRDRLLFVQAIETVRCVEEGVLTS 650 Query: 642 VRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGAR 701 D ++G++FGIGF + GG ++I+ G + VA Q LATQYG RF P L+E A+ Sbjct: 651 TADANVGSIFGIGFAAWTGGALQFINQYGVQDFVARAQYLATQYGERFAPPALLLEKAAK 710 Query: 702 GESF 705 GE+F Sbjct: 711 GEAF 714 Lambda K H 0.319 0.137 0.393 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 992 Number of extensions: 42 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 714 Length of database: 714 Length adjustment: 39 Effective length of query: 675 Effective length of database: 675 Effective search space: 455625 Effective search space used: 455625 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: 55 (25.8 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory