Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate WP_011385249.1 AMB_RS14460 branched-chain amino acid ABC transporter permease
Query= SwissProt::P22729 (425 letters) >NCBI__GCF_000009985.1:WP_011385249.1 Length = 329 Score = 145 bits (365), Expect = 2e-39 Identities = 104/322 (32%), Positives = 161/322 (50%), Gaps = 28/322 (8%) Query: 91 LFLVALLVLAVAW-PFMVSRGTVDIA---TLTMIYIILGLGLNVVVGLSGLLVLGYGGFY 146 L L+A L L AW P S + T MI IL + L+++VG++GL+ LG+ F+ Sbjct: 13 LVLLAALALFPAWGPLAFSAKYAFLLQKLTGIMILAILAMSLDLLVGVAGLVSLGHAAFF 72 Query: 147 AIGAYTFALLN-HYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIV 205 +G Y ALL+ Y W LP A AA ++GF +R G Y +VTL FG++ Sbjct: 73 GLGGYMLALLSPQYEAANAWVVLPAAMGAVAAVSAVVGFLAIRTAGIYFIMVTLAFGQM- 131 Query: 206 RILLLNNTEITGGPNGISQIPKPTL--FGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIF 263 N++++ GG +G KP + FG+ + + F Sbjct: 132 GYYFFNDSKLAGGSDGAYIYVKPNVEAFGITL-----------------VNLESKQAFFF 174 Query: 264 LYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFA 323 + L L+ V L L V+ L P GR A+ +E R LG +P KL AF ++ A A Sbjct: 175 VVLGCLVAVYLWLRVV---LASPFGRVLAAIGVNEGRVRGLGFNPMVYKLVAFALAGALA 231 Query: 324 GFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFN 383 G AG L A + GFVSP + +S VL +V+LGGMG+ F +L A +L ++ + Sbjct: 232 GLAGFLAATQYGFVSPAMLGWHQSGHVLVMVILGGMGTLFGPVLGAFILELAHFGLEAVT 291 Query: 384 EYSMLMLGGLMVLMMIWRPQGL 405 E+ +L +G L++ +++ P+G+ Sbjct: 292 EHWLLPMGVLVITIVLALPKGV 313 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: 341 Number of extensions: 14 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: 425 Length of database: 329 Length adjustment: 30 Effective length of query: 395 Effective length of database: 299 Effective search space: 118105 Effective search space used: 118105 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: 50 (23.9 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