Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate WP_039469452.1 H744_RS03170 ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >NCBI__GCF_000940995.1:WP_039469452.1 Length = 338 Score = 208 bits (529), Expect = 2e-58 Identities = 115/334 (34%), Positives = 192/334 (57%), Gaps = 15/334 (4%) Query: 5 STSGSGAPKSSFSFGRIWDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMV 64 +TSG+ +P++ + R+ +Y + VVF + + +I P F T N+ + ++ G++ Sbjct: 8 ATSGAKSPQN---YKRLISKYAIYVVFIAMCVVMSILSPVFLTVANLLNVVTQMASIGLL 64 Query: 65 ACGMLFCLASGDFDLSVASVIACAGVTTAVVINLTE------------SLWIGVAAGLLL 112 A G+ + + DLS SV+A A V +A + + + + + L + Sbjct: 65 ALGVTIIIITRGIDLSSGSVLAVAAVASASMAQTLDWGMRMYPAMPELPVIVPILVALAV 124 Query: 113 GVLCGLVNGFVIAKLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFG 172 G LCG +NG +IA I I TL M I RG A + SDG+ V +S+ +G G Sbjct: 125 GALCGFINGALIAYTGIPPFIATLGMMIIARGAALLYSDGRPVSSLIDSYQWIGQGTIAG 184 Query: 173 LPAPIWLTVACLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVS 232 +P P+ + + I+ +LLN T FG+ AIGGNE AA ++G+ V + KI+++ +GL++ Sbjct: 185 IPVPVIIFIVMAIVSYILLNYTRFGKYAYAIGGNETAAYVSGINVKKYKILVYTYAGLLA 244 Query: 233 AIAGIILASRMTSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENA 292 IA +IL++R+ SGQP + YEL I++ +GGVS GGIG I + G +I+G ++N Sbjct: 245 GIAALILSARINSGQPGLGVMYELDAIASATVGGVSHAGGIGTIQGTIIGTMIMGVLQNG 304 Query: 293 MNLLNISPFAQYVVRGLILLAAVIFDRYKQKAKR 326 ++LLN+S + Q VV+GL+++ AV+FD +QK + Sbjct: 305 LDLLNVSAYWQQVVKGLVIVVAVVFDMKRQKKSK 338 Lambda K H 0.327 0.141 0.414 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: 318 Number of extensions: 17 Number of successful extensions: 1 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: 328 Length of database: 338 Length adjustment: 28 Effective length of query: 300 Effective length of database: 310 Effective search space: 93000 Effective search space used: 93000 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: 49 (23.5 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