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_023431067.1 N177_RS04545 enoyl-CoA hydratase
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_000496075.1:WP_023431067.1 Length = 738 Score = 392 bits (1007), Expect = e-113 Identities = 242/724 (33%), Positives = 370/724 (51%), Gaps = 29/724 (4%) Query: 7 FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 F + + D IA++ D G MN + ++ II ++ + ++G V S K D F Sbjct: 6 FRIEIDADGIALVIWDTAGRSMNVIDLAVMDELETIIDRVSGEESIKGAVIASGK-DAFS 64 Query: 67 AGADINMIGNC----KTAQEAEALA---------RQGQQLMAEIHALPIQVIAAIHGACL 113 GAD+ M+G T +E + A R+ Q+ + + AI+G + Sbjct: 65 GGADLKMLGGMLEAFHTERERDQTAATQRLFDESRRLSQIYRRLETSGKPWVCAINGTAM 124 Query: 114 GGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQ 173 GG +ELALACH RV ++PK GLPEV++GL PG+GGTQR+ R++ + AL+ +L G+ Sbjct: 125 GGAVELALACHHRVAAENPKAKFGLPEVKVGLFPGAGGTQRVARMMPAADALQYLLQGRD 184 Query: 174 LRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRE-RILAGPLGRALLFKMV 232 L A K+GLVD++VP L+EAA + +P + R+ GP+ A F++ Sbjct: 185 LDFATARKMGLVDEIVPAERLVEAAKAWILGGGSAVKPWDEEKFRLPGGPVYSATGFQVF 244 Query: 233 GKKT---EHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL-RSI 288 +TQ NYP I+ V GL + E+R F + T ++ A+ RS+ Sbjct: 245 PAANAIYRRETQNNYPGARAIMSAVYEGLQLPMDAALRVESRYFAHVLQTKEAAAMIRSL 304 Query: 289 FFASTDVKK--DPGSDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGIN 346 F + ++ K +D P + VG+LG G MG +AYV+A KAGI V + D + + Sbjct: 305 FVSMQELNKLARRPADVPASKARKVGVLGAGFMGAAVAYVSA-KAGIEVVLIDRDVESAE 363 Query: 347 HALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQM 406 Y+ + V R +++ LA I T DY+ DL+IEAVFE+ ++K + Sbjct: 364 RGKAYADTLVSKDVSRGKATHEAKEELLARIDATADYQRLEGCDLVIEAVFEDRDVKADV 423 Query: 407 VAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTS 466 + E + SNTS+ PI +A + RPE+ IG+HFFSPVEKM LVE+I T Sbjct: 424 IQRAEAVVPETAVIGSNTSTFPISSLAKASVRPERFIGIHFFSPVEKMMLVEVIMGEATG 483 Query: 467 AQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKF 526 + +A + + KTPIVV D GFY +R++ YI E ML +G I+ Sbjct: 484 PEALAVALDYCRAIRKTPIVVNDSRGFYTSRVVGTYIREGHLMLAEGVPAAMIENVGRMA 543 Query: 527 GFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPAN---VVSSILNDDRKGRKNGRGF 583 G PVGP+ L DEV +D KI+ + GE P + ++ R GRKNG+GF Sbjct: 544 GMPVGPLALNDEVAVDLAWKILQATKKDLGESAVEPRQEHLLEEMVVKRGRLGRKNGQGF 603 Query: 584 YLYGQKGRKSKKQVDPAIYPLIGTQ-GQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSV 642 Y Y G KK++ P + L + + ++ R +++ E RC +E V+ V Sbjct: 604 YDYPDAG---KKRLWPGLQDLQEIRLDPDTVDVGELKRRFLVMQALETARCFEEGVLTDV 660 Query: 643 RDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARG 702 R+ D+G++ G GF PF GG Y+D +G V + + L ++G RF P + L+ M G Sbjct: 661 READVGSILGFGFAPFTGGTLSYVDGMGTKAFVDLCRALEARHGPRFAPNDLLIAMAENG 720 Query: 703 ESFW 706 E+F+ Sbjct: 721 ETFY 724 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: 992 Number of extensions: 41 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: 738 Length adjustment: 40 Effective length of query: 674 Effective length of database: 698 Effective search space: 470452 Effective search space used: 470452 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