Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Dino:3609042 Length = 328 Score = 175 bits (443), Expect = 2e-48 Identities = 101/300 (33%), Positives = 161/300 (53%), Gaps = 4/300 (1%) Query: 22 WDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSV 81 W+ +LV + F+A + P F N+ + M+A M + SG+ DLSV Sbjct: 23 WETLLLLVAIGI-FVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISGEIDLSV 81 Query: 82 ASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQI 141 AS+IA A + + V GL +G+LCG NG ++ ++ + +++ T+ TM + Sbjct: 82 ASIIALASTAMGAAVQMGVGTPGLVLIGLGVGLLCGAFNGVLVTRMGLPSIVVTIGTMSL 141 Query: 142 VRGLAYIISDGKAVGIEDESF--FALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRN 199 RG++YI+ +A ESF F GY W+ + + L +I+ +LL+KT FGR Sbjct: 142 FRGISYIVLGDQAFRGYPESFSWFGQGYV-WWVISFELVLFAIIAVIYAMLLHKTNFGRA 200 Query: 200 TLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVI 259 AIG N A +G+ V R K I+F+L+GL+S +A I L +R+ S +P ++G+EL V+ Sbjct: 201 VYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLGSTRPSIAMGWELEVV 260 Query: 260 SACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDR 319 + VLGGVS+ GG G I VV ++G V + LLN+ +V G +L+ + R Sbjct: 261 TMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMSIVIGALLIGVIALPR 320 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: 328 Number of extensions: 31 Number of successful extensions: 3 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: 328 Length adjustment: 28 Effective length of query: 300 Effective length of database: 300 Effective search space: 90000 Effective search space used: 90000 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