Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_012400999.1 BPHY_RS08190 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000020045.1:WP_012400999.1 Length = 316 Score = 110 bits (274), Expect = 6e-29 Identities = 83/272 (30%), Positives = 125/272 (45%), Gaps = 25/272 (9%) Query: 8 FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67 F+ NGV+ G +++ G T+++ ++G++NFAH YM+G+YV F + A Sbjct: 4 FVIDALNGVSYGLLLFMLSAGLTLIFSMLGVLNFAHASFYMLGAYVGFSVAA-------- 55 Query: 68 TGWLLVAAGFVGAIVIA----SAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVS 123 AGF A+VIA G ++ER R VR L L+ G + + V Sbjct: 56 ------RAGFWWALVIAPLAVGLMGAALERWLLRRVRPHGHLAELLLTFGAAYLIGEGVK 109 Query: 124 LTEG--SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMG 181 L G + VA+P+ G + FS M AV V LAMLA +R S+ G Sbjct: 110 LVWGLQALSVAVPAALEGPLFEVYGLAFSRYRGFMMAV--AVAMLAMLAAV--LRVSKTG 165 Query: 182 RACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMK 241 RA + LG + V F G A AA+AGV+ + V+ P + G Sbjct: 166 LIVRAALTHPQAVEALGHDVPSVFTWVFAAGTAFAALAGVIGAPLF-VVEPAMAESVGSV 224 Query: 242 AFTAAVLGGIGSIPGAMIGGLILGIAEALSSA 273 F V+GG+GS+ GA+ L++G + + A Sbjct: 225 VFVVVVIGGLGSLGGALAASLVIGCLQTFAVA 256 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: 248 Number of extensions: 13 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: 316 Length adjustment: 27 Effective length of query: 281 Effective length of database: 289 Effective search space: 81209 Effective search space used: 81209 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