Align AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate WP_012706778.1 NGR_RS12340 ABC transporter permease
Query= TCDB::O50183 (232 letters) >NCBI__GCF_000018545.1:WP_012706778.1 Length = 274 Score = 172 bits (436), Expect = 6e-48 Identities = 93/222 (41%), Positives = 134/222 (60%), Gaps = 8/222 (3%) Query: 9 WDSLPLYF----DGLLVTLKLLSISLLIGLLLAVPLALMRVSKQPLVNFPAWLYTYVIRG 64 WD LP Y G+LV+L +L + ++G LLAVPL L++V+ + PA L+ VIRG Sbjct: 47 WDWLPRYLPRLGSGILVSLAMLFSTAILGFLLAVPLGLVQVTGPWFLKAPARLFCTVIRG 106 Query: 65 TPMLVQLFLIYYGLA----QFDAVRESALWPWLSNASFCACLAFAINTSAYTAEILAGSL 120 TP+L+QL+L+YYGL QF A+R S LWP+L A A ++ +AY E++ G+ Sbjct: 107 TPLLLQLWLLYYGLGSLFPQFPAIRHSLLWPYLREAWPYGVAALTLSFAAYEGEVMRGAF 166 Query: 121 KATPHGEIEAAKAMGMSRLKMYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLVDI 180 P GE+EAA+A GM R +RRI LP A+ RALP + E ++ L++T L + +T+VD+ Sbjct: 167 AGVPQGELEAARAYGMGRWTTFRRIWLPRAVHRALPTLNGETVLQLKSTPLVATITVVDV 226 Query: 181 TGAARTVYSQYYLPFEAFITAGLFYLCLTFILVRLFKLAERR 222 V + +L +E + L YLCLT ILV F+ E R Sbjct: 227 YAVISKVRQETFLTYEPLLLLALIYLCLTGILVVAFRYFENR 268 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: 195 Number of extensions: 10 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: 274 Length adjustment: 24 Effective length of query: 208 Effective length of database: 250 Effective search space: 52000 Effective search space used: 52000 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 Apr 09 2024. 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