Align Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale)
to candidate 3610344 Dshi_3725 inner-membrane translocator (RefSeq)
Query= uniprot:A0A0D9B2B6 (307 letters) >FitnessBrowser__Dino:3610344 Length = 294 Score = 137 bits (346), Expect = 2e-37 Identities = 93/307 (30%), Positives = 162/307 (52%), Gaps = 23/307 (7%) Query: 1 MPDIYHFF--QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIA 58 M + HF Q++NGL +G + L+A+G T+++G++ +IN +HGE Y +G+Y A +A+A Sbjct: 1 MAEYLHFVLAPQMLNGLALGVSVILVALGLTIIFGLLDVINMSHGEFYAVGAYGA-LALA 59 Query: 59 GLAM---MGLDSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIP-LISAIGMS 114 + + + VPL+M I +VT Y + R G++R + L+ G+ Sbjct: 60 AFGVNYWVLMAMVPLMM----IPLGIVTERY------LIRRVYDGADRHVSTLLLTFGLG 109 Query: 115 IFLQNTVLLSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFI 174 + ++ + + + N +PG + + I ++ + ++ +L + + Sbjct: 110 LIAEDVLKIIFGPNTQRPENPLPGATDL-----MGIFIPTYRLFLIAISAAVILAVAFVV 164 Query: 175 SRSRLGRACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAG 234 R+RLG RA + D MA LG+ + + F G ALA +A VLL+ Y V P G Sbjct: 165 YRTRLGAIVRAASFDRNMAASLGVRVGWVYSGAFAFGVALAGLAGVLLAPIYSVF-PTMG 223 Query: 235 FLVGLKAFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFR 294 L AFT ++GG+GSI GA++ G+VL +A + + + + + FG++VLVL+FR Sbjct: 224 RDFILIAFTVVIVGGMGSIWGAVVAGIVLTQIQAISSLVISPVWSEPIVFGVMVLVLMFR 283 Query: 295 PTGILGR 301 P G+ GR Sbjct: 284 PQGLFGR 290 Lambda K H 0.327 0.144 0.411 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: 252 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: 307 Length of database: 294 Length adjustment: 27 Effective length of query: 280 Effective length of database: 267 Effective search space: 74760 Effective search space used: 74760 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 (21.7 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