Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_197539624.1 SUTH_RS00445 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000828635.1:WP_197539624.1 Length = 296 Score = 165 bits (417), Expect = 1e-45 Identities = 99/307 (32%), Positives = 170/307 (55%), Gaps = 16/307 (5%) Query: 6 LYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMG 65 L LQ + +G +G YALIA+G+ ++Y +NFA G++ MIG ++ + A+ + G Sbjct: 2 LQLLQLIVSGAAIGCIYALIALGFVLIYKATETVNFAQGDLMMIGGFIG---LTAMTVAG 58 Query: 66 IDTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLT 125 + A F+ IV + +G ER+ RP+ ++ IG+ + V++ Sbjct: 59 LP-----FALAFLLTIVAMALFGMGTERLVLRPLLGQPAFTVVMMTIGLGYLARGLVTMI 113 Query: 126 E--GSRDVALPSLFNGQ--WVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMG 181 G+ LP + + W+ G S+ + ++ V +A+L L F RY+R+G Sbjct: 114 PYWGTETHTLPVPYKDEVIWLGGEGTGLVVSVEHLVIILATVALVALLYL--FFRYTRLG 171 Query: 182 RACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMK 241 A +A +++ A +GI RV L + + AA+ VAG+LL ++ +GF+ G+K Sbjct: 172 IAMQATSQNQLAAFYMGIPVRRVNMLIWGLSAAICGVAGLLLAPIT-FVHANMGFV-GLK 229 Query: 242 AFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILG 301 AF AAV+GG GSIPGA++GGL++GI E+LS YL +KD+ ++ +++++L+V P G+ G Sbjct: 230 AFPAAVVGGFGSIPGALVGGLVIGIVESLSGFYLPEGFKDIAAYVVVLIMLVVKPNGLFG 289 Query: 302 RPEVEKV 308 +KV Sbjct: 290 DNLTKKV 296 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: 226 Number of extensions: 13 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: 296 Length adjustment: 27 Effective length of query: 281 Effective length of database: 269 Effective search space: 75589 Effective search space used: 75589 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