Align AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate 206399 DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family
Query= TCDB::O50183 (232 letters) >MicrobesOnline__882:206399 Length = 337 Score = 131 bits (329), Expect = 2e-35 Identities = 74/214 (34%), Positives = 126/214 (58%), Gaps = 10/214 (4%) Query: 14 LYFDGLLVTLKLLSISLLIGLLLAVPLALMRVSKQPLVNFPAWLYTYVIRGTPMLVQLFL 73 + +GL +TL++ ++++IG++L V L R+S P + + A Y +IRG+P+LVQ+FL Sbjct: 126 ILLEGLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRWLAITYIEIIRGSPLLVQVFL 185 Query: 74 IYYGL-----AQFDAVRESALWPWLSNASFCACLAFAINTSAYTAEILAGSLKATPHGEI 128 Y+ + A F+ V SA+ P + +A AI T AY AEI+ +++ G++ Sbjct: 186 WYFVVGTLLNALFEKVGLSAIPPL-----WYGVMALAIFTGAYVAEIVRAGIQSVHRGQM 240 Query: 129 EAAKAMGMSRLKMYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLVDITGAARTVY 188 EAA+++GMS + R+++LP A RR +P + + I +++ +SL ++ + ++T A R V Sbjct: 241 EAARSLGMSYAQSMRKVILPQAFRRIMPPLAGQFISLVKDSSLLGVIAVRELTKATREVV 300 Query: 189 SQYYLPFEAFITAGLFYLCLTFILVRLFKLAERR 222 + PFE +I L YL LTF L + ERR Sbjct: 301 TTSLQPFELWIVCALLYLVLTFTLSLCVQYLERR 334 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: 184 Number of extensions: 14 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: 337 Length adjustment: 26 Effective length of query: 206 Effective length of database: 311 Effective search space: 64066 Effective search space used: 64066 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: 47 (22.7 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