Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_013519967.1 ALIDE2_RS06405 high-affinity branched-chain amino acid ABC transporter permease LivH
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000204645.1:WP_013519967.1 Length = 308 Score = 360 bits (923), Expect = e-104 Identities = 177/311 (56%), Positives = 243/311 (78%), Gaps = 6/311 (1%) Query: 1 MSEQFLYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAA 60 MSE LQQ+FNG++LG+ YALIAIGYTMVYGIIGMINFAHGE+YMIG+Y + +AA Sbjct: 1 MSEFLPQLLQQLFNGLSLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIGAYAGLVTLAA 60 Query: 61 LMMMGIDTGW---LLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIF 117 + G +G +++A + A+++ YG+ +E+VAY+P+RN RL+ALISAIGMSIF Sbjct: 61 I---GTQSGLPVAVIIALMLLVAVLVTGVYGFVVEQVAYKPLRNGPRLVALISAIGMSIF 117 Query: 118 LQNYVSLTEGSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRY 177 LQN+V+L +G+RD+A+PSL G G F + + +I +VT + M+ALT++IR+ Sbjct: 118 LQNWVALGQGARDMAVPSLLPGALRFGDESGFEVFVPYTRVLIIVVTVVLMIALTLYIRH 177 Query: 178 SRMGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFM 237 SRMGRA RAC++D+ MA LLGI+ +RVI+ TF++GA +AAV GVL+ G +NP+IGF+ Sbjct: 178 SRMGRASRACSQDMHMAGLLGIDVNRVISFTFILGAVLAAVGGVLIALAVGKLNPFIGFI 237 Query: 238 AGMKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPT 297 G+KAFTAAVLGGIGSIPGAM+GG++LG+AE ++AY+S+EYKD+V+F LL+L+LL PT Sbjct: 238 VGVKAFTAAVLGGIGSIPGAMLGGVLLGVAETFAAAYISSEYKDIVAFGLLVLILLFRPT 297 Query: 298 GILGRPEVEKV 308 G+LG+PEVEKV Sbjct: 298 GLLGKPEVEKV 308 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: 346 Number of extensions: 10 Number of successful extensions: 2 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: 308 Length adjustment: 27 Effective length of query: 281 Effective length of database: 281 Effective search space: 78961 Effective search space used: 78961 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