Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_002720083.1 RSPH17029_RS07945 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000015985.1:WP_002720083.1 Length = 336 Score = 132 bits (331), Expect = 1e-35 Identities = 95/316 (30%), Positives = 156/316 (49%), Gaps = 34/316 (10%) Query: 15 GVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDTGWLLVA 74 G+ G+ AL A+G T++YGI+ NFAHG+ G+ V+ + L G+ G L A Sbjct: 18 GLAYGAQLALGALGVTLIYGILRFSNFAHGDTMAFGTMVTILGTWGLQAAGVTGGPLPTA 77 Query: 75 A-GFVGAIVIASAYGWSIERVAYRPVRNSKRL--IALISAIGMSIFLQNYVSLTEGSRDV 131 I + +A + +R YR R K I +I ++G+ + V G ++ Sbjct: 78 LLALPLGIAVTAALVLATDRAVYRFYRRQKAAPTILVIVSLGVMFVMNGIVRFIIGVEEI 137 Query: 132 A-------LPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRAC 184 L + + + + G SE + I T QA+ + + + AL F+ +R G++ Sbjct: 138 GFADGERFLITAGDFRKMTGLSEGLA--IKTTQAITVVTALIVVAALFWFLNRTRTGKSM 195 Query: 185 RACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFT 244 RA +++ +A L GIN +RV+A+T+++ AA+A AGVL G + F + F Sbjct: 196 RAFSDNEDLALLSGINPERVVAVTWILAAALATTAGVLYG-LDKSFKAFTYFQLLLPIFA 254 Query: 245 AAVLGGIGSIPGAMIGGLILGIAEALSS---------------------AYLSTEYKDVV 283 AA++GG+GS GA+ GG ++ +E + +ST+YK V Sbjct: 255 AAIVGGLGSPLGAIAGGFVIAFSEVTVTYAWKKVATYLLPDALAPDGLVQLMSTDYKFAV 314 Query: 284 SFALLILVLLVMPTGI 299 SF +LI+VLL MPTG+ Sbjct: 315 SFTILIIVLLFMPTGL 330 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: 247 Number of extensions: 11 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: 336 Length adjustment: 28 Effective length of query: 280 Effective length of database: 308 Effective search space: 86240 Effective search space used: 86240 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 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