Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_011384432.1 AMB_RS10245 branched-chain amino acid ABC transporter permease
Query= ecocyc::LIVH-MONOMER (308 letters) >NCBI__GCF_000009985.1:WP_011384432.1 Length = 289 Score = 141 bits (355), Expect = 2e-38 Identities = 88/303 (29%), Positives = 161/303 (53%), Gaps = 27/303 (8%) Query: 7 YFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI 66 +F+ + G+ G Y L+A+G ++++G++ ++NFAHG++ ++ Y +F++ L + + Sbjct: 5 FFVNVISAGLLTGLVYGLMALGLSVIFGVMRVVNFAHGDMMVVAMYAAFLLFTKLGIEPV 64 Query: 67 DTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTE 126 L+ FV G+ ++R I + + +++ + N V + Sbjct: 65 PALPLVAGGLFV--------VGYLLQRFLINHFLGVTEHIQFLLLLSVAMIITNVVLMVF 116 Query: 127 G--SRDVALPSLF---NGQWVVGHSENFSASITT--MQAVIWIVTFLAMLALTIFIRYSR 179 G +R++ L + F N W+V A+ T + A++W F RY+ Sbjct: 117 GPDARNIQLDASFESYNLGWLVLDKVRVIAAFTAGGVAALLWA-----------FFRYTT 165 Query: 180 MGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAG 239 G A RACA++ A ++G++ +++ A+TF IG A AG LL V +P++ Sbjct: 166 TGTAIRACADNPVGARVVGLDVEKLYAITFGIGTACVGAAGCLLLLLVDV-HPHLSSDYT 224 Query: 240 MKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGI 299 + F +LGG+GS+ GA++GG+++G++EALS ++ K + SF LLILVLL+ P GI Sbjct: 225 LLGFIIVILGGLGSLGGALLGGILVGLSEALSGVLIAPSLKSMFSFGLLILVLLLRPQGI 284 Query: 300 LGR 302 LG+ Sbjct: 285 LGK 287 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: 235 Number of extensions: 9 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: 289 Length adjustment: 27 Effective length of query: 281 Effective length of database: 262 Effective search space: 73622 Effective search space used: 73622 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 17 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