Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate AZOBR_RS00675 AZOBR_RS00675 ABC transporter permease
Query= reanno::WCS417:GFF4243 (232 letters) >FitnessBrowser__azobra:AZOBR_RS00675 Length = 229 Score = 216 bits (550), Expect = 3e-61 Identities = 107/227 (47%), Positives = 153/227 (67%) Query: 4 DYNVIWEAMPLYLGGLLTTLKLLAISLFFGLLAALPLGLMRVSKQPIVNGAAWLYTYVIR 63 +++++W+++P L G+ TL+L+ ++L FG A + L+R+ + Y +V R Sbjct: 2 NWDLMWDSVPTLLRGVPVTLQLVGLALLFGAGVAFAVALLRLYGNRVTERLMAAYVFVFR 61 Query: 64 GTPMLVQLFLIYYGLAQFEAVRESFLWPLLSSATFCACLAFAINTSAYTAEIIAGSLKAT 123 GTP+LVQ+FLIYYG+ QFE VR SFLW L +CA LA +NT AYT+EI+ G++ + Sbjct: 62 GTPLLVQIFLIYYGMGQFELVRSSFLWVYLREPFWCAILALTLNTGAYTSEILRGAILSV 121 Query: 124 PNGEIEAAKAMGMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGA 183 P G+IEAA+A GMSR L+RRI++P A+R+ LP Y NEVI+M++ +SLAS +TL++ITG Sbjct: 122 PQGQIEAARACGMSRTLLFRRIMMPVAIRQMLPAYGNEVILMVKASSLASTITLLEITGI 181 Query: 184 ARTVNAQFYLPFEAYITAGVFYLCLTFILVRLFKLAERRWLSYLAPR 230 AR + AQ + FE +I AG YL L FI RL + AE R YL R Sbjct: 182 ARKIIAQSFAVFEVFIVAGSIYLLLNFIASRLIRYAEWRMTPYLRAR 228 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: 141 Number of extensions: 4 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: 229 Length adjustment: 23 Effective length of query: 209 Effective length of database: 206 Effective search space: 43054 Effective search space used: 43054 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