Align Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate WP_013418529.1 RVAN_RS04240 3-hydroxyacyl-CoA dehydrogenase
Query= SwissProt::P21177 (729 letters) >NCBI__GCF_000166055.1:WP_013418529.1 Length = 672 Score = 325 bits (833), Expect = 5e-93 Identities = 230/676 (34%), Positives = 345/676 (51%), Gaps = 55/676 (8%) Query: 17 IAELVFDAPG-SVNKLDTATVASLGEAIGVLE---QQSDLKGLLLRSNK-AAFIVGADIT 71 IA VFD G S N L A L + + Q ++GL++ S K +FI GA+I Sbjct: 20 IAWAVFDVKGQSHNTLGREQFAELDRIVTAVAHGAQDRTVRGLVIMSGKDKSFIAGANIK 79 Query: 72 EFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCECVLATDYRLATP 131 EF L EE + + + +VF+R+E LPVP +AA+NG LGGG E LA YR+AT Sbjct: 80 EFDDL--KTEEDVIEAVRAGTAVFDRIEALPVPVVAAINGACLGGGLEFALACHYRIATR 137 Query: 132 D--LRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALKIGLVDGVVK 189 + RIGLPE KLGI+PG GS R R G SA+ + AGK + QA G VD +V Sbjct: 138 EDATRIGLPEVKLGIIPGLNGSARWLRQAGPMSAMPPMLAGKLLRPGQARAAGAVDQLVP 197 Query: 190 AEKLVEGA--KAVLRQAINGDLDWKAKRQPKLEPLKLSKIEATMSFTIAKGMVAQTAGK- 246 ++ A KAVL+ A + QP L E +F +A M +TA K Sbjct: 198 TRHELKWAARKAVLKNAHS---------QPSRAWQPLLMFEPGRAF-LANRMRKETAAKV 247 Query: 247 ---HYPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVKGKA 303 HYPAP + E ++ E K F PL ++++R L +F + +K +A Sbjct: 248 RAEHYPAPFRLIDLFEKHGG-SFDDMKRAETKFFAPLMISDQSRNLRRVFRLSEMLKAEA 306 Query: 304 KKLTKDVETPKQAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQ 363 K D P +A V+GAG MG IA +G+ V ++D + +++ + A K+ Sbjct: 307 PK---DGWRPARAHVIGAGTMGADIAMACVREGMEVSLQDNSPEAVEKALKRADAFFKKR 363 Query: 364 LERGKIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQDTV 423 + R ++ K + + A R D+V+EA+ EN K+AV AE E K++ + Sbjct: 364 M-RSPLEAEKAK---ARLLADPQGAQIHRADVVIEAIYENLDAKRAVFAEVEPKLKPGAL 419 Query: 424 LASNTSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAWASK 483 LA+NTS++ I ++A+AL+ P G+HFFNPV +PLVE+++G S +E I + A+ ++ Sbjct: 420 LATNTSSLKIEDIASALQDPSRLIGLHFFNPVTVLPLVEVVKGADSREEEIRRGAAFVTR 479 Query: 484 MGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYLLDV 543 +GK P++V PGF VNR L PY G Q L +G KID E +FG P+GP L+D+ Sbjct: 480 IGKLPLIVKSSPGFLVNRTLAPYMFGAMQKLAEGTPKEKIDAAAE-EFGMPVGPIELVDI 538 Query: 544 VGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKPKKE 603 VG+D A ++ P + L + G+K G GF+++ + + KP Sbjct: 539 VGLDVALSVAKILKLPTPD------DHPLMQLVAEKKLGKKTGEGFYKWVDGKREKPATA 592 Query: 604 EDAAVEDLLAEVSQPKRDFSEEEIIARMMI-PMVNEVVRCLEEGIIATPAEADMALVYGL 662 + A DL ++ R +I P+++E + L +G++A D V+G Sbjct: 593 PNFAKADL--------------SVLGRELIAPLIDESEKALADGVVADADHVDAGAVFGA 638 Query: 663 GFPPFHGGAFRWLDTL 678 GF PF GG + +L Sbjct: 639 GFAPFRGGPLHYRASL 654 Lambda K H 0.318 0.136 0.399 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: 1123 Number of extensions: 60 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: 729 Length of database: 672 Length adjustment: 39 Effective length of query: 690 Effective length of database: 633 Effective search space: 436770 Effective search space used: 436770 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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