Align BadK (characterized)
to candidate Ac3H11_4006 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4006 Length = 259 Score = 310 bits (794), Expect = 2e-89 Identities = 150/246 (60%), Positives = 194/246 (78%) Query: 13 RVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMAA 72 +VG+ITLNRP LNALND LM+ LG AL AFDAD+ IG +++ G+ +AFAAGADI +MA Sbjct: 14 KVGVITLNRPKQLNALNDQLMNELGAALKAFDADENIGCMIVTGSEKAFAAGADIGAMAK 73 Query: 73 WSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALPE 132 +S++D Y ++ITRNWETIR IRKPV+AAV+G A GGGCELA+ CD +IA +A+F PE Sbjct: 74 YSFADTYKGDYITRNWETIRSIRKPVIAAVSGFALGGGCELAMMCDFIIAADNARFGQPE 133 Query: 133 IKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETVA 192 IKLG++PGAGGTQRLPRA+GK+KAMDM L+ R ++A EA+R GLVSRVV D+L DE + Sbjct: 134 IKLGVIPGAGGTQRLPRAVGKSKAMDMALTGRMMDAAEAERAGLVSRVVPYDKLMDEALG 193 Query: 193 LATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKRA 252 A +A FS A+MA KES+NRAFE TL++G++FERR HA FA+ D +EG+ AF+ KR Sbjct: 194 AAIIVAGFSQLAVMAAKESVNRAFEGTLSDGVMFERRLFHALFATQDQKEGMDAFMNKRP 253 Query: 253 PCFSHR 258 F+H+ Sbjct: 254 ANFTHQ 259 Lambda K H 0.321 0.135 0.389 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: 163 Number of extensions: 4 Number of successful extensions: 1 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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