Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate WP_013451018.1 CALNI_RS04475 branched-chain amino acid ABC transporter permease
Query= SwissProt::P22729 (425 letters) >NCBI__GCF_000183405.1:WP_013451018.1 Length = 313 Score = 165 bits (417), Expect = 2e-45 Identities = 101/320 (31%), Positives = 168/320 (52%), Gaps = 25/320 (7%) Query: 88 KQKLFLVALLVLAVA--WPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGF 145 K LF ++ L +A+ + F+ ++ I MI I LN++ G +G++ LG F Sbjct: 3 KLNLFYLSFLAIAIVLFYIFVDNQFYKSILIYVMINAINASMLNILFGYTGVISLGQAAF 62 Query: 146 YAIGAYTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIV 205 Y IGAYT +L ++G + I ++A+ F++G+P L+L G YLA+ TLGFG I+ Sbjct: 63 YGIGAYTTGILTVHFGYNPLLTILIGIVIASFVAFVVGYPTLKLHGHYLAMATLGFGMIM 122 Query: 206 RILLLNNTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLY 265 IL ++ TGGP+G+ IPK +LFG D F F IF + Sbjct: 123 YILFNEFSDYTGGPSGLVGIPKLSLFGFSLDNE------DKFYVFIS---------IFFF 167 Query: 266 LVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGF 325 + ++LL + ++ L+ ++E E A +S G++ R+KL F + AA Sbjct: 168 IFSILLELFDKSYMSYKLKF--------IKESEFASKSFGVNVSRVKLIVFVVVAAITSL 219 Query: 326 AGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEY 385 G++FA GF+SP SF S + + +GG+GS L A +L EL+ +F +Y Sbjct: 220 TGSVFALYSGFISPISFNLKYSIDIFIMATVGGLGSIVGGTLGATMLTAFPELITNFEDY 279 Query: 386 SMLMLGGLMVLMMIWRPQGL 405 M++ G L+++++++ PQG+ Sbjct: 280 EMIVYGILLLIIIMFFPQGI 299 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: 269 Number of extensions: 9 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: 313 Length adjustment: 29 Effective length of query: 396 Effective length of database: 284 Effective search space: 112464 Effective search space used: 112464 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: 49 (23.5 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