Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate WP_028316571.1 G491_RS0125670 ABC transporter ATP-binding protein
Query= TCDB::P0A9S7 (255 letters) >NCBI__GCF_000429905.1:WP_028316571.1 Length = 256 Score = 223 bits (568), Expect = 3e-63 Identities = 115/251 (45%), Positives = 163/251 (64%) Query: 4 PLLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTIL 63 PLL + L +RFGGL AV N NL + P +I LIGPNGAGKTTVFN +TG PT G +L Sbjct: 2 PLLEIKDLSIRFGGLQAVKNYNLTMNPGDIRGLIGPNGAGKTTVFNMMTGILTPTEGQVL 61 Query: 64 LRDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSF 123 L + +EG QIA G+ RTFQ++ L+R MTV+E++ +A + ++ GLF Sbjct: 62 LNNWSIEGFQPYQIAARGIGRTFQNLCLWRHMTVLEHVKMACYSKITYGLFGAFFGGARR 121 Query: 124 RRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAG 183 +R +++ ++A L +GL + A++ NL YG QRR+EIAR + T P+IL+LDEP AG Sbjct: 122 KREETQMTNKAMDLLALVGLDQFADQLVGNLPYGAQRRMEIARALATDPKILLLDEPTAG 181 Query: 184 LNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIRN 243 +NP+E ++ E+I + + ILLIEH +K VM + +RI + G +A G PE+IRN Sbjct: 182 MNPEELDQIMEIIRLVHGEYKMAILLIEHRLKFVMELCERIQALVFGEVIAEGEPEEIRN 241 Query: 244 NPDVIRAYLGE 254 +P VI AYLG+ Sbjct: 242 HPQVIEAYLGK 252 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: 214 Number of extensions: 13 Number of successful extensions: 1 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: 255 Length of database: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 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: 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