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 YP_428610.1 Rru_A3529 inner-membrane translocator
Query= uniprot:A0A0D9B2B6 (307 letters) >NCBI__GCF_000013085.1:YP_428610.1 Length = 454 Score = 179 bits (454), Expect = 1e-49 Identities = 99/301 (32%), Positives = 168/301 (55%) Query: 3 DIYHFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAM 62 D+ +F QQ +N L V + Y L+A YT++Y + I GE+ MIG+ F +A + Sbjct: 146 DLAYFLQQTLNALPVIALYGLLAASYTLIYALGRTILLVFGELAMIGAMACFAGVALFSG 205 Query: 63 MGLDSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVL 122 +G ++ A + +++ ++ +G ++ R+ +P G L L+++ ++I +Q+ V Sbjct: 206 LGGLGTAGVVGGAVVFALLASAVHGDALRRLVLQPAAGRTPLALLVASFALAIVVQDYVR 265 Query: 123 LSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRA 182 LSQD+ D+ +P L + G V ++ Q+V+ + + L + R R GR Sbjct: 266 LSQDAGDRLLPTLPGRTHVLARAGEFVVAVTDFQLVLVGGAGIVLGALVWGMGRGRFGRC 325 Query: 183 CRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAF 242 RA AED +MA L G++ + A+ F + A LA +A V++ +++G+ N G ++G KA Sbjct: 326 WRAMAEDPQMATLCGVSKTRLWAICFALAATLAGLAGVVVLLRFGLANAFMGAMLGFKAL 385 Query: 243 TAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRP 302 TAAV+GGIG I GA+LG +V+G E + A F ++DV F LL L+ RP G++G Sbjct: 386 TAAVVGGIGRIQGAILGAVVIGGLETYWAAYFDMAWRDVAVFALLAAALVLRPQGLVGLA 445 Query: 303 E 303 E Sbjct: 446 E 446 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: 303 Number of extensions: 13 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: 307 Length of database: 454 Length adjustment: 30 Effective length of query: 277 Effective length of database: 424 Effective search space: 117448 Effective search space used: 117448 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: 50 (23.9 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