Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate AO356_00960 AO356_00960 ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00960 Length = 325 Score = 152 bits (384), Expect = 1e-41 Identities = 99/322 (30%), Positives = 160/322 (49%), Gaps = 3/322 (0%) Query: 7 SGSGAPKSSFSFGRIWDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVAC 66 + S KSS +F + G+ + + +F ++ L I ++A Sbjct: 3 TASAVGKSSGNFYGLGTYLGLAGALLAMVALFSTLSSHFLSYDTFSTLANQIPDLMVLAV 62 Query: 67 GMLFCLASGDFDLSVASVIACAGVTTAV-VINLTESLWIGVAAGLLLGVLCGLVNGFVIA 125 GM F L G DLSV SV+A A T +V V+ S+W G+ + L G V G + Sbjct: 63 GMTFILIIGGIDLSVGSVLALAASTVSVAVLGWGWSVWPSALLGMAVAALAGTVTGSITV 122 Query: 126 KLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLI 185 +I + I +L +++ RGLAY ++ + I D SF L FG+ + + + Sbjct: 123 AWRIPSFIVSLGVLEMARGLAYQMTGSRTAYIGD-SFAWLSNPIAFGISPSFIIALLVIF 181 Query: 186 IFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTS 245 I +L +T FGR + IG NEEA RLAG+ KI++F L GL++ +A + SR+ + Sbjct: 182 IAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISRLEA 241 Query: 246 GQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYV 305 P G EL VI+A V+GG SL GG G + G+LI+ + + + + + + Sbjct: 242 ADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRI 301 Query: 306 VRGLILLAAVIFDRYK-QKAKR 326 + G +++ AV+ D Y+ Q+A R Sbjct: 302 ITGAVIVVAVVLDTYRSQRASR 323 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: 290 Number of extensions: 19 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: 328 Length of database: 325 Length adjustment: 28 Effective length of query: 300 Effective length of database: 297 Effective search space: 89100 Effective search space used: 89100 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 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