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_036260031.1 DL86_RS07960 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_000746085.1:WP_036260031.1 Length = 736 Score = 384 bits (985), Expect = e-110 Identities = 251/728 (34%), Positives = 370/728 (50%), Gaps = 36/728 (4%) Query: 7 FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 F + D IA++T D+ G MN + + ++ +I + + G V S K F Sbjct: 6 FRFELDADGIALLTWDMAGRSMNVITPQVIDELEQVIDHVGAEAAITGCVITSGK-QTFS 64 Query: 67 AGADINMIGNC----------KTAQEAEAL----ARQGQQLMAEIHALPIQVIAAIHGAC 112 GAD++M+G K +EA L AR+ + ++ AAI+G C Sbjct: 65 GGADLSMLGAAAADYQTARQEKGEEEAARLFFESARRLSLVYRKLETCGKPFAAAINGVC 124 Query: 113 LGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGK 172 LGG ELALACH RV DD K +GLPE+++GL PG+GGTQR+ RL+ AL+M+ G+ Sbjct: 125 LGGAFELALACHYRVVADDDKARVGLPEIKVGLFPGAGGTQRVARLMHTGDALQMLFKGE 184 Query: 173 QLRAKQALKLGLVDDVVP-HSILLEAAVELAKKERPSSRPLPVRERILAGPLGRA----- 226 Q+R K A + LV DV P I+ +A +A + + P E P G+ Sbjct: 185 QIRPKAAKTMNLVHDVAPLGEIVGKAKAWIAAGGKGVA---PWDENTFKLPSGKVFSPAG 241 Query: 227 -LLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL 285 +++ +T NYPA + IL V GL EAR F ++ +P++ A+ Sbjct: 242 MMVWPAANAIYRRETHDNYPAAKAILHAVYEGLQLPMDLALRVEARWFAKILRSPEAAAM 301 Query: 286 -RSIFFASTDVKKDPGSDA--PPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINP 342 R++F + ++ K A PA + VGILG G MG GIAYVTA AG+ + D + Sbjct: 302 IRTLFVSMGELNKGARRPAHVSPAAIKRVGILGAGFMGAGIAYVTA-GAGMEGVLIDRDQ 360 Query: 343 QGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLEL 402 + + + +V + K ++++ L I + DY A +L+IEAVFE+ + Sbjct: 361 ASADKGKAFCDQLISSQVLKGRAKGADKEALLGRIKTSADYNDLAGAELVIEAVFEDRTV 420 Query: 403 KQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPH 462 K + + IFASNTS+LPIG +A + PE IG+HFFSPVEKM LVE+I Sbjct: 421 KAEATRKARAAIGPDAIFASNTSTLPIGSLAEADSAPENFIGVHFFSPVEKMLLVEVILG 480 Query: 463 AGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAA 522 A T + +AT + + KTPIVV D GF+ NR + YI E ML +G I+ Sbjct: 481 AKTGDRALATALDYVRAIKKTPIVVNDARGFFANRCVGNYIREGHLMLLEGAPPAMIENI 540 Query: 523 LVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGER---FSAPANVVSSILNDDRKGRKN 579 G PVGP+ L DEVG+D KI+ + G + + ++ R GRKN Sbjct: 541 AKMAGMPVGPLALNDEVGLDLALKILEATKQDLGGAAIDLNQERLLKGLVVEHGRLGRKN 600 Query: 580 GRGFYLYGQKGRKSKKQVDPAIYPLIGTQ-GQGRISAPQVAERCVMLMLNEAVRCVDEQV 638 G+GFY Y +G KS + P + L T+ I + R +++ EA R ++E V Sbjct: 601 GKGFYDYPSQGAKS---LWPGLAALQPTKCDPDAIDIAEFKHRFLVVQALEAARAIEEGV 657 Query: 639 IRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEM 698 + R+ D+G++ G GF PF GG YID +GA V + RL YG RF+P + L++M Sbjct: 658 VTDPREADVGSIIGFGFAPFTGGVLSYIDGMGAANFVVLCDRLRQTYGERFSPPQILIDM 717 Query: 699 GARGESFW 706 E+F+ Sbjct: 718 AKAHETFY 725 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: 1031 Number of extensions: 59 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: 736 Length adjustment: 40 Effective length of query: 674 Effective length of database: 696 Effective search space: 469104 Effective search space used: 469104 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 Apr 09 2024. 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