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 3607421 Dshi_0835 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)
Query= CharProtDB::CH_003230 (714 letters) >FitnessBrowser__Dino:3607421 Length = 737 Score = 410 bits (1053), Expect = e-118 Identities = 260/729 (35%), Positives = 388/729 (53%), Gaps = 38/729 (5%) Query: 7 FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 FT+ D +A+IT DV G+ MN + + + A++ + + ++G++ S K D+F Sbjct: 7 FTMKTDADGVAIITWDVQGKSMNVMNQQGFEDLDALVDKALADDTVKGIIITSGK-DSFA 65 Query: 67 AGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQ----------------VIAAIHG 110 G D+N+I + + + +MA +H + + V AA+ G Sbjct: 66 GGMDLNVIAKMRDDAGDDPARGLFEGVMA-MHGILRKIERAGMDPKTNKGGKPVAAALPG 124 Query: 111 ACLGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILT 170 LG GLE+ LACH D+PK +GLPE+ +G+ PG+GGT R+ R +G A ++L Sbjct: 125 TALGIGLEIPLACHRIFAADNPKAKIGLPEIMVGIFPGAGGTMRVSRKLGAMQAAPILLE 184 Query: 171 GKQLRAKQALKLGLVDDVVPHSILLEAAVE--LAKKERPSSRPLPVRERILAG--PLGRA 226 GK K+A G+VD+VVP LL+AA L+ K+ +P ++ G P A Sbjct: 185 GKLFEPKKAKMAGIVDEVVPAEELLDAAKAWVLSAKDTDIVKPWDLKGYKFPGGAPYHPA 244 Query: 227 LLFKMVGKKT--EHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQA 284 VG KT G YPA + +L V G + EAR F + M P S A Sbjct: 245 GFMTFVGASAMIHSKTMGVYPAAKALLSAVYEGAMVPFDTALKIEARWFTNVLMNPSSSA 304 Query: 285 -LRSIFFASTDVKKDP-GSDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINP 342 +RS+F ++K D P + VGILG G+MG GIAYV+A AGI V + D Sbjct: 305 MIRSLFINKEALEKGAVRPDVPDQKVKKVGILGAGMMGAGIAYVSA-NAGIEVVLIDAAQ 363 Query: 343 QGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLEL 402 + + ++ L+ + R+ + ++D+ LA I+ TTDY DL++EAVFE+ + Sbjct: 364 ESADRGKAHAAGILDKGIARKKVTPEKKDEVLARITATTDYAALEGCDLVVEAVFEDPGV 423 Query: 403 KQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPH 462 K ++ A+ E IFA+NTS+LPI ++A + RPEQ IG+HFFSPV+KM LVEII Sbjct: 424 KAEVTAKAEAVIPGDAIFATNTSTLPISELAKASARPEQFIGIHFFSPVDKMLLVEIIKG 483 Query: 463 AGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAA 522 T +A + ++ KTPIVV D FY NR + PYINE IRM+ +G ++ A Sbjct: 484 RQTGDVAVAKALDFVRQIRKTPIVVNDARFFYANRCIIPYINEGIRMVAEGVTPALVENA 543 Query: 523 LVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPANVVSSIL----NDDRKGRK 578 G P+GP+QL+DE ID G KI +AA G+ + P V +L ++ R GRK Sbjct: 544 AKLVGMPLGPLQLVDETSIDLGVKIAKATKAAMGDAY--PDGAVDEVLFWMADEGRLGRK 601 Query: 579 NGRGFYLYGQKGRKSKKQVDPA-IYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQ 637 + GFY Y + G++ A YP + Q ++A V R +M + EAVR +++ Sbjct: 602 SNAGFYTYDEAGKRGLLWEGLADRYP--AAKEQPELTA--VQHRLLMAQVLEAVRALEDG 657 Query: 638 VIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVE 697 V+ +R+GD+GA+ G GF P+ GGP ++D +GA V I L +G+RFT L E Sbjct: 658 VLMDIREGDVGAILGWGFAPWSGGPLSWLDMIGAARAVEICDALTDTHGARFTTPALLRE 717 Query: 698 MGARGESFW 706 M +GE+F+ Sbjct: 718 MAEKGETFY 726 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: 1090 Number of extensions: 48 Number of successful extensions: 10 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: 737 Length adjustment: 40 Effective length of query: 674 Effective length of database: 697 Effective search space: 469778 Effective search space used: 469778 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 17 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