Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_058929075.1 AU252_RS00670 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_001484605.1:WP_058929075.1 Length = 291 Score = 137 bits (344), Expect = 4e-37 Identities = 88/291 (30%), Positives = 148/291 (50%), Gaps = 9/291 (3%) Query: 12 MFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDTGWL 71 +F G+ LG+ Y L+A G +++YG++G++NFAHG +G++ + I G D W Sbjct: 8 LFTGLGLGALYFLVAAGLSLIYGLMGVLNFAHGAFLTLGAFTGWEIARRT---GSDNWWT 64 Query: 72 LVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEGSRDV 131 + + VGA+ + + E V R + + + ++ +G+S+ V+L +G Sbjct: 65 FLLSLLVGAVA-GAVFAAFTEFVLIRRLYQ-RHIEQVLITVGLSLAA---VALFDGIWGT 119 Query: 132 ALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRACAEDL 191 + W +E A I + + I L +LAL F++ +R G RA E+ Sbjct: 120 DPVFIQGPAWFKETTEILGARIPNDRFICIIAAVLVLLALVFFLKNTRYGMIIRAGVENR 179 Query: 192 KMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAAVLGGI 251 M + LGI+ + L F IG A A + GVL ++G ++P +G + AF V+GG+ Sbjct: 180 SMVTALGIDVRKAFTLVFTIGGAAAGLGGVLASHYFGYVSPLLGGSLLIFAFIVTVIGGL 239 Query: 252 GSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGR 302 GS+ GA I + + + + ++ YL VV A L LVLL P+G+LGR Sbjct: 240 GSLTGAAIAAVAVAVLQQFANFYLGGTGDFVVVLA-LALVLLFRPSGLLGR 289 Lambda K H 0.328 0.141 0.410 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: 225 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: 308 Length of database: 291 Length adjustment: 27 Effective length of query: 281 Effective length of database: 264 Effective search space: 74184 Effective search space used: 74184 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 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