Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_2060 Dsui_2060 branched-chain amino acid ABC-type transport system, permease component
Query= uniprot:Q1MCU0 (300 letters) >FitnessBrowser__PS:Dsui_2060 Length = 293 Score = 165 bits (417), Expect = 1e-45 Identities = 98/293 (33%), Positives = 159/293 (54%), Gaps = 13/293 (4%) Query: 6 QQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLP 65 QQLLN LTLGS+Y L A+G+T+V+G++ +IN +HG +FM+G +AAL + L + Sbjct: 4 QQLLNALTLGSVYALFALGFTLVFGVLAVINLSHGAVFMVGSYAALAMVSHLNA------ 57 Query: 66 VAVLLLVMLVVAMLMTSLWNWTIERVAYRPL--RGSFRLAPLITAIGMSITLSNFIQVTQ 123 L V ++ AM+++ ++ + +PL R + L P+I IG+ I L++ Q Sbjct: 58 ---PLWVAMLGAMVVSGTIGLLVDVLVLKPLRARNAPHLIPMIATIGVGIMLTSAAQGLF 114 Query: 124 GPRNKPIPP--MVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQ 181 G P M + + G++ V +I I+ I +L+ + + I+ RT LGRA RA + Sbjct: 115 GAEVLRFPEDVMPAGEFMVGDVHVRALEIAIVAIAFLLMAVLFTILKRTQLGRALRAIAE 174 Query: 182 DRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLG 241 K A LLG+NV+ IT + AAL +AG + + + + G K +LG Sbjct: 175 SPKAAYLLGINVEGLFHITSFVAAALGGIAGVLIGLNFNAITPFMGQPMLHKGIAVIILG 234 Query: 242 GIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGR 294 G+G + GA+ GGL +G E + AY + D F +L +L+ +P+G+ GR Sbjct: 235 GMGDIRGALIGGLFLGFAEVISKAYLSSQMGDAVAFGLLFLILLVRPSGLFGR 287 Lambda K H 0.329 0.143 0.421 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: 262 Number of extensions: 19 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: 300 Length of database: 293 Length adjustment: 26 Effective length of query: 274 Effective length of database: 267 Effective search space: 73158 Effective search space used: 73158 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