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_013075626.1 BTUS_RS08110 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A0D9B2B6 (307 letters) >NCBI__GCF_000092905.1:WP_013075626.1 Length = 289 Score = 164 bits (415), Expect = 2e-45 Identities = 95/293 (32%), Positives = 159/293 (54%), Gaps = 14/293 (4%) Query: 9 QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLDSV 68 Q +++GL +G YALIA+G+ V+ + G+INFA G+ +G+ L M + Sbjct: 6 QLVLSGLALGGIYALIAVGFVTVFKVCGLINFAQGDFATVGAL-------SLVMFFASGL 58 Query: 69 PLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQDSK 128 P M A +IVV + G + R+ LR + +I+ IG+SI LQ+ L S+ Sbjct: 59 PTWM--ALFGAIVVAAIVGGVLHRVFLDKLRDQAETVQIIATIGLSIVLQSVGQLLMGSQ 116 Query: 129 DKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRACAE 188 +++ +PG GGA + +V+ V + + L F +S G A RA Sbjct: 117 PRAVSPFLPGQPYHFMGGA----VPRQDVVILVTVAILFVLLFFFFEKSYAGAALRAVML 172 Query: 189 DIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTAAVLG 248 + A LLGI+ ++ +FVIGAA+A + +++ +++ + G +GLK F AAV+G Sbjct: 173 NRDSARLLGISARSMATFSFVIGAAVAGLGGAVIA-PVTLVSYDMGLTLGLKGFVAAVVG 231 Query: 249 GIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGR 301 G+ +PGA+ G +LG+ E+ GA YK+ +AF +L+++LL+RP G+ G+ Sbjct: 232 GLSDVPGAVAGAFILGMLESVGAGFVSSAYKEAIAFVVLIVILLWRPNGLFGK 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: 259 Number of extensions: 14 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: 307 Length of database: 289 Length adjustment: 26 Effective length of query: 281 Effective length of database: 263 Effective search space: 73903 Effective search space used: 73903 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 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