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 6938034 Sama_2167 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= CharProtDB::CH_003230 (714 letters) >FitnessBrowser__SB2B:6938034 Length = 706 Score = 823 bits (2127), Expect = 0.0 Identities = 409/708 (57%), Positives = 544/708 (76%), Gaps = 6/708 (0%) Query: 3 MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKP 62 M F+L+ R D IA++T+DVPGE MNTLKA+FA ++ AI+++++ + ++G+V +S K Sbjct: 1 MEKTFSLSRRDDGIALLTMDVPGETMNTLKAQFAPEITAILQEIKADSSIKGLVLISGKA 60 Query: 63 DNFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALA 122 D+F+AGADI+M+ C+TA++A L+RQG + AE+ L I V+AAIHGACLGGGLELALA Sbjct: 61 DSFVAGADISMLDACETAEDARLLSRQGHHVFAELEGLNIPVVAAIHGACLGGGLELALA 120 Query: 123 CHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKL 182 CH RVC+D KT+LG+PEVQLGLLPG GGTQRLPRLIG++ AL+++LTGKQ+R KQA+K+ Sbjct: 121 CHQRVCSDSSKTMLGVPEVQLGLLPGGGGTQRLPRLIGIAKALDLMLTGKQVRPKQAVKM 180 Query: 183 GLVDDVVPHSILLEAAVELAKKERPSSRPL--PVRERILAG-PLGRALLFKMVGKKTEHK 239 GLVDDVVP SILL+ A+E+A + + +PL P+ ++L G P+GR ++F K+ K Sbjct: 181 GLVDDVVPESILLDTAIEMALAGKKTRKPLKQPLVTKLLEGTPVGRNIMFDQATKQVLKK 240 Query: 240 TQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDP 299 TQGNYP+ +I++ V G+A+G G + EA FG L TP+S ALRSIFFA+T++KK+ Sbjct: 241 TQGNYPSPLKIIDCVREGMAKGMEKGLEVEAAHFGALVATPESAALRSIFFATTEMKKET 300 Query: 300 GS-DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEG 358 G+ DA P + +LGGGLMGGGIA VT KA +PVR+KDI+ +G+++AL Y++ L+ Sbjct: 301 GAGDAKPRKVAKAVVLGGGLMGGGIASVTTTKAKVPVRVKDISDKGLSNALGYAYKLLDK 360 Query: 359 KVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHT 418 V+RRH+ ++ERDK +AL++ TT+YRG D+++EAVFE+L LK QMV ++E+ C HT Sbjct: 361 GVKRRHMTSAERDKLMALMTTTTEYRGVKDADIVVEAVFEDLNLKHQMVRDIERECGEHT 420 Query: 419 IFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAK 478 IFASNTSSLPI IAA A+RPE VIGLH+FSPVEKMPLVE+I H TS +TIATTV A+ Sbjct: 421 IFASNTSSLPITQIAAAASRPENVIGLHYFSPVEKMPLVEVIAHEKTSPETIATTVAFAR 480 Query: 479 KQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDE 538 KQGKTPIVV+D AGFYVNRILA Y+NEA ++L +G+ V+H+D ALVKFGFPVGP+ LLDE Sbjct: 481 KQGKTPIVVKDCAGFYVNRILALYMNEAAQLLLEGQAVDHLDKALVKFGFPVGPMTLLDE 540 Query: 539 VGIDTGTKIIPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVD 598 VGID G KI P+LE GERF APA ++ DDRKGRKNG+GFYLYG+ +K KK VD Sbjct: 541 VGIDVGAKISPILEKELGERFKAPA-AFDKLMADDRKGRKNGKGFYLYGKAAKKGKK-VD 598 Query: 599 PAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPF 658 ++Y L+G A ++AERCV+ MLNEAVRC++E +I S RDGDIGA+FGIGFPPF Sbjct: 599 ESVYSLLGLTPATGKEAGEIAERCVVQMLNEAVRCLEEGIIASPRDGDIGAIFGIGFPPF 658 Query: 659 LGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706 LGGPFRY+D+LGA ++V +++ ++YG RF P L M A G++F+ Sbjct: 659 LGGPFRYMDTLGAAKMVRLLEGYQSKYGDRFAPAALLKAMAAEGKTFY 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: 1125 Number of extensions: 42 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: 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