Align ABC transporter for L-Arginine, permease component 1 (characterized)
to candidate AO353_01530 AO353_01530 amino acid ABC transporter permease
Query= reanno::BFirm:BPHYT_RS07680 (237 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01530 Length = 236 Score = 324 bits (830), Expect = 1e-93 Identities = 155/232 (66%), Positives = 194/232 (83%) Query: 1 MIDILNQFWRAFLYWDGQRMSGLAVTLWLLVASVGIGFCAAIPLAVARVSKKRWLSTPVR 60 MI++L +W+ FLY DG ++GLA+TLWLL AS+ IGF ++PL++ARVS K ++ PV+ Sbjct: 1 MIELLQDYWKPFLYSDGYHITGLAMTLWLLSASIFIGFLVSVPLSIARVSNKLYVRWPVQ 60 Query: 61 LYTYVFRGTPLYVQLLLIYTGMYSLEFVRSHQLLDAFFRSGFHCAILAFALNTCAYTTEI 120 YTY+FRGTPLY+QLL+ YTG+YSL VR+ LLDAFFR +C ILAFALNTCAYTTEI Sbjct: 61 FYTYLFRGTPLYIQLLICYTGIYSLAAVRAQPLLDAFFRDAMNCTILAFALNTCAYTTEI 120 Query: 121 FAGAIRSTSHGEVEAARAYGMSWFTMYRRIVIPSALRRALPLYSNEVILMLHATTVAFTA 180 FAGAIRS +HGEVEAA+AYG++ + +Y +++PSALRR+LP YSNEVILMLH+TTVAFTA Sbjct: 121 FAGAIRSMNHGEVEAAKAYGLTGWKLYAYVIMPSALRRSLPYYSNEVILMLHSTTVAFTA 180 Query: 181 TVPDILKVARDANSATYQSFDAFGLAALIYLVVSFVLVALFRRAERHWLGYL 232 TVPDILKVARDANSAT+ +F +FG+ ALIYL+V+F LV LFR AER WL +L Sbjct: 181 TVPDILKVARDANSATFLTFQSFGITALIYLLVTFALVGLFRIAERRWLAFL 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: 252 Number of extensions: 10 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: 236 Length adjustment: 23 Effective length of query: 214 Effective length of database: 213 Effective search space: 45582 Effective search space used: 45582 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