Align AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate GFF3834 PGA1_262p02380 putative histidine transport system permease protein HisM
Query= TCDB::O50183 (232 letters) >FitnessBrowser__Phaeo:GFF3834 Length = 258 Score = 154 bits (388), Expect = 2e-42 Identities = 83/225 (36%), Positives = 129/225 (57%), Gaps = 8/225 (3%) Query: 6 SVIWDSLPLY----FDGLLVTLKLLSISLLIGLLLAVPLALMRVSKQPLVNFPAWLYTYV 61 S+ WD +P Y +GL T+ +L ++ ++G LAVPL L + ++ PA ++ V Sbjct: 29 SLRWDWIPTYAPLALEGLWTTIWILVVTSILGFALAVPLGLAQAVGPWYLSTPARIFCTV 88 Query: 62 IRGTPMLVQLFLIYYGLA----QFDAVRESALWPWLSNASFCACLAFAINTSAYTAEILA 117 IRGTP+L+Q++L+YYGL QF +R S LWP+L A A LA ++ + Y E++ Sbjct: 89 IRGTPLLLQIWLLYYGLGSLFPQFPWIRSSELWPYLRQAWPYAVLALTLSYAGYEGEVMR 148 Query: 118 GSLKATPHGEIEAAKAMGMSRLKMYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTL 177 G+ G++EAAKA GM RL M+RRI LP A+R LP E I+ L+ T L + +T+ Sbjct: 149 GAFSGVAKGQLEAAKAYGMPRLTMFRRIWLPQAVRNVLPTLGGETILQLKATPLVATITV 208 Query: 178 VDITGAARTVYSQYYLPFEAFITAGLFYLCLTFILVRLFKLAERR 222 +DI + V S ++ +E + L Y+ + ++ FK E R Sbjct: 209 LDIYAVSSRVRSDTFIVYEPLLLLALVYMAIAGVITLAFKRFEDR 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: 187 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: 258 Length adjustment: 24 Effective length of query: 208 Effective length of database: 234 Effective search space: 48672 Effective search space used: 48672 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