Align Histidine transport system permease protein HisM (characterized)
to candidate HSERO_RS10770 HSERO_RS10770 amino acid ABC transporter permease
Query= SwissProt::P0AEU3 (238 letters) >FitnessBrowser__HerbieS:HSERO_RS10770 Length = 221 Score = 117 bits (294), Expect = 1e-31 Identities = 73/206 (35%), Positives = 113/206 (54%), Gaps = 10/206 (4%) Query: 22 GVAITLWLLILSVVIGGVLALFLAIGRVSSNKYIQFPIWLFTYIFRGTPLYVQLLVFYSG 81 GV TL + S++ G VL LA+ R+ + I +P ++ + RGTPL VQ+ V Y G Sbjct: 19 GVGYTLLFALASMLGGLVLGFVLAVARIVPWRPIHWPAAIYVSMMRGTPLLVQIFVVYYG 78 Query: 82 MYTLEIVKGTEFLNAFFRSGLNCTVLALTLNTCAYTTEIFAGAIRSVPHGEIEAARAYGF 141 + + G EF S L VL L+LN AY +E GAI V G+ AA + G Sbjct: 79 LPGM----GIEF------SPLTAGVLTLSLNASAYLSESLRGAILGVTRGQWNAAFSVGL 128 Query: 142 STFKMYRCIILPSALRIALPAYSNEVILMLHSTALAFTATVPDLLKIARDINAATYQPFT 201 + F+ R II+P A+RIA+P+ SN +I ++ T+L TV +L+ +++ A T++P Sbjct: 129 TYFQTLRYIIVPQAVRIAVPSMSNTLISLIKDTSLVSVITVTELMLATKEVIAVTFRPLP 188 Query: 202 AFGIAAVLYLIISYVLISLFRRAEKR 227 + AA +Y ++S +L R EK+ Sbjct: 189 LYVAAAAIYWMLSLCFEALQHRLEKK 214 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: 100 Number of extensions: 4 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: 238 Length of database: 221 Length adjustment: 23 Effective length of query: 215 Effective length of database: 198 Effective search space: 42570 Effective search space used: 42570 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