Align ABC transporter for L-Arginine, permease component 1 (characterized)
to candidate BPHYT_RS05500 BPHYT_RS05500 histidine/lysine/arginine/ornithine ABC transporter permease HisM
Query= reanno::BFirm:BPHYT_RS07680 (237 letters) >FitnessBrowser__BFirm:BPHYT_RS05500 Length = 237 Score = 370 bits (949), Expect = e-107 Identities = 174/232 (75%), Positives = 206/232 (88%) Query: 1 MIDILNQFWRAFLYWDGQRMSGLAVTLWLLVASVGIGFCAAIPLAVARVSKKRWLSTPVR 60 MI+I+ ++WR +LY DG R++G+ +TLWLLV S+G+GFC +IPLAVARVSKK+WLS V Sbjct: 1 MIEIIQEYWRNYLYTDGYRLTGVVITLWLLVVSIGLGFCLSIPLAVARVSKKKWLSRLVW 60 Query: 61 LYTYVFRGTPLYVQLLLIYTGMYSLEFVRSHQLLDAFFRSGFHCAILAFALNTCAYTTEI 120 LYTYVFRGTPLYVQLLL YTG+YSLE +R+H+L +AFFR G HC +LAF LNTCAYTTEI Sbjct: 61 LYTYVFRGTPLYVQLLLCYTGLYSLEIIRNHELTNAFFRDGMHCTLLAFTLNTCAYTTEI 120 Query: 121 FAGAIRSTSHGEVEAARAYGMSWFTMYRRIVIPSALRRALPLYSNEVILMLHATTVAFTA 180 FAGAI++T +GE+EAARAYGMS FT+YRR+++PSALRRALP YSNEVILMLHATTVAFTA Sbjct: 121 FAGAIKATPYGEIEAARAYGMSSFTLYRRVILPSALRRALPYYSNEVILMLHATTVAFTA 180 Query: 181 TVPDILKVARDANSATYQSFDAFGLAALIYLVVSFVLVALFRRAERHWLGYL 232 TVPDILK+ARD NSATYQSF+AFG+AAL+YL +SF LV LFRRAER WL YL Sbjct: 181 TVPDILKIARDVNSATYQSFNAFGIAALLYLCISFALVWLFRRAERRWLAYL 232 Lambda K H 0.331 0.139 0.437 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: 307 Number of extensions: 7 Number of successful extensions: 1 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: 237 Length of database: 237 Length adjustment: 23 Effective length of query: 214 Effective length of database: 214 Effective search space: 45796 Effective search space used: 45796 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (22.0 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