Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate 16257 b2148 beta-methylgalactoside transporter inner membrane component (NCBI)
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Keio:16257 Length = 336 Score = 154 bits (388), Expect = 4e-42 Identities = 99/321 (30%), Positives = 162/321 (50%), Gaps = 26/321 (8%) Query: 30 VFAVLFIACAIFV---PNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVIA 86 ++ VL + AI + P F + +N+ + S+ ++A G+ + + DLS + Sbjct: 18 IYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVG 77 Query: 87 CAGVTTAVVIN--------LTESLWIGVAAGLLL----GVLCGLVNGFVIAKLKINALIT 134 A V A ++ E + +A +L+ G + GL+NG +IA L + IT Sbjct: 78 LAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFIT 137 Query: 135 TLATMQIVRGLAYIISDGKAVGIEDESFFALGYANW---------FGLPAPIWLTVACLI 185 TL TM IV G+ + D VG S F G++ + F L + + + Sbjct: 138 TLGTMIIVYGINSLYYD--FVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVA 195 Query: 186 IFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTS 245 +L NKT FG+N AIGGN EAA+++GV V ++I+ LSG+ A G++ A R+ S Sbjct: 196 FVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGS 255 Query: 246 GQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYV 305 YEL I+ACV+GGVS GG+G + VV G++I + + + ++P+ QY+ Sbjct: 256 ATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYI 315 Query: 306 VRGLILLAAVIFDRYKQKAKR 326 ++G I++ AV D K K+ Sbjct: 316 IKGAIIIFAVALDSLKYARKK 336 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: 343 Number of extensions: 26 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 328 Length of database: 336 Length adjustment: 28 Effective length of query: 300 Effective length of database: 308 Effective search space: 92400 Effective search space used: 92400 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 17 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