Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_011156794.1 TX73_RS06280 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000195775.1:WP_011156794.1 Length = 290 Score = 175 bits (443), Expect = 1e-48 Identities = 103/303 (33%), Positives = 174/303 (57%), Gaps = 14/303 (4%) Query: 6 LYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMG 65 L F+QQ+ G+ LG Y LIA+G+ ++Y ++NFA GE+ M+G+++SF IA L + Sbjct: 2 LDFVQQVIGGIALGCVYGLIALGFVLIYKATEVVNFAQGEIMMLGAFLSFTFIATLGL-- 59 Query: 66 IDTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLT 125 W GF+ +V + G ++ER+ RP+ + +++ IG+ + +++ V + Sbjct: 60 --NYWF----GFLLCVVSMAVLGAAMERLVVRPILGYPQFSIVMATIGLGLVIRSLVGII 113 Query: 126 EGSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACR 185 G+ D+ + + F G G + ++ I + T L L F R++++G A + Sbjct: 114 WGTDDLRIETPFTG----GVIQLGGLVLSQDSLSIIVATALLCAVLYAFFRFTKIGIAMQ 169 Query: 186 ACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTA 245 A ++++ A +GI R+ +L + + A +A AGVLL I+ +GF+ G+KAF A Sbjct: 170 ATSQNMLAAYYMGIPVKRMFSLIWSLSAIVACCAGVLLAPIT-FIHANLGFL-GIKAFPA 227 Query: 246 AVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEV 305 AVLGG GSIPGA+ GG+ +GI E+LS YL +KDV ++ +L+ VLL P G+ G + Sbjct: 228 AVLGGFGSIPGALAGGITIGIVESLSGFYLPEGFKDVAAYIVLLAVLLWRPQGLFGSNAL 287 Query: 306 EKV 308 +KV Sbjct: 288 KKV 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: 249 Number of extensions: 16 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