Align ABC transporter permease (characterized, see rationale)
to candidate WP_012400001.1 BPHY_RS02955 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000020045.1:WP_012400001.1 Length = 316 Score = 397 bits (1020), Expect = e-115 Identities = 201/316 (63%), Positives = 249/316 (78%), Gaps = 7/316 (2%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 MDI +QQ+INGLVLGS+YA+IALGYTMVYGI+ +INFAHG+VLM+GA+ + S IG++Q Sbjct: 1 MDIFIQQVINGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAIGVLQNH 60 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 PG L +A +IA +V A + + IE+VAYRPLR +PRLAPLITAIG+SILLQTLAM Sbjct: 61 FPGLGNVPTLCIALVIAAIVCAVVGYTIERVAYRPLRKAPRLAPLITAIGVSILLQTLAM 120 Query: 121 IIWKPNYKPYPTMLPSSPFEI-------GGAFITPTQILILGVTAVALASLVYLVNHTNL 173 +IW N P+P +LP+ P + GA I+ T+I+I+ V + +A L+ LV+ T L Sbjct: 121 MIWSRNPLPFPQLLPTDPLNVIKATDTTPGAVISMTEIVIIVVAFLVMAGLLLLVHKTKL 180 Query: 174 GRAMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGL 233 GRAMRA AENP VASLMGV P+ VISATF+IG+ LAA+AG+M AS YG A MGF+PGL Sbjct: 181 GRAMRAIAENPGVASLMGVNPNFVISATFMIGSALAALAGVMIASEYGNAHFYMGFIPGL 240 Query: 234 KAFTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIIL 293 KAFTAAV GGIGNL GA+VGG++LGLIE +G+GYIG LTGG+ GS+Y D+FAFIVLII+L Sbjct: 241 KAFTAAVLGGIGNLGGAMVGGVILGLIEQLGAGYIGNLTGGVFGSNYQDVFAFIVLIIVL 300 Query: 294 TLRPSGLLGERVADRA 309 RPSGLLGERVADRA Sbjct: 301 VFRPSGLLGERVADRA 316 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: 328 Number of extensions: 10 Number of successful extensions: 2 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: 316 Length adjustment: 27 Effective length of query: 282 Effective length of database: 289 Effective search space: 81498 Effective search space used: 81498 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