Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_029134157.1 A3GO_RS0115370 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000428045.1:WP_029134157.1 Length = 293 Score = 174 bits (441), Expect = 2e-48 Identities = 103/306 (33%), Positives = 173/306 (56%), Gaps = 16/306 (5%) Query: 5 FLYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMM 64 F LQ + G+T+GSTYAL+ +G+ ++Y ++NF+ GE MIG+ ++A+ + Sbjct: 2 FDQILQFLLTGITVGSTYALVGLGFAIIYNASDVVNFSQGEFVMIGA------MSAVALS 55 Query: 65 GIDTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSL 124 DTG L AA + A++I + G +++R A P R + + +I IG SIFL+ L Sbjct: 56 AGDTGLPLWAAA-LAAVLITTLVGMALQRFAIXPARGASVVTTIIITIGASIFLRGVALL 114 Query: 125 TEGSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLAL--TIFIRYSRMGR 182 G ALP G+ + T + +W++ A+L F ++ +G+ Sbjct: 115 VWGKDLFALPPFS------GNEPIXIGNATVLPQSLWVMGGAAVLVFGAQYFFTHTTLGK 168 Query: 183 ACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKA 242 A AC+ + A L+GIN ++ + + + AA+ A+AG+L+ + G M G+K Sbjct: 169 AILACSCNKTAAHLVGINVGVMLLVAYGLSAALGAMAGILVAPIT-FASYDTGVMLGLKG 227 Query: 243 FTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGR 302 F+AA+LGG+G+ GA+ GGL+LG+ E+LS+ +S+ YKD + F +L+LVL P+G+ G+ Sbjct: 228 FSAAILGGMGNPMGAVAGGLLLGLIESLSAGLISSGYKDAIGFIILLLVLFFRPSGLFGK 287 Query: 303 PEVEKV 308 VE+V Sbjct: 288 ASVERV 293 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: 260 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: 293 Length adjustment: 27 Effective length of query: 281 Effective length of database: 266 Effective search space: 74746 Effective search space used: 74746 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