Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate 8500845 DvMF_1583 ABC transporter related (RefSeq)
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__Miya:8500845 Length = 240 Score = 195 bits (496), Expect = 6e-55 Identities = 109/252 (43%), Positives = 155/252 (61%), Gaps = 16/252 (6%) Query: 9 LPLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRV 68 + +L L FGG+ A+ + +V QG I LIGPNGAGKTTLFN ++ F P +G+V Sbjct: 1 MSMLEIRKLSMFFGGLAALHDVNFDVRQGEILALIGPNGAGKTTLFNCVNGFYTPSEGQV 60 Query: 69 IFDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQV 128 +F G+PI L+PH++ Q G+ RTFQV + LSR+SV +N+L +A + Sbjct: 61 LFKGQPISGLKPHKVCQMGIARTFQVVKPLSRMSVFDNVLASAFLRN------------- 107 Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188 K Q+ A +L GL + + GL G+RK LE+ RAL T P+ +LLDE A Sbjct: 108 --PTRKGAQDVADEVLHFTGLWDDRDQLSKGLPLGKRKRLEIARALATQPEFLLLDESFA 165 Query: 189 GVNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQ 248 G+NP +D D I+ +Q G+T +IIEH+M VIM++ DR+ VL GQ +A+GTPA+I Sbjct: 166 GLNPAELDVSID-IIRGIKQQGITVMIIEHHMKVIMAISDRIVVLNFGQKIAEGTPAQIS 224 Query: 249 TNSQVLEAYLGK 260 + QV+EAYLG+ Sbjct: 225 ADRQVVEAYLGE 236 Lambda K H 0.319 0.136 0.391 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: 161 Number of extensions: 8 Number of successful extensions: 3 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: 260 Length of database: 240 Length adjustment: 24 Effective length of query: 236 Effective length of database: 216 Effective search space: 50976 Effective search space used: 50976 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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