Align BadI (characterized)
to candidate Pf6N2E2_1147 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1147 Length = 257 Score = 104 bits (259), Expect = 2e-27 Identities = 79/267 (29%), Positives = 126/267 (47%), Gaps = 23/267 (8%) Query: 1 MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60 M +E ++ EI++ V I +NRP +NA EL +AL D +G IVL G+ + Sbjct: 1 MSYETILLEIKDRVGLITLNRPQALNALNAQIVSELNQALDSLEADPKIGCIVLTGS-KK 59 Query: 61 AFCTGGD-----QSTHDGNYDGRGTVGLPMEELHT---AIRDVPKPVIARVQGYAIGGGN 112 AF G D + T+ Y +++L + + + KP+IA V G+A+GGG Sbjct: 60 AFAAGADIKEMAELTYPQIY---------LDDLFSDSDRVANRRKPIIAAVNGFALGGGC 110 Query: 113 VLATICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEA 172 LA +CD + + A FGQ +G + GT L R VG+ KA E+ + EA Sbjct: 111 ELALMCDFILAGDNAKFGQPEVNLGVLPGMGGTQRLTRAVGKAKAMEMCLTGRFIDAVEA 170 Query: 173 EAMGLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALK 232 E G+ VP DEL + K + +S + K S N A + ++ + + Sbjct: 171 ERCGIVARIVPADELLDDALKTAALIASKSVPISMMVKESVN--RAFEVSLSEGVRFERR 228 Query: 233 LY---YDTDESREGVKALQEKRKPEFR 256 ++ + T + +EG+ A KR EF+ Sbjct: 229 VFHAAFATQDQKEGMAAFVAKRAAEFQ 255 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: 151 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: 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