Align BadI (characterized)
to candidate WP_073037062.1 BUB04_RS03725 enoyl-CoA hydratase-related protein
Query= metacyc::MONOMER-892 (260 letters) >NCBI__GCF_900129305.1:WP_073037062.1 Length = 263 Score = 143 bits (360), Expect = 4e-39 Identities = 94/260 (36%), Positives = 139/260 (53%), Gaps = 6/260 (2%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 M F+++++E+R+GVA I NRP +NA T +EL +A+ A D V +VL GAGD+ Sbjct: 1 MDFQNILFEVRDGVALITFNRPKALNALNPQTLEELARAVAAARDDDAVRVVVLTGAGDK 60 Query: 61 AFCTGGD-QSTHDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICD 119 AF G D N +++ ++ D+PKPVIA V G+A+GGG LA CD Sbjct: 61 AFVAGADITELQKMNPLEARLFAQKGQDVFFSLEDLPKPVIACVNGFALGGGCELAMSCD 120 Query: 120 LTICSEKAIFGQVGPKMGSVDPGY-GTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLA 178 S+KA FGQ +G + PG+ GT LAR+VG KA+E+ + ++A+ +GL Sbjct: 121 FIYASDKAKFGQPEINLGII-PGFGGTQRLARLVGRAKAKELCMTGEMIDAQQAKELGLV 179 Query: 179 NLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFN--MDTAHQAGIAGMGMYALKLYYD 236 PH+ L E K + +S TAL K + MD + G A + A + + Sbjct: 180 AKVFPHEALLEETLKAATAMAAKSCTALRAIKHVVDRGMDADLKTGCA-LEAEAFGVCFA 238 Query: 237 TDESREGVKALQEKRKPEFR 256 +++EG A EKRKP F+ Sbjct: 239 GQDAKEGTTAFLEKRKPVFK 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: 188 Number of extensions: 11 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: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 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