Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_028998315.1 H537_RS0113285 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000430725.1:WP_028998315.1 Length = 290 Score = 179 bits (453), Expect = 9e-50 Identities = 109/300 (36%), Positives = 167/300 (55%), Gaps = 14/300 (4%) Query: 9 LQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDT 68 +Q +F+G+T+G+ YAL A+G+T++Y G+INFA G+ M+G ++ ++ A M G+ Sbjct: 5 MQFVFSGLTIGAIYALAALGFTLIYNASGVINFAQGDFLMLGGMIAAALLGANMPYGVAI 64 Query: 69 GWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEGS 128 + VG I+ Y W+I RP + + +I IG SIF+Q V + G Sbjct: 65 VLSVACTVLVGVIL----YRWAI-----RPAGEASAVSLIIVTIGASIFIQGVVQVVLGK 115 Query: 129 RDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRACA 188 LP+ F+G + + A + + V L ++A +F R + G+A A A Sbjct: 116 NQHTLPA-FSGDEAL---QVLGAYVLPQSLWMCGVAALLVVACVVFFRRTLSGKAMLAVA 171 Query: 189 EDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAAVL 248 + A +GI T R++ L+F + A + AVAGV+ + IG M GMK F AA L Sbjct: 172 ANRLAARAVGIPTTRILQLSFGLSALLGAVAGVVAAPITTTVYD-IGLMLGMKGFVAATL 230 Query: 249 GGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVEKV 308 GG+GS GA++GGLI+G+ EAL + Y+S+ YKD V F L+I+VLL MP G+ G E+V Sbjct: 231 GGLGSPLGAVVGGLIVGLLEALIAGYVSSAYKDAVPFVLIIVVLLAMPHGLFGARVTERV 290 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: 252 Number of extensions: 10 Number of successful extensions: 4 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: 290 Length adjustment: 27 Effective length of query: 281 Effective length of database: 263 Effective search space: 73903 Effective search space used: 73903 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 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