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 WP_028320915.1 H567_RS0107410 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A0D9B2B6 (307 letters) >NCBI__GCF_000422285.1:WP_028320915.1 Length = 291 Score = 152 bits (385), Expect = 7e-42 Identities = 98/294 (33%), Positives = 151/294 (51%), Gaps = 16/294 (5%) Query: 7 FFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLD 66 F Q LV G+ G Y LI +G +++ G++G+IN AHG++ M+ Y+ F+ L + Sbjct: 4 FLQTLVAGILKGGLYGLIGMGMSLIMGVMGIINLAHGQLMMVAMYITFVCFTYLGLDPYA 63 Query: 67 SVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIP---LISAIGMSIFLQNTVLL 123 ++ + M A F+ G I+R A PL L+P ++ +G+ + L Sbjct: 64 ALLITMPALFLL--------GALIQRYALNPLMEVESLLPENQVLMTVGIGMVLTEIARF 115 Query: 124 SQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRAC 183 S KS+ + G + V ++ F + L+ + F+ ++ LGRA Sbjct: 116 IFSSDYKSVQTAYSSSSFFLRGISFSVALT----AAFFIALLFTGFMFWFLLKTDLGRAI 171 Query: 184 RACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFT 243 RA A+D A L+G++ I LTF IG+AL A A LL Y + P+ G KAF Sbjct: 172 RATAQDKDAALLMGVDAKRITILTFGIGSALVAAAGTLLMPIYYLF-PDIGSPFTRKAFV 230 Query: 244 AAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTG 297 +LGG+GS GA+ GGL LG+AEAFGA G + D++ + +LVLLF P+G Sbjct: 231 ITILGGLGSTVGAIFGGLTLGLAEAFGATYIGMAFDDMIGLLIFILVLLFLPSG 284 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: 268 Number of extensions: 21 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: 291 Length adjustment: 27 Effective length of query: 280 Effective length of database: 264 Effective search space: 73920 Effective search space used: 73920 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 Apr 09 2024. 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