Align BadI (characterized)
to candidate GFF2389 Psest_2437 Enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__psRCH2:GFF2389 Length = 257 Score = 118 bits (295), Expect = 1e-31 Identities = 88/263 (33%), Positives = 121/263 (46%), Gaps = 17/263 (6%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 M FE L+ +I+ VA I +NRP +NA G EL +AL + D +G IVL G+ + Sbjct: 1 MTFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSA-K 59 Query: 61 AFCTGGDQSTHDGNYDGRGTVGLPMEELHTAIRDVP------KPVIARVQGYAIGGGNVL 114 AF G D + P L D KP+IA V GYA+GGG L Sbjct: 60 AFAAGADIKE-------MAELTYPQIYLDDFFADADRIATRRKPLIAAVAGYALGGGCEL 112 Query: 115 ATICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEA 174 A +CD+ ++ A FGQ +G + GT L R VG+ KA ++ ++ EAE Sbjct: 113 ALLCDMIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAER 172 Query: 175 MGLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFN--MDTAHQAGIAGMGMYALK 232 GL P + L E K + E+S A + K S N +T GI Sbjct: 173 AGLVARVFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIR-FERRVFH 231 Query: 233 LYYDTDESREGVKALQEKRKPEF 255 + T + +EG+ A EKRKPEF Sbjct: 232 AVFATADQKEGMAAFSEKRKPEF 254 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: 145 Number of extensions: 12 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: 257 Length adjustment: 24 Effective length of query: 236 Effective length of database: 233 Effective search space: 54988 Effective search space used: 54988 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