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 YP_004145058.1 Mesci_6001 3-hydroxyacyl-CoA dehydrogenase NAD-binding protein
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_000185905.1:YP_004145058.1 Length = 739 Score = 413 bits (1062), Expect = e-119 Identities = 256/725 (35%), Positives = 391/725 (53%), Gaps = 29/725 (4%) Query: 7 FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 F L+ D IA++T D+PG MN E ++ AI+ ++ + ++G V S K D F Sbjct: 6 FALDTDADGIALVTWDMPGRSMNVFTEEAMRELNAIVDKVAGDAAIKGAVITSGK-DTFS 64 Query: 67 AGADINMIGNCKTAQEAE----------AL---ARQGQQLMAEIHALPIQVIAAIHGACL 113 GADI+++ T AE AL A L ++ ++AI+G C+ Sbjct: 65 GGADISLLQKMLTTFAAEKGKDAEKATKALFDNAGMMTGLFRKLETCGKPWVSAINGTCM 124 Query: 114 GGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQ 173 GG EL+LACHGRV D K + LPEV++G+ PG+GGTQR+PRL AL+M+ +G+ Sbjct: 125 GGAFELSLACHGRVAADSDKVKMALPEVKIGIFPGAGGTQRVPRLTDQQQALQMLTSGQT 184 Query: 174 LRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG-----PLGRALL 228 L ++A +GL+ ++ + L+E A + + P + L G P G L Sbjct: 185 LSPQKAKSMGLIHEIAEPTRLVETAKAMIRNGLKPVAPWDEKGFKLPGGQIYSPAGFNLW 244 Query: 229 FKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL-RS 287 + +T GNYPA IL+ V GL + E R F E+ T ++ A+ RS Sbjct: 245 PPAIAI-LRRETYGNYPAAAAILKCVYEGLLVPFDTALRIEQRYFTEIMQTREAAAMIRS 303 Query: 288 IFFASTDVKKDPGSDA--PPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGI 345 +F + ++ K A P +GILG G MG GIAYVTA KAGIPV + D + + Sbjct: 304 LFVSLQELNKGARRPAGVPETKFKKIGILGAGFMGAGIAYVTA-KAGIPVVLLDRDLESA 362 Query: 346 NHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQ 405 +S + +V++ K ++DK L+LI+ T DY A DL++EAVFE+ +K+ Sbjct: 363 AKGKAHSDSLVSDQVKKGRAKPEDKDKLLSLITPTADYADLAGCDLVVEAVFEDSGVKKS 422 Query: 406 MVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGT 465 + E IFASNTS++PI +A ++ RP+ IG+HFFSPV+KM LVEII T Sbjct: 423 ATEQAEAVLKPSAIFASNTSTIPISSLAKNSARPKNFIGIHFFSPVDKMMLVEIILGKKT 482 Query: 466 SAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVK 525 + +AT + + KTPIVV D GFYVNR + Y++EA +ML +G I+ A Sbjct: 483 GDKALATAIDFVRAIKKTPIVVNDTRGFYVNRCVLRYMSEAYKMLIEGVPAPMIENAAKA 542 Query: 526 FGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPAN--VVSSILND-DRKGRKNGRG 582 G PVGP+ L DE ID KI+ G++ P +++++++D R GRKNG+G Sbjct: 543 AGMPVGPLALTDETAIDLAQKIMKQTIRDLGDKAVDPKQMALINTMVDDHGRFGRKNGKG 602 Query: 583 FYLYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSV 642 FY Y K +KK++ P + L ++ ++ +R ++ + EA R ++E ++ Sbjct: 603 FYDYPAK--PAKKKLWPGLKELYPQLAPEKVDYEELQQRLLVTIALEAARVMEEGIVTDP 660 Query: 643 RDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARG 702 R+ D+G++ GF P+ GG YID +GA V I + L +YG+ F + L++M +G Sbjct: 661 READVGSILAFGFAPYTGGALSYIDGIGAKAFVKIARNLQKKYGAEFKAPKLLLDMAEKG 720 Query: 703 ESFWK 707 ESF++ Sbjct: 721 ESFYQ 725 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: 975 Number of extensions: 34 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 714 Length of database: 739 Length adjustment: 40 Effective length of query: 674 Effective length of database: 699 Effective search space: 471126 Effective search space used: 471126 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