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_093395264.1 BM091_RS09340 ABC transporter ATP-binding protein
Query= TCDB::P0A9S7 (255 letters) >NCBI__GCF_900114975.1:WP_093395264.1 Length = 242 Score = 206 bits (524), Expect = 4e-58 Identities = 109/254 (42%), Positives = 164/254 (64%), Gaps = 16/254 (6%) Query: 1 MSQPLLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGG 60 M+ P+L V + M FGGL AV+ V + P EIV++IGPNGAGKTT+FN ++G+ KPT G Sbjct: 1 MNSPVLRVESVTMAFGGLRAVDGVTFNVMPGEIVAIIGPNGAGKTTIFNVISGYLKPTRG 60 Query: 61 TILLRDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKT 120 + +D+ + G P ++A+MG+ RTFQ V+ F ++V+EN++V L++ Sbjct: 61 KVFFQDRDITGKPPYELAQMGIGRTFQIVKPFSSLSVLENVMV-----------GALIR- 108 Query: 121 PSFRRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEP 180 R++++A A L+ IGL + A+ AS L ++RLEIA+ + +P +L+LDE Sbjct: 109 ---HRSKADAESHAGEILKFIGLADKADTAASGLTLAWRKRLEIAKALSLEPSLLLLDEV 165 Query: 181 AAGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQ 240 AGLNP E E ELI ++R+ T+LLIEH+M++VM +S R+ V+N G +A G+P + Sbjct: 166 MAGLNPAEVAETVELIKQIRD-RGVTVLLIEHNMRVVMSLSSRVIVLNYGEKIAEGSPAE 224 Query: 241 IRNNPDVIRAYLGE 254 + NP VIRAYLGE Sbjct: 225 VAKNPVVIRAYLGE 238 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: 152 Number of extensions: 5 Number of successful extensions: 3 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: 242 Length adjustment: 24 Effective length of query: 231 Effective length of database: 218 Effective search space: 50358 Effective search space used: 50358 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: 46 (22.3 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