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 AO353_01155 AO353_01155 3-hydroxyacyl-CoA dehydrogenase
Query= CharProtDB::CH_003230 (714 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01155 Length = 714 Score = 388 bits (996), Expect = e-112 Identities = 267/724 (36%), Positives = 376/724 (51%), Gaps = 31/724 (4%) Query: 3 MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAK 61 MT A D I V+TID+PG+ NT+ A + + + +L +K+ + GV+ SAK Sbjct: 1 MTDAIRYEKGQDQIVVLTIDMPGQSANTMNAVYREAMADCVARLVADKDSITGVIITSAK 60 Query: 62 PDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGLE 118 F AG D+N + +Q A+A L A++ L V+AAI+GA LGGG E Sbjct: 61 K-TFFAGGDLNELIKVGKSQ-AKAFYDMVLLLKAQLRTLETLGKPVVAAINGAALGGGWE 118 Query: 119 LALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQ 178 + LACH RV D+P +GLPEV LGLLPG GG R+ RL+G+ AL +L GK++R++Q Sbjct: 119 ICLACHHRVALDNPSVQIGLPEVTLGLLPGGGGVVRMVRLLGLEKALPYLLEGKKVRSQQ 178 Query: 179 ALKLGLVDDVVPHSILLEAAVELAKKERPS-SRPLPVRERILAGPLGR----ALLFKMVG 233 AL+ GLVD++ L A P+ +P + + G A + + Sbjct: 179 ALQAGLVDELAADRDELLAKARAWIATNPTVKQPWDMSGYQIPGGTPSSPKVAQMLAIAP 238 Query: 234 KKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAST 293 KTQG PA E+IL G + E R F EL ++ + F+ Sbjct: 239 SILRSKTQGCLPAPEKILCAAVEGAQVDFDTAQLIETRYFTELTTGQVAKNMIGTFWFQL 298 Query: 294 DVKKDPGSDAP---PAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALK 350 + GS P +G+LG G+MG GIAYV+A AGI V +KDIN Sbjct: 299 NEINAGGSRPAGFAPHATKKLGVLGAGMMGAGIAYVSAV-AGIDVVLKDINLAAAEKGKA 357 Query: 351 YSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEV 410 +S L+ KV R L A++RD LA I + A DLIIEAVFE+ ELK ++ + Sbjct: 358 HSAALLDKKVARGQLSAAQRDATLARIKTSEQGADLAGCDLIIEAVFEDRELKARVSSAA 417 Query: 411 EQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTI 470 ++ A + ASNTS+LPI +A + IGLHFFSPV+KMPLVEII TS +T+ Sbjct: 418 QKVVGADAVIASNTSTLPISGLATAVPDQSKFIGLHFFSPVDKMPLVEIIKGVNTSDETL 477 Query: 471 ATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPV 530 A + KTPIVV D GF+ +R+ + NE I ML +G I+ K G P+ Sbjct: 478 ARGFDFVLQIKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGISAPMIETEARKAGMPI 537 Query: 531 GPIQLLDEVGIDTGTKI-IPVLEAAYGERFSAPAN----VVSSILND-DRKGRKNGRGFY 584 GP+ + DEV + + I + E PA+ V+ +LN+ R G+ G GFY Sbjct: 538 GPLAISDEVSLSLMSHIRQQAAKDLQAEGKPLPAHPAFAVIDLLLNECQRPGKAAGGGFY 597 Query: 585 LYGQKGRKSKKQVDPAIYPLIGT---QGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRS 641 Y G+K ++P + T + G+IS V +R + + E VRCV+E V+ S Sbjct: 598 EYPAGGQKH-------LWPELKTRFEKADGQISPQDVRDRLLFVQAIETVRCVEEGVLLS 650 Query: 642 VRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGAR 701 D +IG++FGIGF + GG ++I+ G + VA Q LA QYG RFTP L+E A+ Sbjct: 651 TADANIGSIFGIGFAAWTGGALQFINQYGVKDFVARAQYLAEQYGERFTPPALLLEKAAK 710 Query: 702 GESF 705 G F Sbjct: 711 GALF 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: 41 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