Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate HSERO_RS07530 HSERO_RS07530 amino acid ABC transporter permease
Query= TCDB::Q52665 (434 letters) >FitnessBrowser__HerbieS:HSERO_RS07530 Length = 216 Score = 101 bits (251), Expect = 2e-26 Identities = 67/223 (30%), Positives = 121/223 (54%), Gaps = 23/223 (10%) Query: 216 LPEVDSDQFGGFLLA----LVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVR 271 L E D F L A L++ A + G ++AL R S + ++ LS I+ ++ Sbjct: 2 LAEFSFDNFVFLLEAARWTLLLSALAFLGGGIAGFIVALMRTSHLAPLRLLSAVYIQIIQ 61 Query: 272 GVPLITLLFTASLLLQYF---LPPGTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRG 328 G P++ LLF + L F LPP ++ I +T++++AY+ E+ RG + A+P Sbjct: 62 GTPVLILLFLSFYGLAIFGYKLPP------MVAATIAMTIYSSAYLGEIWRGCIEAVPVP 115 Query: 329 QYEAADALGLDYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISN 388 Q+EA+ AL + WQ R +I+PQA++IS+P V + + K+T++ + +GL + Sbjct: 116 QWEASTALAMTRWQQLRYVILPQAVRISLPPTVGFLVQIVKNTSIASIIGLVE------- 168 Query: 389 VVRSDMAWKGTYWEPYI---FVALIFFLFNFSMSRYSMYLERK 428 + ++ ++P++ VA I+F+F + +SR++ LERK Sbjct: 169 LAQAGKLVSNATFQPFLVFPIVAGIYFVFCYPLSRFAFALERK 211 Lambda K H 0.329 0.143 0.457 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: 264 Number of extensions: 17 Number of successful extensions: 2 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: 434 Length of database: 216 Length adjustment: 27 Effective length of query: 407 Effective length of database: 189 Effective search space: 76923 Effective search space used: 76923 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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