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_043916947.1 jaqu_RS00375 enoyl-CoA hydratase/isomerase family protein
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_000877395.1:WP_043916947.1 Length = 727 Score = 416 bits (1069), Expect = e-120 Identities = 268/732 (36%), Positives = 380/732 (51%), Gaps = 40/732 (5%) Query: 7 FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 FT+ D +AVIT DVPG+ MN + E + A+I ++ ++G+V S KPD+F Sbjct: 4 FTMEKGADGVAVITWDVPGKSMNVMSMEAWPEFEALIDDALADEAVKGIVVTSGKPDSFA 63 Query: 67 AGADINMIGNCKTAQEAEA-----------------LARQGQQLMAEIHALPIQVIAAIH 109 G D+N+I K + + L R G P V AA+ Sbjct: 64 GGMDLNVIAKMKESAGDDPARGLFEGLMGAHGILRKLERAGMDPKTSKGGKP--VAAALP 121 Query: 110 GACLGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMIL 169 G LG GLE+ LACH C D+PK +GLPE+ +G+ PG GGT RL R +G A +L Sbjct: 122 GTALGIGLEIPLACHRIFCADNPKAKIGLPEIMVGIFPGMGGTTRLVRKMGAMAASPYLL 181 Query: 170 TGKQLRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG-----PLG 224 GK + +A GL+D+VV L AA E E +P + + G P G Sbjct: 182 EGKMMAPAKAKSAGLIDEVVDDP--LAAAKEWVLSEPKIVKPWDEKGYKMPGGAPYHPSG 239 Query: 225 RALLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQA 284 L F KT+G YPA + +L V G + EAR F + M P S A Sbjct: 240 -FLTFVGASAMVNGKTKGVYPAAKALLSAVYEGALVPFDTALKVEARWFTHVLMNPSSAA 298 Query: 285 L-RSIFFASTDVKKDPGSDAPPAP---LNSVGILGGGLMGGGIAYVTACKAGIPVRIKDI 340 + RS+F ++K G++ P AP + VGILG G+MG GIAYV+A AGI V + D Sbjct: 299 MIRSLFINKEALEK--GANRPEAPDQKVRKVGILGAGMMGAGIAYVSA-NAGIEVVLIDR 355 Query: 341 NPQGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENL 400 N YS L+ + R+ + ++ + L I+ TTD DLI+EAVFE++ Sbjct: 356 EQAAANKGKSYSEGLLDKGISRKKVTEEKKAEVLGRITATTDLGALEGCDLIVEAVFEDV 415 Query: 401 ELKQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEII 460 +K +M +VE IFA+NTS+LPI ++A + RPEQ IG+HFFSPV+KM LVEII Sbjct: 416 GVKAEMTKKVEAVVGEDCIFATNTSTLPITELAKASERPEQFIGIHFFSPVDKMLLVEII 475 Query: 461 PHAGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHID 520 A T + +A + ++ KTPIVV D FY NR + PYINE IRM+ +G I+ Sbjct: 476 KGAKTGDRAVAKALDFVRQIRKTPIVVNDARFFYANRCIIPYINEGIRMVKEGVEPALIE 535 Query: 521 AALVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPANVVSSILNDD-RKGRKN 579 A G P+GP+QL DE +D G KI +AA G+ + + V + + R GRK+ Sbjct: 536 NAAKLLGMPLGPLQLTDETSVDLGVKIAKATKAAMGDAYDDTTDEVLFFMEEQGRLGRKS 595 Query: 580 GRGFYLYGQKGRKSKKQVD-PAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQV 638 GFY Y +KG++ +P+ TQ +V R + + EAVR ++E V Sbjct: 596 NAGFYEYDEKGKRQLLWDGLSERFPVADTQP----DLHEVQNRLMFAQVLEAVRALEEDV 651 Query: 639 IRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEM 698 + +R+GD+GA+ G GF P+ GGPF ++D +GA V L ++G+RF + L EM Sbjct: 652 LLDIREGDVGAILGWGFAPWSGGPFGWLDIVGAAWAVDKTAELTEKFGARFETPKTLTEM 711 Query: 699 GARGESFWKTTA 710 G +F+ A Sbjct: 712 AKSGATFYGDAA 723 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: 1046 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: 727 Length adjustment: 40 Effective length of query: 674 Effective length of database: 687 Effective search space: 463038 Effective search space used: 463038 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