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_085636206.1 MGEO_RS08035 3-hydroxyacyl-CoA dehydrogenase
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_002115805.1:WP_085636206.1 Length = 728 Score = 400 bits (1029), Expect = e-116 Identities = 265/724 (36%), Positives = 372/724 (51%), Gaps = 33/724 (4%) Query: 7 FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 FT+ D IA IT DVP + MN L E + ++ ++ ++G++ S K D F Sbjct: 4 FTMTKDADGIATITWDVPEKSMNVLSFEGLQTLNDLVDDALADEAVKGIIITSGKAD-FA 62 Query: 67 AGADINMIGNCKTAQEAEA--------------LARQGQQLMAEIHALPIQVIAAIHGAC 112 AG D+N++ K A AEA + R G P V A + G Sbjct: 63 AGMDLNVLATLKEAG-AEAVFDGIMKMHGVLRKIERAGMDAKTNKGGKP--VAAVLPGTA 119 Query: 113 LGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGK 172 LG GLE+ LACH D+PK +GLPE+ +G+ PG+GGT R+ R +G A +L GK Sbjct: 120 LGIGLEIPLACHRVFAADNPKAKIGLPEILVGIFPGAGGTTRVARKMGAMAASPFLLEGK 179 Query: 173 QLRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG--PLGRALLFK 230 +A GL+D+V + A L+ + +P + + G P A Sbjct: 180 LSDPAKAKAAGLIDEVSADPMADARAWVLSAGDADILKPWDAKGYKMPGGAPYHPAGFMT 239 Query: 231 MVGKKT--EHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL-RS 287 VG KT+G YPA + +L V G + EAR F + M P S A+ RS Sbjct: 240 FVGASAMVNGKTKGVYPAAKALLSAVYEGALVPFDTALKIEARWFTSVIMNPSSSAMIRS 299 Query: 288 IFFASTDVKKDP--GSDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGI 345 +F ++K +D + VG+LG G+MG GIA V+A +AGI V + D + Sbjct: 300 LFINKQALEKGAVRPADVDDQRVKKVGVLGAGMMGAGIALVSA-QAGIDVVLLDRDQAAA 358 Query: 346 NHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQ 405 + YS D V RR + + D LA I+ TTDY A DLI+EAVFE+ ++K Sbjct: 359 DKGKAYSADYAAKGVSRRKITQDKADAMLARITATTDYNDLAGCDLIVEAVFEDPKIKAD 418 Query: 406 MVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGT 465 + A+VE IFA+NTS+LPI D+A + RPEQ IG+HFFSPVEKM LVEII T Sbjct: 419 VTAQVEAVIGEDCIFATNTSTLPISDLAKASKRPEQFIGIHFFSPVEKMMLVEIIKGKET 478 Query: 466 SAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVK 525 + +A + ++ KTPIVV D FY NR + PYINE IRM+ +G I+ A Sbjct: 479 GDRAVAKALDFVRQIRKTPIVVNDARFFYANRCIIPYINEGIRMVKEGVAPALIENAAKM 538 Query: 526 FGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERF--SAPANVVSSILNDDRKGRKNGRGF 583 G P+GP+QL+DE ID G KI +AA G+ + A V+ + + R GRK GF Sbjct: 539 VGMPLGPLQLVDETSIDLGAKIARATKAAMGDAYPDGAVDEVIFWMEGEGRLGRKAKAGF 598 Query: 584 YLYGQKG-RKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSV 642 Y Y KG R+ V A YP Q + + V R + + EAVR +++ V+ + Sbjct: 599 YDYDDKGKRQGLSSVVAAQYP----QAEDQPDLIDVQHRLLFVQSLEAVRALEDGVLMDI 654 Query: 643 RDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARG 702 R+GD+GA+ G GF P+ GGP ++D LG+ +L YG RF + L EM A+G Sbjct: 655 REGDVGAILGWGFAPWSGGPLSWLDMLGSEYAAERCDQLVETYGDRFACPDLLREMAAKG 714 Query: 703 ESFW 706 +SF+ Sbjct: 715 QSFY 718 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: 1048 Number of extensions: 50 Number of successful extensions: 8 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: 728 Length adjustment: 40 Effective length of query: 674 Effective length of database: 688 Effective search space: 463712 Effective search space used: 463712 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