Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate Dsui_2060 Dsui_2060 branched-chain amino acid ABC-type transport system, permease component
Query= ecocyc::LIVH-MONOMER (308 letters) >FitnessBrowser__PS:Dsui_2060 Length = 293 Score = 198 bits (503), Expect = 1e-55 Identities = 114/297 (38%), Positives = 176/297 (59%), Gaps = 17/297 (5%) Query: 10 QQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDTG 69 QQ+ N +TLGS YAL A+G+T+V+G++ +IN +HG V+M+GSY AAL M+ Sbjct: 4 QQLLNALTLGSVYALFALGFTLVFGVLAVINLSHGAVFMVGSY------AALAMVSHLNA 57 Query: 70 WLLVAAGFVGAIVIASAYGWSIERVAYRPVR--NSKRLIALISAIGMSIFLQNYVSLTEG 127 L VA +GA+V++ G ++ + +P+R N+ LI +I+ IG+ I L + G Sbjct: 58 PLWVA--MLGAMVVSGTIGLLVDVLVLKPLRARNAPHLIPMIATIGVGIMLTSAAQGLFG 115 Query: 128 SRDVALPS--LFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACR 185 + + P + G+++VG + ++ I + FL M L ++ +++GRA R Sbjct: 116 AEVLRFPEDVMPAGEFMVG-----DVHVRALEIAIVAIAFLLMAVLFTILKRTQLGRALR 170 Query: 186 ACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTA 245 A AE K A LLGIN + + +T + AA+ +AGVL+G + I P++G K Sbjct: 171 AIAESPKAAYLLGINVEGLFHITSFVAAALGGIAGVLIGLNFNAITPFMGQPMLHKGIAV 230 Query: 246 AVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGR 302 +LGG+G I GA+IGGL LG AE +S AYLS++ D V+F LL L+LLV P+G+ GR Sbjct: 231 IILGGMGDIRGALIGGLFLGFAEVISKAYLSSQMGDAVAFGLLFLILLVRPSGLFGR 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: 226 Number of extensions: 14 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: 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 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