Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 175 bits (444), Expect = 1e-48 Identities = 101/309 (32%), Positives = 170/309 (55%), Gaps = 12/309 (3%) Query: 26 GMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVI 85 G ++ +L IA + NFAT+ N+ + + G++A GM F + SG DLSV S+ Sbjct: 42 GPVIGLVLLCIAGTLLNSNFATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSVGSMA 101 Query: 86 ACAGVTTAVVINLTE--------SLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLA 137 A + + +N ++ +G+ ++LG + GLV+G +I K +I I TL Sbjct: 102 ALIAGSVILFMNAMAPVLGSPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFIVTLG 161 Query: 138 TMQIVRGLAYIISDGKAVGIEDES---FFALGYANWFGLPAPIWLTVACLIIFGLLLNKT 194 T+ I R S+G A+ +E++ + + YAN G+P P+W+ + I+ G++LN+T Sbjct: 162 TLGIFRAYLTYFSNGGAITLENDLSDIYSPVYYANLLGVPIPVWIFLLVAIVGGVILNRT 221 Query: 195 TFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGY 254 +GR AIG NE+ A+ A V V + KI+ ++L G+ IA ++ R+ S P T + + Sbjct: 222 AYGRYVQAIGSNEQVAQYAAVDVHKIKILTYMLLGVCVGIATLLYVPRLGSASPTTGLLW 281 Query: 255 ELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLN-ISPFAQYVVRGLILLA 313 EL I+A ++GG LKGG G I+ V G ++L + N +NL + IS + V+G +++A Sbjct: 282 ELEAIAAVIVGGTVLKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAAVQGFVIIA 341 Query: 314 AVIFDRYKQ 322 R K+ Sbjct: 342 VAFMQRGKR 350 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: 17 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: 350 Length adjustment: 28 Effective length of query: 300 Effective length of database: 322 Effective search space: 96600 Effective search space used: 96600 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