Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate WP_011842444.1 RSPH17029_RS17975 branched-chain amino acid ABC transporter permease
Query= SwissProt::P22729 (425 letters) >NCBI__GCF_000015985.1:WP_011842444.1 Length = 331 Score = 179 bits (453), Expect = 1e-49 Identities = 115/328 (35%), Positives = 172/328 (52%), Gaps = 24/328 (7%) Query: 94 VALLVLAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTF 153 VAL ++AV + + + TL I+ L + +V++G +G L L +G + +GAY Sbjct: 14 VALFLVAVTLALRLDDYLLYVVTLGAIFATLAVSFDVLLGYTGYLSLAHGALFGVGAYAC 73 Query: 154 ALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNT 213 +L ++G FW LP AGL+A AAG ++ R RG Y A++TLG G I L L Sbjct: 74 GILTAHHGWPFWAALPAAGLVAGAAGAVIALLAFRTRGLYFAVLTLGIGLIGHQLFLVLA 133 Query: 214 EITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVALLLVV 273 +TGG G IP P G + GW+ L+AL L++ Sbjct: 134 GLTGGVGGFVGIPSP---GRPDWVPLDQNGWNA-------------------LLALALLL 171 Query: 274 LSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAAR 333 + +R LG A A+RED ++LG+ + +L AF SA F GFAG LFAA Sbjct: 172 ATFLAAQLFVRSRLGAACLAVREDLTLAQALGIRVGQARLAAFVFSAIFTGFAGALFAAI 231 Query: 334 QGFVSPESFTFAESAF-VLAIVVLGGMGSQFAVILAAILLVVSRELMRDFNEYSMLMLGG 392 FV+PESFT + F ++A+VV+GGMG+ + IL A LL E +R + YS++ G Sbjct: 232 SNFVAPESFTVLGAGFQLVALVVVGGMGTLWGPILGAALLTALPEALRVASGYSLIAYGV 291 Query: 393 LMVLMMIWRPQGLLPMTRPQL-KLKNGA 419 L+++ +I+ P+GL + L +L+ GA Sbjct: 292 LLLVFVIFAPRGLASLATDGLARLRTGA 319 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: 279 Number of extensions: 12 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: 331 Length adjustment: 30 Effective length of query: 395 Effective length of database: 301 Effective search space: 118895 Effective search space used: 118895 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 Apr 10 2024. 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