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 WP_090447062.1 BLS63_RS17605 3-hydroxyacyl-CoA dehydrogenase
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_900100495.1:WP_090447062.1 Length = 714 Score = 392 bits (1006), Expect = e-113 Identities = 269/721 (37%), Positives = 378/721 (52%), Gaps = 25/721 (3%) Query: 3 MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAK 61 MT A D I V+TID+PG+ NT+ A++ + ++++L K+ + GV+ SAK Sbjct: 1 MTDAIRYEKGQDAIVVLTIDMPGQSANTMNAQYREAMGQVVERLEAEKDSIAGVIVTSAK 60 Query: 62 PDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGLE 118 F AG D+N + A +A+A R ++ ++ L V+AAI+GA LGGG E Sbjct: 61 K-TFFAGGDLNELIKVSKA-DADAFYRMILKIKGQLRRLECLGKPVVAAINGAALGGGWE 118 Query: 119 LALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQ 178 + LACH R+ D LGLPEV LGLLPG GG R+ RL+G+ AL + GK++R + Sbjct: 119 ICLACHHRIALDSSSVQLGLPEVTLGLLPGGGGVVRMVRLLGLEKALPYLAEGKKVRPEA 178 Query: 179 ALKLGLVDDVVPHS--ILLEAAVELAKKERPSSRPLPVRERILAGPLGRALLFKMVG--- 233 ALK GL+D++ +L +A +A P +I G + +M+ Sbjct: 179 ALKAGLIDELASDKDDLLAKARAWIAANPAPRQPWDLPGYKIPGGTPSSPNVAQMLAIAP 238 Query: 234 KKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAST 293 KT+G +PA E+IL G + EAR F EL ++ + F+ Sbjct: 239 SVLRDKTKGCFPAPEKILCAAVEGAQVDFDTAQLIEARYFTELTTGQVAKNMIGTFWFQL 298 Query: 294 DVKKDPGSDAP---PAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALK 350 + GS P VG+LG G+MG GIAYV+A AGI V +KDI+ + Sbjct: 299 NEINAGGSRPQGFAPYLTKKVGVLGAGMMGAGIAYVSAL-AGIEVVLKDISLEAAEKGKS 357 Query: 351 YSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEV 410 YS LE KV R + A +RD LA I+ T FA DLIIEAVFE+ +LK + A Sbjct: 358 YSAKLLEKKVGRGQMSAEKRDAILARIATTDKDADFAGCDLIIEAVFEDRDLKANVTAAA 417 Query: 411 EQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTI 470 E+ A + ASNTS+LPI +A + ++ IGLHFFSPV+KMPLVEII TS +T+ Sbjct: 418 ERAALAEAVIASNTSTLPITGLANAVQKQDRFIGLHFFSPVDKMPLVEIIRGERTSDETL 477 Query: 471 ATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPV 530 A + KTPIVV D GF+ +R+ + NE I ML +G I+ K G PV Sbjct: 478 ARGFDYVMQIKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVSAALIENEARKAGMPV 537 Query: 531 GPIQLLDEVGIDTGTKI-IPVLEAAYGERFSAPAN----VVSSILND-DRKGRKNGRGFY 584 GP+ + DEV + I L+ E S P + V+ S+L + R G+ G GFY Sbjct: 538 GPLAISDEVSLSLMQHIRQQTLKDLAEEGKSLPEHPAFAVIESMLGEYKRPGKAAGGGFY 597 Query: 585 LYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRD 644 Y G KK + P + + +I V +R + + E VRCV+E V+ S D Sbjct: 598 EYPAGG---KKYLWPELKSRF-EKADRQIPQEDVRDRILFIQAIETVRCVEEGVLNSTAD 653 Query: 645 GDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGES 704 +IG++FGIGF + GG ++I+ G + VA Q LA QYG RF P L+E A+GES Sbjct: 654 ANIGSIFGIGFAAWTGGALQFINQYGIQDFVARAQYLAEQYGERFLPPALLLEKAAKGES 713 Query: 705 F 705 F Sbjct: 714 F 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: 1020 Number of extensions: 38 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 24 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