Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::P0A9S7 (255 letters) >FitnessBrowser__Keio:18115 Length = 510 Score = 129 bits (324), Expect = 1e-34 Identities = 80/253 (31%), Positives = 141/253 (55%), Gaps = 10/253 (3%) Query: 1 MSQPLLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGG 60 M+ P +S+ G+ FG + A+ +VNL +YP EI +L+G NGAGK+T+ L+G ++PT G Sbjct: 1 MATPYISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKG 60 Query: 61 TILLRDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKT 120 TI + + L + A++G+ +Q + + E+TV+ENL + +H K G + Sbjct: 61 TITINNISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKK---ICG-VNI 116 Query: 121 PSFRRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEP 180 +R E RAA L R+GL + + +NL+ ++ LEIA+ ++ +++++DEP Sbjct: 117 IDWR----EMRVRAAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEP 172 Query: 181 AAGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQ 240 + L KE L ++ +LR T I+ I H + + I DR V+ G+ + +G Sbjct: 173 TSSLTNKEVDYLFLIMNQLRK-EGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSD 231 Query: 241 IRNNPDVIRAYLG 253 + +N D++R +G Sbjct: 232 V-SNDDIVRLMVG 243 Score = 64.3 bits (155), Expect = 5e-15 Identities = 49/214 (22%), Positives = 103/214 (48%), Gaps = 11/214 (5%) Query: 21 VNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLRDQHLEGLPGQQIARM 80 V +++ + EI+ G G+G+T + NCL G K GG I L + + + Sbjct: 279 VRDISFSVCRGEILGFAGLVGSGRTELMNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKK 338 Query: 81 GVVRTFQHVR---LFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRRAQSEALDRAATW 137 G+ + R F ++ +N+ +++ LK G + G + F + A Sbjct: 339 GMAYITESRRDNGFFPNFSIAQNMAISR--SLKDGGYKGAMGL--FHEVDEQRT--AENQ 392 Query: 138 LERIGLLEHA-NRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGLNPKETKELDELI 196 E + L H+ N+ + L+ G+Q+++ I++ + PE+++ DEP G++ E+ +++ Sbjct: 393 RELLALKCHSVNQNITELSGGNQQKVLISKWLCCCPEVIIFDEPTRGIDVGAKAEIYKVM 452 Query: 197 AELRNHHNTTILLIEHDMKLVMGISDRIYVVNQG 230 +L + IL++ ++ ++ + DRI V +G Sbjct: 453 RQLAD-DGKVILMVSSELPEIITVCDRIAVFCEG 485 Lambda K H 0.320 0.137 0.395 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: 277 Number of extensions: 15 Number of successful extensions: 4 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: 255 Length of database: 510 Length adjustment: 29 Effective length of query: 226 Effective length of database: 481 Effective search space: 108706 Effective search space used: 108706 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 (21.8 bits) S2: 49 (23.5 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