Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_086508346.1 BZY95_RS02050 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >NCBI__GCF_002151265.1:WP_086508346.1 Length = 243 Score = 233 bits (594), Expect = 2e-66 Identities = 111/221 (50%), Positives = 163/221 (73%) Query: 10 EALPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLV 69 + + Y+ GLV T +L+ LSL+ GL+ A+PL + R S + +++ ++YTYV RGTP+L+ Sbjct: 20 QTIGYYWDGLVLTTQLVFLSLVAGLVLAIPLAIGRSSGRRWISLPIYVYTYVFRGTPLLI 79 Query: 70 QLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIE 129 QL++IYYG+ F+ ++++FLWP L A + A +AF +NT+AYT EI G+++ATP GEIE Sbjct: 80 QLYIIYYGVVFFDGIQQTFLWPILREAFYPALIAFTLNTAAYTTEIFRGAIKATPRGEIE 139 Query: 130 AAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNA 189 AA+A GMS+ M +RI+LPSA RRALP Y NEVI ML +++AS+VTL+DITGAAR V A Sbjct: 140 AARAYGMSQGLMMRRIVLPSAFRRALPAYGNEVIFMLHASAIASVVTLMDITGAARFVYA 199 Query: 190 QYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGYLAPR 230 ++Y PFEA++ A YLC+TF ++ F+ E + L +L P+ Sbjct: 200 RFYAPFEAFLFAAAIYLCLTFAILYFFRYLEKKLLAHLKPQ 240 Lambda K H 0.329 0.139 0.427 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: 185 Number of extensions: 6 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: 232 Length of database: 243 Length adjustment: 23 Effective length of query: 209 Effective length of database: 220 Effective search space: 45980 Effective search space used: 45980 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 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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