Align AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein
Query= TCDB::O50183 (232 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3326 Length = 260 Score = 119 bits (299), Expect = 4e-32 Identities = 69/210 (32%), Positives = 111/210 (52%), Gaps = 9/210 (4%) Query: 15 YFDGLLVTLKLLSISLLIGLLLAVPLALMRVSKQPLVNFPAWLYTYVIRGTPMLVQLFLI 74 + DG TL L IS +GL+L AL R ++ +V + A Y +VIRGTP+LVQ+ + Sbjct: 52 FSDGARTTLWLTLISGSVGLVLGTGAALARTARWAVVRWAASFYIWVIRGTPLLVQILFV 111 Query: 75 YYGLAQFDAVRESALWPWLSNASFCAC-LAFAINTSAYTAEILAGSLKATPHGEIEAAKA 133 Y+ L L P L+ F A LA +N AY AE + L A P G+ EAAKA Sbjct: 112 YFALP--------VLVPGLNLPDFAAAVLALGLNVGAYNAEAIRAGLLAVPRGQTEAAKA 163 Query: 134 MGMSRLKMYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLVDITGAARTVYSQYYL 193 +G+ R+ ++ ++ P A + +LP + + +L+ +SLA + +V++T + S + Sbjct: 164 LGLGRMHVFFDVVFPQAFKISLPPLVSNFVALLKDSSLAYAIGVVELTNVGNRIQSATFQ 223 Query: 194 PFEAFITAGLFYLCLTFILVRLFKLAERRW 223 P T + YL LT ++ ++ E R+ Sbjct: 224 PIATLSTVAITYLLLTTLVTQISNAVEYRF 253 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: 140 Number of extensions: 6 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: 260 Length adjustment: 24 Effective length of query: 208 Effective length of database: 236 Effective search space: 49088 Effective search space used: 49088 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 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