Align HAD family hydrolase (characterized, see rationale)
to candidate N515DRAFT_0084 N515DRAFT_0084 2-haloacid dehalogenase
Query= uniprot:A0A0L7BRC5 (209 letters) >FitnessBrowser__Dyella79:N515DRAFT_0084 Length = 206 Score = 99.8 bits (247), Expect = 3e-26 Identities = 63/207 (30%), Positives = 101/207 (48%), Gaps = 14/207 (6%) Query: 6 ITDVIFDFCGVLLDWNTRACLEGKFPDDV-----VNRICANDDPCGFFHYEDRMDAGEDL 60 I V+FD GVL+DWN R F D+ + +IC + ++ DAG Sbjct: 2 IDTVVFDLGGVLIDWNPRYLYRQLFDDEAAMEHFLTKICTGP-------WNEQQDAGRPW 54 Query: 61 ADILPDVRREQGDELAAIFEYYIAHYDDALPRTLPGMVELLEDLKAHGYGVWGLTNWSHE 120 ++ + + E A + + +++ L + G VELL +LKA G ++ LTNWS+E Sbjct: 55 SEAIARLSAEHPAH-APLIAAFRERWEEMLAGPIAGSVELLAELKARGVRLYALTNWSNE 113 Query: 121 TFHLAFEKFPRLEELLQGTVVSGVEKMHKPNADIYELALNHFGLTAGNCVFFDDTAKNIV 180 TF A E + L +G VVSG E++ KP+ IY+ +G+ ++ DD +N+ Sbjct: 114 TFPRALELYDFLH-WFEGIVVSGEERLIKPDPRIYQCLFERYGVEPSRALYIDDARRNVD 172 Query: 181 GANEVGIHGLLFENALQARESLAQLGV 207 A +G+ F+ A R LA G+ Sbjct: 173 AAAALGMQAWWFQGAEGLRTWLASHGL 199 Lambda K H 0.323 0.142 0.445 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: 10 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: 209 Length of database: 206 Length adjustment: 21 Effective length of query: 188 Effective length of database: 185 Effective search space: 34780 Effective search space used: 34780 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 (21.9 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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