Align BadI (characterized)
to candidate CA265_RS20005 CA265_RS20005 enoyl-CoA hydratase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__Pedo557:CA265_RS20005 Length = 259 Score = 119 bits (297), Expect = 8e-32 Identities = 83/259 (32%), Positives = 132/259 (50%), Gaps = 7/259 (2%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 M +++LI EI+ + ++ INR +NA T EL + AG +V ++L GAG++ Sbjct: 1 MAYQNLISEIKENILYVTINREKALNALNKDTLAELADVIAFAGRTDEVRGVILTGAGEK 60 Query: 61 AFCTGGDQSTHDGNYDGRGTVGLPM---EELHTAIRDVPKPVIARVQGYAIGGGNVLATI 117 AF G D +Y G+ L E + AI + KP IA + G+A+GGG LA Sbjct: 61 AFVAGADIKEFS-DYSGKQGEELAKRGHELVFNAIENSSKPFIAAINGFALGGGLELAMA 119 Query: 118 CDLTICSEKAIFGQVGPKMGSVDPGY-GTAFLARVVGEKKAREIWYMCKRYSGKEAEAMG 176 C + I S+ A G +G + PGY GT L ++VG+ KA E+ + +AE +G Sbjct: 120 CHIRIASDNAKLGLPEVTLGLI-PGYGGTQRLTQLVGKGKAIEMITTANMITATDAEKIG 178 Query: 177 LANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLYYD 236 L N+ VP +L + ++ + +R+P A++ A +S + G A + ++ Sbjct: 179 LVNVVVPQADLIGKAEEMLNVIKQRAPLAISAAIKSVIASINNTNGYA-TEIEEFGKCFE 237 Query: 237 TDESREGVKALQEKRKPEF 255 T + +EGV A EKRK F Sbjct: 238 TADFKEGVTAFVEKRKAIF 256 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: 160 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: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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 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