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_004300927.1 C665_RS04215 NAD-binding 3-hydroxyacyl-CoA dehydrogenase
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_000310185.1:WP_004300927.1 Length = 671 Score = 333 bits (853), Expect = 2e-95 Identities = 227/662 (34%), Positives = 347/662 (52%), Gaps = 37/662 (5%) Query: 16 IAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGADINMIG 75 +A + +D N L A+ ++ ++ L + + +V SAKP FIAGADI Sbjct: 21 LAWLDLDKAEASANVLSADVLAEFAGVLDVL-DAVPPKALVIASAKPAGFIAGADIEEFS 79 Query: 76 NCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTDDPKTV 135 + A L +G L + A+ +A I G C+GGGLELALAC R+ D+P T Sbjct: 80 RLDSVLAARMLVERGWLLFNRLAAVSYPTLALIRGHCMGGGLELALACRHRIVVDEPGTK 139 Query: 136 LGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVPHSILL 195 L LPEV LG++PG GG RLP LIG + AL+++LTGK + AK+A +LGL DD VP ++ Sbjct: 140 LALPEVMLGIVPGWGGMLRLPALIGPAAALDLMLTGKSVDAKKAKRLGLADDCVPPRVM- 198 Query: 196 EAAVELAKKERPSSRPLPVRERILA----GPLGRALLFKMVGKKTEHKTQGNYPATERIL 251 E+A + + +PLP +ER L GP + K + + NYPA I+ Sbjct: 199 ESAARILALSGVAKKPLPFKERALRWAMNGPARAKVADKARAQAARKVGRENYPAPFAIV 258 Query: 252 EVVET--GLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPGSDAPPAPLN 309 ++ E G A +G + + + +P ++ L +F +K G D+ P + Sbjct: 259 DIWERHGGNALDVPAG---DRSSLDTIFSSPTARNLVRVFHLQERLKAF-GKDSDFTPRH 314 Query: 310 SVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKVRRRHLKASE 369 V ++G G+MGG IA V A + G+ V ++D + + I A+ + E RRH K Sbjct: 315 -VHVVGAGVMGGDIAAVCALR-GMTVTLQDQSVERIAPAIARAAKLFE----RRH-KGDA 367 Query: 370 RDKQLALISGTTDYRG--FAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASNTSSL 427 R + L D +G A D+IIEA+FENLE+K+ + AE+E + A+NTSSL Sbjct: 368 RQVRFTLDRLIPDPKGEGAARADVIIEAIFENLEVKRSLFAELEARAKPDAVLATNTSSL 427 Query: 428 PIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKTPIVV 487 + DIA P +++G+HFF+PV +PLVE++ T A+ + ++ K P+ V Sbjct: 428 RLEDIATALKDPSRLVGIHFFNPVPMLPLVEVVQGEATDAEVLRRATGFVRRIDKLPLPV 487 Query: 488 RDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVGIDTGTKI 547 + GF VN +L PY+ EA+R + +G E +DAALV FG P+GP++L+D VG+D Sbjct: 488 KSAPGFLVNSVLGPYMLEALRCVEEGVAPEMVDAALVAFGMPMGPVELVDTVGLDIA--- 544 Query: 548 IPVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLY-GQKGRKSKKQVDPAIYPLIG 606 + +A GE PA ++ ++ + + GRK+G G+Y + K K+ + + G Sbjct: 545 VAAGKALAGEGAEPPARLL-KLVGEGKLGRKSGEGYYRWVDGKAVKAGDEDERK-----G 598 Query: 607 TQGQGRISAPQ------VAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLG 660 + R AP +AER + +L RCV+ V+ D G +FG GF P G Sbjct: 599 GLWRKRRPAPPPPIPAGLAERVLAPLLAATRRCVELGVVGDADLADAGVIFGTGFAPHTG 658 Query: 661 GP 662 GP Sbjct: 659 GP 660 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: 989 Number of extensions: 44 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: 671 Length adjustment: 39 Effective length of query: 675 Effective length of database: 632 Effective search space: 426600 Effective search space used: 426600 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: 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