Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS19445 BPHYT_RS19445 metal-dependent hydrolase
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__BFirm:BPHYT_RS19445 Length = 254 Score = 202 bits (515), Expect = 4e-57 Identities = 111/248 (44%), Positives = 155/248 (62%), Gaps = 7/248 (2%) Query: 1 MGDEVMTGQPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGS 60 M + + P+L V+G+ YG + AL G + V G+IVS+IG NGAGKSTL+ I G+ Sbjct: 1 MENTMNAASPILDVDGLSVRYGKVEALHGAAIKVRPGQIVSVIGPNGAGKSTLLNAIMGA 60 Query: 61 PQAR---TGSVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNL- 116 G+V+++G D++ +P + + PE R +F MTV +NL +GA Sbjct: 61 LPTTGHAKGAVLYQGEDVSAVPVEKRVARGMCLVPEKRELFASMTVEDNLVLGAYRRKRA 120 Query: 117 --KHFAEDVEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGL 174 ++F + +E +FTLFPRL+ER Q GTLSGGE+QML++GRALM +P LL+LDEPSLGL Sbjct: 121 GERNFLDQLEPVFTLFPRLRERRKQAAGTLSGGERQMLAVGRALMGKPDLLMLDEPSLGL 180 Query: 175 APLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLAN 234 APLIVK IF I L + G+ L+EQNA AAL++S YV+ G++ + G +L N Sbjct: 181 APLIVKEIFHIISALRQT-GVATLLIEQNARAALQISDYGYVLETGELALEGPAADLAQN 239 Query: 235 PEVRAAYL 242 P V YL Sbjct: 240 PRVIETYL 247 Lambda K H 0.320 0.137 0.387 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: 186 Number of extensions: 8 Number of successful extensions: 4 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: 247 Length of database: 254 Length adjustment: 24 Effective length of query: 223 Effective length of database: 230 Effective search space: 51290 Effective search space used: 51290 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 (21.8 bits) S2: 46 (22.3 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