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 Ac3H11_1693 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= TCDB::Q7A2H0 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1693 Length = 260 Score = 195 bits (496), Expect = 7e-55 Identities = 103/252 (40%), Positives = 157/252 (62%), Gaps = 7/252 (2%) Query: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 +L +G+ K FGG++A+ + I + +G + GLIGPNGAGKTT FN+++ PD G Sbjct: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 Query: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130 G+P + H++A+ G+ RTFQ R + ++ LEN+++ +TG + + + Sbjct: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190 EE + ++A LL+ VG+ K A A LS G ++ LE+ RAL T+P+LI LDEPAAG+ Sbjct: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188 Query: 191 NPR---LIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEI 247 N + ++ DRI R D T L+IEH++ ++M LCDRV VL G+ +A+G PAE+ Sbjct: 189 NATEKVQLRELIDRI----RNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244 Query: 248 QTNSQVLEAYLG 259 Q N +V+EAYLG Sbjct: 245 QKNEKVIEAYLG 256 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: 158 Number of extensions: 5 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: 260 Length of database: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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: 47 (22.7 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