Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate AZOBR_RS18070 AZOBR_RS18070 polar amino acid ABC transporter permease
Query= reanno::WCS417:GFF4243 (232 letters) >FitnessBrowser__azobra:AZOBR_RS18070 Length = 223 Score = 114 bits (286), Expect = 1e-30 Identities = 66/210 (31%), Positives = 108/210 (51%), Gaps = 9/210 (4%) Query: 3 FDYNVIWEAMPLYLGGLLTTLKLLAISLFFGLLAALPLGLMRVSKQPIVNGAAWLYTYVI 62 FDY+ I E P+ L GL+TT++L I FG+ + R + Y +I Sbjct: 5 FDYSWIAEYWPVILKGLVTTVELTLIGTLFGVALGIACAWTRSLGPRWLRPPVVAYVELI 64 Query: 63 RGTPMLVQLFLIYYGLAQFEAVRESFLWPLLSSATFCACLAFAINTSAYTAEIIAGSLKA 122 R TP L+QLF I++GL F A LA IN AY+ EII ++A Sbjct: 65 RNTPFLIQLFFIFFGLPSLGVQMTEFQ---------AAVLAMVINLGAYSGEIIRAGIEA 115 Query: 123 TPNGEIEAAKAMGMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITG 182 TP G+ EA ++ M+R++ +R ++L +L+R P S+++++++ +++ S + DIT Sbjct: 116 TPRGQFEAGASLAMTRFETFRHVVLIPSLQRIWPALSSQIVIVMLGSAVVSQIAAEDITF 175 Query: 183 AARTVNAQFYLPFEAYITAGVFYLCLTFIL 212 AA + ++ + FE+Y YL L L Sbjct: 176 AANFIQSRTFRAFESYFLTTGLYLLLALAL 205 Lambda K H 0.329 0.140 0.422 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: 131 Number of extensions: 9 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: 232 Length of database: 223 Length adjustment: 22 Effective length of query: 210 Effective length of database: 201 Effective search space: 42210 Effective search space used: 42210 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 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