Align BadI (characterized)
to candidate Ac3H11_2775 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2775 Length = 279 Score = 105 bits (262), Expect = 1e-27 Identities = 77/251 (30%), Positives = 113/251 (45%), Gaps = 5/251 (1%) Query: 9 EIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCTGGD- 67 E R GV WI++NRPD++NA + AL + D V IV+ GAG R FC G D Sbjct: 27 ERRGGVGWIVLNRPDQINAINDDIRRGVPAALAELDSDPSVRVIVIRGAGARGFCAGADI 86 Query: 68 QSTHDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDLTICSEKA 127 + + + A+ KPVIA + GY +GGG LA CDL + A Sbjct: 87 KERRAAETSVQVRRRMQKSRWIEALDRTEKPVIAAIHGYCMGGGMELALACDLRFAASDA 146 Query: 128 IFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGL-ANLCVPHDE 186 +F +G + G GT L VVG +A ++ R + A +GL + D Sbjct: 147 VFALPETGLGLIPGGGGTQRLGAVVGPGRALDLLLTGDRVDARRAFDIGLITRMADSADS 206 Query: 187 LDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMY--ALKLYYDTDESREGV 244 L AEV E + ++ PTA AK++ H +G+ + + ++ +E Sbjct: 207 LLAEVTALAERIAQKPPTATLFAKQAARA-ACHLDLKSGLDLELDLFAMLVPMNDVKEAA 265 Query: 245 KALQEKRKPEF 255 A +EKR P F Sbjct: 266 LAFREKRAPCF 276 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: 182 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: 279 Length adjustment: 25 Effective length of query: 235 Effective length of database: 254 Effective search space: 59690 Effective search space used: 59690 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