Align Histidine transport system permease protein HisM (characterized)
to candidate AZOBR_RS15680 AZOBR_RS15680 amino acid ABC transporter permease
Query= SwissProt::P0AEU3 (238 letters) >FitnessBrowser__azobra:AZOBR_RS15680 Length = 216 Score = 110 bits (276), Expect = 2e-29 Identities = 70/211 (33%), Positives = 115/211 (54%), Gaps = 10/211 (4%) Query: 18 YRFTGVAITLWLLILSVVIGGVLALFLAIGRVSSNKYIQFPIWLFTYIFRGTPLYVQLLV 77 + + V TL L ++ + G + L +A+ R S K ++ + +F+GTPL +QL + Sbjct: 11 FLLSAVQWTLALSAIAFIGGATVGLVIALARTSDIKAVRLAATGYIQLFQGTPLLMQLFL 70 Query: 78 FYSGMYTLEIVKGTEFLNAFFRSGLNCTVLALTLNTCAYTTEIFAGAIRSVPHGEIEAAR 137 + G V G + LN + + L LTLN A+ EI+ G I++VP G+ EAA Sbjct: 71 VFFGA----TVMGLD-LNPWAAAALG-----LTLNASAFLGEIWRGCIQAVPRGQWEAAS 120 Query: 138 AYGFSTFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIARDINAATY 197 A G + R +ILP A+++A+P ++ ++ ST+LA +L + + +N AT+ Sbjct: 121 ALGLRYPGLMRYVILPQAVKVAVPPTVGFLVQLIKSTSLAAIIGFTELTRAGQIVNNATF 180 Query: 198 QPFTAFGIAAVLYLIISYVLISLFRRAEKRW 228 QPF FGI AVLY ++ + L L R E+R+ Sbjct: 181 QPFLVFGIVAVLYFLMCWPLSLLSARLERRY 211 Lambda K H 0.330 0.142 0.438 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: 117 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: 238 Length of database: 216 Length adjustment: 22 Effective length of query: 216 Effective length of database: 194 Effective search space: 41904 Effective search space used: 41904 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 (21.9 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