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 Dsui_0842 Dsui_0842 ABC-type branched-chain amino acid transport systems, ATPase component
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__PS:Dsui_0842 Length = 593 Score = 190 bits (483), Expect = 5e-53 Identities = 107/249 (42%), Positives = 156/249 (62%), Gaps = 3/249 (1%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 LL A G+ K FGG+ A ++ + V G + LIGPNGAGK+T+FN +S P +GR+ F Sbjct: 345 LLQAEGVTKRFGGLVANKDMALTVQAGEVMALIGPNGAGKSTMFNCISGVNPPSEGRISF 404 Query: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130 G+P+ L+ IA+ G+ RTFQ R LS ++VLEN+ + A + N+ L+ + Sbjct: 405 LGQPVAGLEARDIARLGLSRTFQHVRLLSGMTVLENVAIGAHLRGRHNYLAAGLRLERA- 463 Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190 EE +L +A +E VGLA+ ++ AG L+ G+++++E+ RAL +P L+LLDEPAAG+ Sbjct: 464 -EEARLLAEAARQIERVGLAEHMFDAAGSLALGKQRIIEIARALAADPCLLLLDEPAAGL 522 Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250 L +L R +GM L++EH+MD +M L DRV V+ G+ LA+G P EIQ N Sbjct: 523 R-YLEKQALAELLRKLRGEGMGILLVEHDMDFVMGLADRVVVMEFGEKLAEGLPEEIQKN 581 Query: 251 SQVLEAYLG 259 VLEAYLG Sbjct: 582 PAVLEAYLG 590 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: 353 Number of extensions: 19 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: 593 Length adjustment: 30 Effective length of query: 230 Effective length of database: 563 Effective search space: 129490 Effective search space used: 129490 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: 50 (23.9 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