Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit
Query= uniprot:B2TBJ7 (240 letters) >NCBI__GCF_900156495.1:WP_083710231.1 Length = 589 Score = 96.7 bits (239), Expect = 9e-25 Identities = 61/195 (31%), Positives = 106/195 (54%), Gaps = 14/195 (7%) Query: 25 TVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLVIYLFYFGGSTL 84 T+ L++ + +G + G ++A A +SR R LR IYT +FRG+P ++VI + G + Sbjct: 366 TLILSVVSGVLGTILGMVLAVAGISRSRWLRWPARIYTDIFRGLPAVVVILVVGLGIGPV 425 Query: 85 VTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRGELEAARSIGMPT 144 V ++ G P+ +GA+A+ +++ AY E++RS + +V G+LEA+R+IG Sbjct: 426 VKNL---------TGNNPYWLGAVALALLAAAYIGEIFRSGIQSVDDGQLEASRAIGFSY 476 Query: 145 LTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGL----AELLRTSQVAAGSTHQY 200 R +++PQ +R LP + N + +KDS+L+ GL EL + T Sbjct: 477 RQSMRLVVVPQGVRRVLPALMNQFISLIKDSSLVYFLGLLASQRELFAVGRDLNAQTGN- 535 Query: 201 FTFFVVGGALYLIMT 215 + V G +YL++T Sbjct: 536 LSPLVAAGLIYLVLT 550 Lambda K H 0.327 0.141 0.403 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: 209 Number of extensions: 7 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: 240 Length of database: 589 Length adjustment: 30 Effective length of query: 210 Effective length of database: 559 Effective search space: 117390 Effective search space used: 117390 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 (21.7 bits) S2: 50 (23.9 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