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 WP_073040798.1 BUB04_RS14480 ABC transporter ATP-binding protein
Query= TCDB::Q7A2H0 (260 letters) >NCBI__GCF_900129305.1:WP_073040798.1 Length = 264 Score = 194 bits (492), Expect = 2e-54 Identities = 99/239 (41%), Positives = 155/239 (64%), Gaps = 1/239 (0%) Query: 21 FGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQLQP 80 FGG+ A++ R +V +G + +IGPNGAGKTTL N +S + P +GR+ F G +++ P Sbjct: 11 FGGVTALKGIRYQVPRGIVQSIIGPNGAGKTTLLNCISGVLHPTEGRISFLGRRVEREPP 70 Query: 81 HQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEEKQLQEQA 140 H+IA GM RTFQ ++SVLEN+++ +T FW L+ + + +EE + A Sbjct: 71 HRIAALGMSRTFQHVALFPQMSVLENVMVGRHVRTRSGFWAAGLRTRSMRREEAAIGRDA 130 Query: 141 MFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGVNPRLIDDICD 200 L+ VGLA A+ AG L G++K+LE+ RAL T+P L+LLDEPA G+N R +++ Sbjct: 131 RAWLDFVGLADAAHLPAGALPLGKQKILEIARALATDPALLLLDEPAGGLNTRETEEL-G 189 Query: 201 RILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNSQVLEAYLG 259 ++ ++ G T +++EH+M+++M++ DR+ VL GQ LA G P EI+ N +V++AYLG Sbjct: 190 ELIGRIKERGTTVILVEHDMNLVMTISDRILVLYYGQPLASGVPDEIKENPEVIQAYLG 248 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: 153 Number of extensions: 6 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: 264 Length adjustment: 25 Effective length of query: 235 Effective length of database: 239 Effective search space: 56165 Effective search space used: 56165 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 24 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