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 GFF3113 HP15_3056 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= uniprot:A0A0D9B2B6 (307 letters) >FitnessBrowser__Marino:GFF3113 Length = 307 Score = 404 bits (1038), Expect = e-117 Identities = 197/307 (64%), Positives = 251/307 (81%) Query: 1 MPDIYHFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL 60 M D+ +F QQL+NGLT+GSTYALIAIGYTMVYGIIGMINFAHGE+YMIG+Y A IAI GL Sbjct: 1 MQDLLYFSQQLINGLTIGSTYALIAIGYTMVYGIIGMINFAHGEIYMIGAYTALIAITGL 60 Query: 61 AMMGLDSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT 120 A +G+ +PL++ A + +++V+SS G+++ER+AYRP+RG +RLIPLISAIGMSIFLQN Sbjct: 61 AALGIAWLPLILIVALLCAMIVSSSMGWAVERVAYRPVRGRHRLIPLISAIGMSIFLQNY 120 Query: 121 VLLSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLG 180 V L+Q S++ P LI G F G G ++ +SYMQI +F+ TL+ M L+LFISRSR G Sbjct: 121 VHLAQGSRNIGFPALIDGGFNFGSGDGFQMSLSYMQITIFITTLICMTALSLFISRSRTG 180 Query: 181 RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLK 240 RACRA ++D+ MANLLGI+TN II+ TFVIGAALAA+A +LL M YG ++P GF+ GLK Sbjct: 181 RACRAVSQDLGMANLLGIDTNRIISATFVIGAALAAVAGLLLGMYYGSVDPLFGFIAGLK 240 Query: 241 AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILG 300 AFTAAVLGGIGSIPGAMLGGL+LGVAE+ + +YKDV++F LL+L+LLF+PTG+LG Sbjct: 241 AFTAAVLGGIGSIPGAMLGGLILGVAESMTSGYLSGEYKDVISFSLLILILLFKPTGLLG 300 Query: 301 RPEVEKV 307 +PEVEK+ Sbjct: 301 KPEVEKI 307 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: 371 Number of extensions: 15 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: 307 Length adjustment: 27 Effective length of query: 280 Effective length of database: 280 Effective search space: 78400 Effective search space used: 78400 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