Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate GFF136 Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= TCDB::Q52814 (384 letters) >FitnessBrowser__psRCH2:GFF136 Length = 229 Score = 82.8 bits (203), Expect = 9e-21 Identities = 64/213 (30%), Positives = 105/213 (49%), Gaps = 15/213 (7%) Query: 174 GLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPLITVLFMASVM 233 G +TL L V + L V + L + R SR +R L +I RG PL+ LF+ Sbjct: 16 GAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPYGYIFFFRGTPLLVQLFLVYYG 75 Query: 234 LPLFLPTGWNV------DKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADSLGLG 287 + F + D A+I +++ T+AY+AE+IRG +Q +P G+ E A +LG+ Sbjct: 76 MAQFDVVRQSALWPYLRDPYWCAIITMTLHTAAYIAEIIRGAIQNVPHGEIEAARALGMS 135 Query: 288 YWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLLGIVKLNFSDANWASAV 347 Q II+P+A ++ +P+ N I K ++L + I + +L G+ A +A Sbjct: 136 RSQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLELTGM-------ARKIAAR 188 Query: 348 TPITGLIF--AGFIFWLFCFGMSRYSGFMERHL 378 T + +F AG I+ L F + + +ER L Sbjct: 189 TYLHEEMFLTAGLIYLLIAFILMQGFKLLERWL 221 Lambda K H 0.330 0.145 0.469 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: 257 Number of extensions: 16 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: 384 Length of database: 229 Length adjustment: 26 Effective length of query: 358 Effective length of database: 203 Effective search space: 72674 Effective search space used: 72674 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 (21.8 bits) S2: 48 (23.1 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