Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__Burk376:H281DRAFT_02703 Length = 333 Score = 201 bits (510), Expect = 3e-56 Identities = 115/309 (37%), Positives = 178/309 (57%), Gaps = 8/309 (2%) Query: 26 GMLVVFAVLFIAC---AIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVA 82 G+ +FA L I C +I P F T + + + +S+ G+ A G F + + DLSV Sbjct: 25 GIGPLFAALVIICIALSIASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITSGIDLSVG 84 Query: 83 SVIACAGVTTAVVI--NLTESLWIGVA---AGLLLGVLCGLVNGFVIAKLKINALITTLA 137 S++A G+ A V+ + ++ +G+A A L +G G +NG +A L++ I TLA Sbjct: 85 SLVALTGMVAATVMAGSSPGAIGLGIAGLCAALAVGAAAGALNGLAVAWLRLVPFIVTLA 144 Query: 138 TMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFG 197 M + RGL ISDG+ +F A G GLP P+ + + +I +LL KTTFG Sbjct: 145 MMAMARGLTLAISDGRTKFDFPNAFTAFGAKTVAGLPMPMIVMLVIFVIGHVLLRKTTFG 204 Query: 198 RNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELI 257 A+GGN+EAARLAG+PV R + ++L+G+ +AIAGI+LA R+ S P + G EL Sbjct: 205 HQVFAVGGNQEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSALPSAANGLELQ 264 Query: 258 VISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIF 317 VI+A V+GG SL GG G I G++++G + ++LL ++PF ++G ++ AAV+ Sbjct: 265 VIAAVVIGGTSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQGGVIFAAVLL 324 Query: 318 DRYKQKAKR 326 D Q+ K+ Sbjct: 325 DALSQRRKQ 333 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: 345 Number of extensions: 16 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: 333 Length adjustment: 28 Effective length of query: 300 Effective length of database: 305 Effective search space: 91500 Effective search space used: 91500 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