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_023432923.1 N177_RS13530 3-hydroxyacyl-CoA dehydrogenase
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_000496075.1:WP_023432923.1 Length = 715 Score = 326 bits (836), Expect = 2e-93 Identities = 223/683 (32%), Positives = 345/683 (50%), Gaps = 36/683 (5%) Query: 14 DNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGADINM 73 DN+A + ID G NTL A+ +++ ++++ ++ +G+V SAK FIAGADI Sbjct: 37 DNVAWLVIDKEGASANTLSADVLAELDRALEEIERDRP-KGLVIRSAKKSGFIAGADITE 95 Query: 74 IGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTDDPK 133 + + E + +++ + L I +A +HG LGGGLE+ALAC R+ P+ Sbjct: 96 FRGIRDPKVVEEKISEANRVVDRLDRLDIPTVAIMHGYALGGGLEIALACDRRLAL--PE 153 Query: 134 TVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVPHSI 193 T LG PEV LGL PG GGT R L+ A+ M+LTGK A++A ++GL+D+V+ Sbjct: 154 TKLGFPEVLLGLHPGLGGTVRSTFLMDPVQAMTMMLTGKSHPARRAKRMGLIDEVIEERH 213 Query: 194 LLEAAVELAKKERPSSRPLPVRERILAGPLGRALLFKMVGKKTEHKTQG-NYPATERILE 252 +L AAV+ A SR R+R L+ GR + +TE K +YPA ++ Sbjct: 214 VL-AAVKAAVSGGSKSRDRSFRDRALSSGPGRRFAAGRMRGETESKAPAEHYPAPHALIA 272 Query: 253 VVETGLAQGTSSGYDA----EARAFGELAMTPQSQALRSIFFASTDVKKDPGSDAPPAPL 308 + E YD E ++F L +T +Q L +FF +K Sbjct: 273 LWEEH-----GGDYDQMKAEEIKSFARLLVTDTAQNLIRVFFLREHMK---AIGKGKTTF 324 Query: 309 NSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEGKVRRRHLKAS 368 V ++G G MGG IA A + G+ V + D+ P+ + A++ + +L KV + K Sbjct: 325 GHVHVVGAGAMGGEIAAWCALR-GLTVTLADMKPEVLGKAIRNA-HRLYEKVAKDGAKI- 381 Query: 369 ERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHTIFASNTSSLP 428 RD LI G + G H D++IEAV E +++K+++ +VE I A+NTSS+ Sbjct: 382 -RDAMDRLIPGINGH-GIRHADIVIEAVPEKVDIKRKVYEQVEPLLKPGAILATNTSSIR 439 Query: 429 IGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAKKQGKTPIVVR 488 + ++ H P + GLHFF+PV +M LVE++ H S +T+ + + P V+ Sbjct: 440 LEELRGHLKDPSRFAGLHFFNPVSRMQLVEVVSHDQASEETLKKLERFTTSIDRLPAPVK 499 Query: 489 DKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDEVGIDTGTKII 548 GF VNR L PY+ E + ML +G E ID A +FG P+GPI+L D+VG+D + Sbjct: 500 SAPGFLVNRALMPYLMEGLLMLDEGTPKEVIDRAAEEFGMPMGPIELADQVGLDICLDVA 559 Query: 549 PVLEAAYGERFSAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKSKKQVDPAIYPLIGTQ 608 +L A + + + GRK G+G Y + + G+ K G+ Sbjct: 560 DMLRANLDAELPQTPAWLREKVENGELGRKTGKGLYDW-KDGKVQKNDKG-------GSY 611 Query: 609 GQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDS 668 +G + +R ++ MLN V C VI + D +FG GF PF GGP +Y Sbjct: 612 DRG------ITDRLILPMLNACVTCYRTGVIDDLDTLDGAMIFGTGFAPFRGGPIKYAHD 665 Query: 669 LGAGEVVAIMQRLATQYGSRFTP 691 +V+A ++RL Q+G+RF P Sbjct: 666 RRITDVIASLKRLEKQHGARFAP 688 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: 1036 Number of extensions: 51 Number of successful extensions: 6 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: 715 Length adjustment: 39 Effective length of query: 675 Effective length of database: 676 Effective search space: 456300 Effective search space used: 456300 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