Align AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate WP_023433914.1 N177_RS18360 amino acid ABC transporter permease
Query= TCDB::O50183 (232 letters) >NCBI__GCF_000496075.1:WP_023433914.1 Length = 224 Score = 112 bits (280), Expect = 6e-30 Identities = 74/216 (34%), Positives = 116/216 (53%), Gaps = 10/216 (4%) Query: 12 LPLYFDGLLVTLKLLSISLLIGLLLAVPLALMRVSKQPLVNFPAWLYTYVIRGTPMLVQL 71 LP+ L +TL+L + + LLLA LA++RV + P+++ L+ RGTP+LVQL Sbjct: 13 LPVLLSYLPLTLQLAVTGMALALLLACLLAVVRVLQVPVLDPLVRLFISFFRGTPLLVQL 72 Query: 72 FLIYYGLAQFDAVRESALWPWLSNASFCACLAFAINTSAYTAEILAGSLKATPHGEIEAA 131 FL YYGL Q A + N + ++ +AY AE + ++ + EAA Sbjct: 73 FLFYYGLPQVFAFLTAI------NGITATIIGLTLHFAAYMAESIRAAIVGIDRSQTEAA 126 Query: 132 KAMGMSRLKMYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLVDITGAARTVYSQY 191 ++GM+ +M RRI+LP A R A P N I M+++TSLA + + ++ GA + + Sbjct: 127 LSIGMTTSQMMRRIVLPQAARVAAPTLMNYFIDMIKSTSLAFTLGVTELMGATQKEAAGS 186 Query: 192 YLPFEAFITAGLFYLCLTFILVRLFKLAERRWLAYL 227 +L FEAFIT + Y +I+V +RR +L Sbjct: 187 FLYFEAFITVAVIY----WIVVEGLSWVQRRMEVFL 218 Lambda K H 0.330 0.140 0.425 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: 124 Number of extensions: 5 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: 224 Length adjustment: 23 Effective length of query: 209 Effective length of database: 201 Effective search space: 42009 Effective search space used: 42009 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 (21.9 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