Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate Pf6N2E2_163 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_163 Length = 325 Score = 152 bits (385), Expect = 8e-42 Identities = 104/325 (32%), Positives = 163/325 (50%), Gaps = 9/325 (2%) Query: 7 SGSGAPKSSFSF---GRIWDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGM 63 + S KSS +F G G L+ LF A + ++ TF + I + Sbjct: 3 TASAVGKSSGNFYGLGTYLGLAGALLAMVALFSALSSHFLSYDTFSTLAN---QIPDLMV 59 Query: 64 VACGMLFCLASGDFDLSVASVIACAGVTTAV-VINLTESLWIGVAAGLLLGVLCGLVNGF 122 +A GM F L G DLSV SV+A A T +V V+ S+W G+ + L G V G Sbjct: 60 LAVGMTFILIIGGIDLSVGSVLALAASTVSVAVLGWGWSVWPSALLGMAVAALAGTVTGS 119 Query: 123 VIAKLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVA 182 + +I + I +L +++ RGLAY ++ + I D SF L FG+ + + Sbjct: 120 ITVAWRIPSFIVSLGVLEMARGLAYQMTGSRTAYIGD-SFAWLSNPIAFGISPSFIIALL 178 Query: 183 CLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASR 242 + I +L +T FGR + IG NEEA RLAG+ KI++F L GL++ +A + SR Sbjct: 179 VIFIAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGVAALFQISR 238 Query: 243 MTSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFA 302 + + P G EL VI+A V+GG SL GG G + G+LI+ + + + + Sbjct: 239 LEAADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPT 298 Query: 303 QYVVRGLILLAAVIFDRYK-QKAKR 326 + ++ G +++ AV+ D Y+ Q+A R Sbjct: 299 KRIITGAVIVVAVVLDTYRSQRASR 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: 289 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