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_013011149.1 DACET_RS09435 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A0D9B2B6 (307 letters) >NCBI__GCF_000025725.1:WP_013011149.1 Length = 287 Score = 166 bits (421), Expect = 5e-46 Identities = 103/299 (34%), Positives = 157/299 (52%), Gaps = 13/299 (4%) Query: 9 QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLDSV 68 Q L +GLT GS Y L+A+G+ ++Y G+INFA GE MIG + + M GL Sbjct: 2 QFLYSGLTSGSIYGLVALGFNIIYNTTGIINFAQGEFVMIGGMLIYTFFV---MYGLP-- 56 Query: 69 PLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQDSK 128 AF ++ G ER R + N L + I SI L++ + Sbjct: 57 ---FPIAFFGAVACAFLIGIVFERFFIRLTKIKNELNLITVTIAASIILRDVAMHLWGRD 113 Query: 129 DKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRACAE 188 + IP PGG +IS I+V V+L+ LGL +F+ +SR G+A RA + Sbjct: 114 SLPVKEFIPVFNIDMPGG----VISSQSILVVAVSLMVALGLNIFLKKSRYGKAMRASFD 169 Query: 189 DIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTAAVLG 248 D A GI +NI ++F + A L A+A V+++ + + G + GLK F+AA+LG Sbjct: 170 DPVAAETCGIKVSNIRVMSFAVAALLGAVAGVIIA-PIMFVTYDDGIMTGLKGFSAAILG 228 Query: 249 GIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRPEVEKV 307 G+G+ A+ GGL+LG+ E+F A I KD VAF +++++L +P G+ GR +V +V Sbjct: 229 GLGNFGAAIAGGLLLGIFESFSASIIPSGLKDAVAFLVILVILFVKPDGLFGRKKVHRV 287 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: 248 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: 287 Length adjustment: 26 Effective length of query: 281 Effective length of database: 261 Effective search space: 73341 Effective search space used: 73341 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