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_085772004.1 B1812_RS13170 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
Query= CharProtDB::CH_003230 (714 letters) >NCBI__GCF_002117405.1:WP_085772004.1 Length = 728 Score = 405 bits (1041), Expect = e-117 Identities = 257/728 (35%), Positives = 374/728 (51%), Gaps = 34/728 (4%) Query: 7 FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 F +V D +A++T D+PG MN + E S++ +++++ + ++G V S K + F Sbjct: 6 FRFDVGADGVALLTWDMPGRSMNVITEEVMSELAQVVEKVAADAAIKGCVIASGK-NAFS 64 Query: 67 AGADINMIGNC----------KTAQEAEAL----ARQGQQLMAEIHALPIQVIAAIHGAC 112 GAD++M+ K A+EA L AR+ QL + AIHG C Sbjct: 65 GGADLSMLQKSRAAHGKALGEKGAEEANRLFFESARKLSQLYRRLETCGKPFAIAIHGVC 124 Query: 113 LGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGK 172 LGG ELALACH RV DD KT +GLPEV++GL PG+GGTQR+ R++ AL+ + G+ Sbjct: 125 LGGAFELALACHHRVLADDDKTKVGLPEVKVGLFPGAGGTQRVARIMPTGDALQFLFKGE 184 Query: 173 QLRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAGPLGRA------ 226 QL K A GL ++ P S ++ A + + P ++ P GR Sbjct: 185 QLSGKAAKAAGLAQELAPQSEIVSRAKDWILGGGKAIAPWDQKD--FKPPSGRIFSPGGM 242 Query: 227 LLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL- 285 +++ +T NYPA + IL V GL G EAR F + + ++ A+ Sbjct: 243 MIWMPANAIYRRETYDNYPAVKAILHCVYEGLQLPIDQGLTVEARWFAHILRSKEAAAMI 302 Query: 286 RSIFFASTDVKKDPG--SDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQ 343 RS+F + ++ K D PP L +G+LG G MG G+ YV+A G+ V + D + + Sbjct: 303 RSLFLSKNELDKGARRPKDEPPTQLKKIGVLGAGFMGAGVGYVSALN-GLEVVLIDRDQE 361 Query: 344 GINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELK 403 + + G+V R AS ++ LA + T DY DLI+EAVFE+ +K Sbjct: 362 SADKGKATIDKLISGQVSRGKATASAKEALLARVEATPDYERLKGCDLILEAVFEDRAVK 421 Query: 404 QQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHA 463 + + +FASNTS+LPI +A + +PE IG+HFFSPVEKM LVEII Sbjct: 422 AEATKRAQAAVGPDVVFASNTSTLPITSLAETSLKPENFIGVHFFSPVEKMLLVEIILGE 481 Query: 464 GTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAAL 523 TS + +AT + + KTPIVV D GF+ NR + Y+ E ML +G I+ A Sbjct: 482 KTSDKALATALDFVRMIKKTPIVVNDSRGFFANRCVLAYVREGQTMLVEGVPPAMIENAA 541 Query: 524 VKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPA--NVVSSIL-NDDRKGRKNG 580 G PVGP+ L DEVG+D G KI+ + G PA V+ ++ + R GRKNG Sbjct: 542 RMAGMPVGPLSLNDEVGLDLGWKILQATKKDLGAAAVDPAQERVLGFLVEKNGRFGRKNG 601 Query: 581 RGFYLYGQKGRKSKKQVDPAIYPLI-GTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVI 639 +GFY Y G KK + P + L T I ++ R ++ EA R E V+ Sbjct: 602 KGFYDYPASG---KKTLWPGLAGLAEKTLDPDAIDVKELERRFLVAQAVEAARTFAEHVV 658 Query: 640 RSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMG 699 R+ D+G++ G GF PF GG YID +G VA+ LA +YG RF P + L +M Sbjct: 659 TDPREADVGSILGFGFAPFTGGALSYIDGMGLKAFVALCDTLAAKYGPRFAPPQLLRDMA 718 Query: 700 ARGESFWK 707 GE+F++ Sbjct: 719 REGETFYR 726 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: 1019 Number of extensions: 52 Number of successful extensions: 9 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: 728 Length adjustment: 40 Effective length of query: 674 Effective length of database: 688 Effective search space: 463712 Effective search space used: 463712 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