Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 194 bits (494), Expect = 2e-54 Identities = 110/311 (35%), Positives = 170/311 (54%), Gaps = 11/311 (3%) Query: 24 QYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVAS 83 ++ L+ +L + ++ F T N + +S++ ++ GM + + DLSV S Sbjct: 6 KFQSLIALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSVGS 65 Query: 84 VIACAGVTTAVVIN---LTESLWI--------GVAAGLLLGVLCGLVNGFVIAKLKINAL 132 ++A G TA +I E L + V G+ LG G NG+ I + K+ Sbjct: 66 ILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPF 125 Query: 133 ITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLN 192 + TLA + I RGL + + G + E F LG + G+P P+W+T + + LL Sbjct: 126 VATLAMLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIPMPVWITAVIVALAVLLTK 185 Query: 193 KTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSI 252 KT FGR AIGGNE AARL+G+ + R K+ ++ ++G ++A+ G+I+ SR+ S QP I Sbjct: 186 KTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPNAGI 245 Query: 253 GYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILL 312 YEL I+A V+GG SL GG G I V G +I+G + N + LLN+SPF Q VV+G ++L Sbjct: 246 SYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKGAVIL 305 Query: 313 AAVIFDRYKQK 323 AV+ D+ K Sbjct: 306 LAVVIDKANSK 316 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: 323 Number of extensions: 20 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: 318 Length adjustment: 28 Effective length of query: 300 Effective length of database: 290 Effective search space: 87000 Effective search space used: 87000 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