Align BadI (characterized)
to candidate WP_057507779.1 ABB28_RS05820 enoyl-CoA hydratase
Query= metacyc::MONOMER-892 (260 letters) >NCBI__GCF_001431535.1:WP_057507779.1 Length = 259 Score = 106 bits (265), Expect = 4e-28 Identities = 81/249 (32%), Positives = 113/249 (45%), Gaps = 16/249 (6%) Query: 17 IIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCTGGDQSTHD--GN 74 + + RP+K+NA G T L A +A D V ++L GAG +AF G D S + Sbjct: 16 VTVQRPEKLNALNGETLRALAAAFEQAAQDPAVRVVILTGAGPKAFVAGADISEMNTLSA 75 Query: 75 YDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDLTICSEKAIFGQVGP 134 +GR L + L I +PKPVIARV G+A+GGG LA C L I + A GQ Sbjct: 76 VEGRD-FSLLGQRLMRQIERMPKPVIARVNGFALGGGLELAMACHLRIAVDTARLGQPEI 134 Query: 135 KMGSVDPGY-GTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANLCVPHDELDAEVQK 193 +G + PG+ G+ L R+ G A E+ + A +GL N D+LDA V Sbjct: 135 TLGLI-PGFGGSQRLLRLCGRAAALELCLLGTPIDAARALQLGLVNEVASADDLDARVAG 193 Query: 194 WGEELCERSPTALAIAKRSFNMDTAHQAGIAGM------GMYALKLYYDTDESREGVKAL 247 E L +P A+ +D H G + L + T + REG A Sbjct: 194 LAERLANAAPLAVRAL-----LDAVHVGGECSLESGLEYESAQFGLLFATHDMREGTSAF 248 Query: 248 QEKRKPEFR 256 E+R F+ Sbjct: 249 LERRAAMFQ 257 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: 144 Number of extensions: 8 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 24 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