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 5209977 Shew_2425 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= CharProtDB::CH_003230 (714 letters) >FitnessBrowser__PV4:5209977 Length = 706 Score = 815 bits (2104), Expect = 0.0 Identities = 417/710 (58%), Positives = 538/710 (75%), Gaps = 9/710 (1%) Query: 3 MTSAFTLNVRLDN-IAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAK 61 M +FTLN RLDN IAV+T+DVPGE MNTL+AEF ++ ++ +++ + +RGVV +S K Sbjct: 1 MDKSFTLN-RLDNGIAVLTMDVPGETMNTLRAEFGPEICEMLAEIKADAGIRGVVIISGK 59 Query: 62 PDNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELAL 121 D+F+AGADI+M+ C TA++A L++QG ++ + +L I V+AAI+GACLGGGLELAL Sbjct: 60 KDSFVAGADISMLDACATAEDARELSKQGHEVFFALESLSIPVVAAINGACLGGGLELAL 119 Query: 122 ACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALK 181 ACH RVCTD KT+LGLPEVQLGLLPG GGTQRLPRL+G++ +L+M+LTGKQLRAKQALK Sbjct: 120 ACHQRVCTDSNKTMLGLPEVQLGLLPGGGGTQRLPRLVGIAKSLDMMLTGKQLRAKQALK 179 Query: 182 LGLVDDVVPHSILLEAAVELAKK-ERPSSRP-LPVRERILAG-PLGRALLFKMVGKKTEH 238 +GLVDDVVP SILL+ A+E+A RP+ +P L E++L G P+GR ++F+ K+ Sbjct: 180 MGLVDDVVPESILLQTAIEMALAGARPAKKPKLSTVEKLLEGTPVGRNIIFEQALKQVNK 239 Query: 239 KTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKD 298 KTQGNYPA E+I++ V G+ +G G + EA+ FG+L ++ +S+ALRSIFFA+T++KK+ Sbjct: 240 KTQGNYPAPEKIIDCVRQGVTKGIVKGLEVEAQHFGDLVVSNESEALRSIFFATTEMKKE 299 Query: 299 PGS-DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLE 357 G+ D P +N V +LGGGLMGGGIA VT KA IPVR+KDI+ G+++AL Y++ L Sbjct: 300 SGAGDVSPKAVNKVMVLGGGLMGGGIASVTTTKAKIPVRVKDISEIGLSNALAYAYKLLA 359 Query: 358 GKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAH 417 V+RRH+ + RD +AL++ TT+Y+G D+++EAVFE+L LK QMV +VE+ C H Sbjct: 360 KGVKRRHMTPAVRDNLMALMTTTTEYKGIKDADMVVEAVFEDLNLKHQMVKDVERECGEH 419 Query: 418 TIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLA 477 TIFASNTSSLPI IA A RPE VIGLH+FSPVEKMPLVE+I H TS QTIATTV A Sbjct: 420 TIFASNTSSLPIKQIAEAAERPENVIGLHYFSPVEKMPLVEVIAHDKTSPQTIATTVAFA 479 Query: 478 KKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLD 537 +KQGKTPIVV+D AGFYVNRILA Y+NEA +L +G+ V+H+D ALVKFGFPVGP+ LLD Sbjct: 480 RKQGKTPIVVKDGAGFYVNRILALYMNEAANLLLEGQSVDHLDKALVKFGFPVGPMTLLD 539 Query: 538 EVGIDTGTKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQV 597 EVGID G KI P+LE GERF APA +L DDRKGRKNG+GFY YG K + KK V Sbjct: 540 EVGIDVGAKISPILEKELGERFKAPA-AFDKLLADDRKGRKNGKGFYQYGAKSK--KKLV 596 Query: 598 DPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPP 657 D ++Y ++G +AERCV+ MLNEAVRC++E +I S RDGDIGA+FGIGFPP Sbjct: 597 DESVYGVLGLTPGADGEPIALAERCVVQMLNEAVRCLEEGIIASPRDGDIGAIFGIGFPP 656 Query: 658 FLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFWK 707 FLGGPFRY+DSLGA +V ++R Q+G RF PC+RLVEM G F++ Sbjct: 657 FLGGPFRYMDSLGAKHLVETLKRYQDQFGDRFAPCDRLVEMAESGSKFYE 706 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: 1190 Number of extensions: 53 Number of successful extensions: 5 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: 706 Length adjustment: 39 Effective length of query: 675 Effective length of database: 667 Effective search space: 450225 Effective search space used: 450225 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