Align ABC transporter for L-Histidine, periplasmic substrate-binding component 2 (characterized)
to candidate AZOBR_RS07675 AZOBR_RS07675 ABC transporter substrate-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2562 (321 letters) >FitnessBrowser__azobra:AZOBR_RS07675 Length = 339 Score = 90.1 bits (222), Expect = 7e-23 Identities = 80/269 (29%), Positives = 129/269 (47%), Gaps = 26/269 (9%) Query: 6 VKWTSLAAAAACVMAL------AAPAQAQDTKIVLGMSGWTGFAPLTLADKAGIFKKNGL 59 ++ S+ AAAA V+A A + +D K+ +G + PLT+A++ G FK+ GL Sbjct: 1 MRMKSVIAAAAVVLAFGIGGANAQQVEKKDLKLAVGGKPLLYYLPLTVAERLGYFKEAGL 60 Query: 60 DVEIKMIPQKDRHL-ALASKSIQCAATTVETHVAWNANGVPIVQIFQMDKSYGADGIAVR 118 +VEI + L AL S + V A G PI + + + G AV Sbjct: 61 NVEINDFGGGAKSLQALVGGSADIVTGAFDHTVQMQAKGQPITAVALLGRYPGIVLAAVN 120 Query: 119 --GDIKSFADLKGKTIGVDAPGTAPYFGLAWMLSKNGMSLKDVKTTTLSPQAAAQAFV-A 175 G I S +LKGK IGV APG++ F + ++L+++GM+ +DV + +A A V Sbjct: 121 KAGTITSIKELKGKKIGVTAPGSSTNFMVNYLLTQHGMTPEDVSFIGVGGGPSAVAAVKR 180 Query: 176 GQNDAAMTYEPYLSTVRDNPAAGKI--LATTLDYPMVMDTVG---------CDPTWLKAN 224 G+ DA +P +S + A G + +A T +DT G P ++K N Sbjct: 181 GEIDAIANLDPVISQLE---ADGDVTTIADTRTEKGTLDTYGGPYPAAVLYTTPAFIKEN 237 Query: 225 GKAAQALANSYFQALDMIKADPAKSNEIM 253 K QAL + + + L + D AK+ +++ Sbjct: 238 PKTTQALVDVFVRTLKWL--DQAKTEDVL 264 Lambda K H 0.317 0.129 0.374 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: 210 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 321 Length of database: 339 Length adjustment: 28 Effective length of query: 293 Effective length of database: 311 Effective search space: 91123 Effective search space used: 91123 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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