Align ABC transporter permease (characterized, see rationale)
to candidate WP_086510701.1 BZY95_RS14925 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_002151265.1:WP_086510701.1 Length = 335 Score = 130 bits (328), Expect = 3e-35 Identities = 95/329 (28%), Positives = 166/329 (50%), Gaps = 37/329 (11%) Query: 8 IINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAPGW 67 II G V GS+YA+ A+G T+++ I++ +FAH +++ GA + ++ A PG G Sbjct: 12 IIAGSVTGSIYAIGAIGVTLIFSIMRFAHFAHADMMTFGAFM----VLLLTLAFPGVGGV 67 Query: 68 VIL---LLATIIACVVAATLNFVIEKVAYRPLRSS--PRLAPLITAIGMSILLQ------ 116 V L ++ +A ++ A L I+KV Y+PLR+ + +I ++G++++LQ Sbjct: 68 VGLPTPIVMLPLAMILTAALAVGIDKVFYKPLRAHGVKPIVIVIGSLGVTLMLQGLIRLF 127 Query: 117 --TLAMIIWKPNYKPYPTMLPSSPFEIGGA--FITPTQILILGVTAVALASLVYLVNHTN 172 T A ++ + L PFE+ +T QI++ +T + L +N T Sbjct: 128 AGTSAQNMYLAGERKEIYRL-DVPFELATRPIIVTEPQIILFILTIACVVGLHVFLNRTR 186 Query: 173 LGRAMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPG 232 LG+AMRA ++NP +A G+ + ++S T++I LAAIAG + + + T + + F Sbjct: 187 LGKAMRAMSDNPDLARASGINTNYIVSVTWVIAGSLAAIAGTLLSLDV-TFKPDLSFFLL 245 Query: 233 LKAFTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTG----------------GLL 276 L F AA+ GG+G+ GA+ GG ++G E + L + Sbjct: 246 LPIFAAAIVGGVGHPYGAIAGGFVVGFAETLAVFNWAVLLRPIAHLFPEWIEIPRNLAFV 305 Query: 277 GSHYTDIFAFIVLIIILTLRPSGLLGERV 305 G+ Y + F +L+ IL RP+G+ +V Sbjct: 306 GTEYKIVVPFFILVAILVWRPTGIFKGKV 334 Lambda K H 0.327 0.142 0.419 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: 249 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: 309 Length of database: 335 Length adjustment: 28 Effective length of query: 281 Effective length of database: 307 Effective search space: 86267 Effective search space used: 86267 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