Align BadI (characterized)
to candidate WP_092487896.1 BM299_RS18360 enoyl-CoA hydratase-related protein
Query= metacyc::MONOMER-892 (260 letters) >NCBI__GCF_900115975.1:WP_092487896.1 Length = 260 Score = 134 bits (336), Expect = 2e-36 Identities = 88/268 (32%), Positives = 136/268 (50%), Gaps = 22/268 (8%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 M + +L+ E G+A + INRP +NA T EL A+ + G D +V I+L GAG++ Sbjct: 1 MGWNNLLLEKEAGIAVLTINRPKVLNALNAETLQELDAAMDQLGNDDEVRVIILTGAGEK 60 Query: 61 AFCTGGD----QSTHDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLAT 116 AF G D Q+ +G +++ + I ++PKPVIA + G+A+GGG L+ Sbjct: 61 AFVAGADIAFMQTLKPLEAKNFARLG---QKVFSKIENLPKPVIAAINGFALGGGCELSM 117 Query: 117 ICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMG 176 CD+ I SE A GQ +G + GT L R+V A+EI + Y + A +G Sbjct: 118 ACDIRIASENAKLGQPEVNLGLIAGFGGTQRLTRLVNPGLAKEILFTADMYDAEAAHRIG 177 Query: 177 LANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFN----MDT----AHQAGIAGMGM 228 L N VP EL + + + R P A+ ++K++ N MD H+A + G Sbjct: 178 LVNHVVPAGELMNFCKNMAKRIAARGPVAVQLSKQAVNDGLEMDLEKAFVHEADLFG--- 234 Query: 229 YALKLYYDTDESREGVKALQEKRKPEFR 256 L + T++ EG+ A K+KPEF+ Sbjct: 235 ----LVFATEDREEGIAAFLGKKKPEFK 258 Lambda K H 0.319 0.138 0.418 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: 167 Number of extensions: 9 Number of successful extensions: 3 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: 260 Length of database: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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 (21.7 bits) S2: 47 (22.7 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