Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate WP_083439157.1 AKL27_RS18995 ABC transporter ATP-binding protein
Query= SwissProt::P22729 (425 letters) >NCBI__GCF_001189915.1:WP_083439157.1 Length = 613 Score = 148 bits (374), Expect = 4e-40 Identities = 99/326 (30%), Positives = 159/326 (48%), Gaps = 28/326 (8%) Query: 93 LVALLVLAVAWPFMVSRGTVD----IATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAI 148 L+ +LV+A + + + D I + +Y + G+NV+VG +G LG G +A Sbjct: 31 LLGVLVIAAIAAVLAALASNDYYLRILFMICVYFMCATGMNVLVGFAGQKSLGQAGLFAA 90 Query: 149 GAYTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRIL 208 GAYT A+L + W + AG++A G L+ P LR++G YLA+VTL FG ++ + Sbjct: 91 GAYTAAILTVNFNWSPWLAMAAAGVVAGVCGVLIALPSLRVKGPYLAMVTLAFGTVIEKI 150 Query: 209 LLNNTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVA 268 + +I GG GI I KP G P V +++ Sbjct: 151 VTEWDDIFGGAAGIYGI-KPLSLG----------------------EAPLSNVQWVWFGI 187 Query: 269 LLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGT 328 L V L + N +LR LGR+ +L+ DEIA S+G+ R K+ AF I+A G AG Sbjct: 188 ALCAVTHLLLRN-VLRGRLGRSLLSLQADEIAAASVGIKVYRAKVLAFVIAAVTCGIAGA 246 Query: 329 LFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSML 388 + A + +++ + F S F+L +V+ GG GS +L A+LL V ++ + Sbjct: 247 MVAQQNQYINSDFINFNLSVFILLLVLFGGAGSTLGPLLGAVLLTVIDAMLSRWPSAQHF 306 Query: 389 MLGGLMVLMMIWRPQGLLPMTRPQLK 414 + G L++ + PQG+ + P L+ Sbjct: 307 VYGALLLFALYAMPQGVAGLLAPLLR 332 Lambda K H 0.330 0.145 0.436 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: 420 Number of extensions: 22 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: 425 Length of database: 613 Length adjustment: 34 Effective length of query: 391 Effective length of database: 579 Effective search space: 226389 Effective search space used: 226389 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 (21.8 bits) S2: 52 (24.6 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