Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate BPHYT_RS31745 BPHYT_RS31745 ABC transporter ATP-binding protein
Query= TCDB::P74455 (372 letters) >FitnessBrowser__BFirm:BPHYT_RS31745 Length = 389 Score = 78.6 bits (192), Expect = 3e-19 Identities = 46/118 (38%), Positives = 64/118 (54%), Gaps = 17/118 (14%) Query: 5 YLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLLSLRGL-------- 56 Y + ++ A Y + ALGLN+ GFAGL++ G++AF +GAY LL+ L Sbjct: 47 YGVRVLDFAMLYVMLALGLNIVVGFAGLLDLGYIAFYAVGAYTAALLTSPHLAAHFEWIG 106 Query: 57 ---------PIPLAVLVGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANN 105 P + V M LA G+ +G TLRLR DYLAIVT+G E++R+ NN Sbjct: 107 HMWPSGFHAPYWFVMPVAMVLAAIAGICLGAPTLRLRGDYLAIVTLGFGEIVRIFMNN 164 Score = 67.8 bits (164), Expect = 5e-16 Identities = 54/188 (28%), Positives = 84/188 (44%), Gaps = 15/188 (7%) Query: 189 LTAYVPGVVSLYNYSGKAGLMLLALTLLALTY------AGLEFWV-----HSPWGRILKA 237 +T P V+ +N S + T + + Y + L WV HS GR A Sbjct: 178 ITGVAPVTVAGFNLSETHAFLGFQFTTVYMYYYVFVLCSLLVVWVCTRLQHSRIGRAWAA 237 Query: 238 IREDEEIPRALGKNVFWYKLQAFMGGGAIAGLAGALFAWQLTSIYPSNFDTLLTFNAWII 297 IREDE +A+G N KL AF G + GL+GA+FA + P +F + Sbjct: 238 IREDEIAAKAMGINTRNVKLLAFAMGASFGGLSGAMFAGFQGFVSPESFTLWESVTVLAC 297 Query: 298 VVLGGAGSNAGTVLGTIIFWAYDSLTRFLLP--QIAFLDQ--SQAGALRVMVIGLILMVL 353 VVLGG G G + G ++ + R + Q A +R ++ GL ++++ Sbjct: 298 VVLGGMGHIPGVIFGAVLLAILPEILRSTMTPLQNAIFGHVIVDTEVIRQLLYGLAMVII 357 Query: 354 MVWRPQGI 361 M+ RP+G+ Sbjct: 358 MLRRPEGL 365 Lambda K H 0.327 0.143 0.442 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: 305 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 372 Length of database: 389 Length adjustment: 30 Effective length of query: 342 Effective length of database: 359 Effective search space: 122778 Effective search space used: 122778 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 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