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_041096229.1 SUTH_RS00440 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_000828635.1:WP_041096229.1 Length = 720 Score = 422 bits (1084), Expect = e-122 Identities = 271/717 (37%), Positives = 385/717 (53%), Gaps = 25/717 (3%) Query: 11 VRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGAD 70 V + IA + D P + N L A+ +++ + ++G+V SAK D FIAG D Sbjct: 6 VDAEGIATVEFDYPEKSQNILNAKSMGAYADAMQKALADPAVKGIVVASAKKD-FIAGGD 64 Query: 71 INMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTD 130 + +G A A +LM I V AA++G LGGG+E+AL CH RV D Sbjct: 65 LAELGAATDAAAFHASISAWHKLMRAIELGGKPVAAALNGTTLGGGMEVALGCHYRVAAD 124 Query: 131 DPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVP 190 +PK G PEV LGLLPG+GGTQRLPRL G+ A +++ GK+++A +A K+G++ VV Sbjct: 125 NPKARFGFPEVTLGLLPGAGGTQRLPRLAGMMAAAPLLMEGKRIKAAEAQKIGMIHAVVT 184 Query: 191 HSILLEAAVE-----LAKKERPSSRPLPVRERILAG-----PLGRALLFKMVGKKTEHKT 240 AA + LA +P +P ++ + G P G +L E KT Sbjct: 185 VGAERTAARQWVADTLAAGTKPL-QPWDMKGAKIPGGGPNTPNGMQMLMAANAMLRE-KT 242 Query: 241 QGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQ-ALRSIFFASTDVKKDP 299 NYPA + IL V GL+ +G EAR F L M+P S+ +RS+FF + K Sbjct: 243 CDNYPAPKHILSCVYEGLSTNIDTGLAIEARYFTNLVMSPVSKNMIRSLFFGMQEANKLA 302 Query: 300 GSDA--PPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLE 357 A P + +G+LG G+MG GIA TA AG+ + + D + Y+ Q Sbjct: 303 SRPAGVPTQKYSKIGMLGAGMMGAGIAMSTAT-AGMAIVLLDTTQEAAEKGKDYARKQWS 361 Query: 358 GKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQ----N 413 +V + + A + LA I T DY +L+IEAVFE E+K + + E + Sbjct: 362 KQVAKGRMTADAMEALLARIHPTADYADLKSCELVIEAVFEKREIKADVTKKAEAVLLAD 421 Query: 414 CAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATT 473 A IFASNTS+LPI +A + RP IGLHFFSP EKMPLVEII TS T+A + Sbjct: 422 PAPDAIFASNTSTLPITGLAEASARPANFIGLHFFSPAEKMPLVEIIVGKATSDATLARS 481 Query: 474 VKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPI 533 + + GKTPIVV D GFY +R+ Y++E + +L +G ID A + G PVGP+ Sbjct: 482 MDYVRAIGKTPIVVNDSRGFYTSRVFGTYVSEGMALLEEGVPPALIDKAGLIAGMPVGPL 541 Query: 534 QLLDEVGIDTGTKIIPVLEAAYGERF--SAPANVVSSILND-DRKGRKNGRGFYLYGQKG 590 L DEV I+ KI A G + A V + ++ D R GRK+G GFY Y G Sbjct: 542 ALADEVSIELVHKIAQQTRADLGSAYVERAADRVAAKMVADLGRLGRKSGAGFYDYPADG 601 Query: 591 RKSKKQVDPAIYPL-IGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGA 649 K +P+ +G G ++ Q+ ER +++ E VRC++E+V+R+ D D+GA Sbjct: 602 PKHLWSGLAQHFPVRVGADGTAALTLEQIVERLILVQSVETVRCLEEKVLRAPIDADVGA 661 Query: 650 VFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706 + G G+PPF GGP ++ +LG+ + VA + RLA Q G RFTP + L +M ARGE+F+ Sbjct: 662 ILGWGYPPFRGGPIGWLHTLGSAKSVAALDRLAEQNGPRFTPPKLLRDMAARGENFY 718 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: 983 Number of extensions: 36 Number of successful extensions: 7 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: 720 Length adjustment: 40 Effective length of query: 674 Effective length of database: 680 Effective search space: 458320 Effective search space used: 458320 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