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_046010135.1 OLEAN_RS16520 3-hydroxyacyl-CoA dehydrogenase
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_000967895.1:WP_046010135.1 Length = 723 Score = 358 bits (919), Expect = e-103 Identities = 251/715 (35%), Positives = 373/715 (52%), Gaps = 32/715 (4%) Query: 15 NIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGADINMI 74 NI + +D P N + EF + A +++LR++ + G++F SAK F AG +++ + Sbjct: 14 NIVHLILDKPNAGANLMDNEFTDSLTAAVEKLRQD-DYAGIIFRSAK-STFFAGGNLDDL 71 Query: 75 GNCKTAQEAEALARQGQQLMAEIHALPIQ---VIAAIHGACLGGGLELALACHGRVCTDD 131 + A+ L +L + L Q V+A I+GA LGGG ELAL+ H RV + Sbjct: 72 FTTHK-ENADVLYDMVNRLKLAMRELETQGKPVVACINGAALGGGWELALSAHYRVALNK 130 Query: 132 PKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVPH 191 +LGLPEV LGLLPG GG R+ RL+GV A+ +L GKQ + ++ LKLGL+++VV Sbjct: 131 G-VILGLPEVTLGLLPGGGGIIRMTRLLGVQAAMPYLLEGKQFKPEKGLKLGLINEVVDS 189 Query: 192 -SILLEAAVELAKKERPSS----RPLPVRERILAGPLGR----ALLFKMVGKKTEHKTQG 242 + +L++A++ K + +P V+ + G L A + + KT+G Sbjct: 190 PAAMLQSAIQWIKANSSADCNVQQPYDVKGHKVPGGLPHQPALAKMLPIAPTLIRAKTKG 249 Query: 243 NYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFASTDVKKDPGSD 302 PA E IL V+ GL + E+R F EL + ++ + F+ + K G+ Sbjct: 250 TLPAPESILAVMVEGLQVDIDTAMRIESRYFVELVCSQVAKNMIGTFWYQMNEIK-AGAA 308 Query: 303 APP----APLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLEG 358 P +N +G+LG G+MG GIAY +A K GI V +KD++ + YS + + Sbjct: 309 RPKNIERKKVNKLGVLGAGMMGAGIAYSSAMK-GIDVVLKDVDIESAEKGKAYSENIVNK 367 Query: 359 KVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQNCAAHT 418 KV++ L + D L+ I T + + A DL+IEAVFEN ELK ++ E E + Sbjct: 368 KVKQGRLSQDKADALLSAILATDNAQHLAGCDLVIEAVFENRELKAKVTQEAEVQLSTQA 427 Query: 419 IFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATTVKLAK 478 +FASNTS+LPI +A + RP+ IGLHFFSPV+KMPLVEII TS +T+A + Sbjct: 428 VFASNTSTLPITGLAQASARPQNFIGLHFFSPVDKMPLVEIICGEKTSDETLALAYDYVQ 487 Query: 479 KQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPIQLLDE 538 + GK PIVV D GFY +R+ + NE I ML +G I+ A GFPVGP+ + DE Sbjct: 488 QIGKIPIVVNDSRGFYTSRVFGTFANEGIAMLGEGIPAAAIENAAFLTGFPVGPLAVTDE 547 Query: 539 VGIDTGTKI---IPVLEAAYGERF--SAPANVVSSILNDDRKGRKNGRGFYLYGQKGRKS 593 V + KI + AA G+ F V +L +R G+ G GFY Y Q K Sbjct: 548 VSLTLVEKIRKQTMLDMAAEGKDFVHHPGEKTVDKMLAMERAGKLAGAGFYDYPQSDSKE 607 Query: 594 KKQVDPAIYPLIGTQGQGRISAPQVAE---RCVMLMLNEAVRCVDEQVIRSVRDGDIGAV 650 K+ ++ + + A +AE R + + E VRC +E V+ SVRD +IG++ Sbjct: 608 NKK--KHLWAGLKDTFEDNTVAFDLAEIKDRLLYIQAIETVRCFEENVLTSVRDANIGSI 665 Query: 651 FGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESF 705 GIGFP + GG ++I+ G + + L G RF L +M F Sbjct: 666 MGIGFPVWTGGILQFINQTGFDAFIERAEYLFETCGERFRVPNLLKDMAKDNRVF 720 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: 976 Number of extensions: 46 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: 723 Length adjustment: 40 Effective length of query: 674 Effective length of database: 683 Effective search space: 460342 Effective search space used: 460342 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