Align L-arabinose-binding periplasmic protein; ABP (characterized)
to candidate BPHYT_RS16935 BPHYT_RS16935 arabinose ABC transporter substrate-binding protein
Query= SwissProt::P02924 (329 letters) >FitnessBrowser__BFirm:BPHYT_RS16935 Length = 332 Score = 306 bits (784), Expect = 5e-88 Identities = 155/323 (47%), Positives = 217/323 (67%), Gaps = 2/323 (0%) Query: 5 TKALAAIGLAAVMSQSAMAENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVP 64 T A AA G+ + A+ +K+GFLVKQPEEPWFQ EWKFA+ A K+ GF ++KI P Sbjct: 8 TLAAAATGVLFNAPVAQAADPVKIGFLVKQPEEPWFQDEWKFAEIAAKEKGFTLVKIGAP 67 Query: 65 DGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPMD 124 GEK ++AID+L+A A+GFVICTPD KLG IVAKA+ +K++ VDD+ V+ GKP+ Sbjct: 68 SGEKVMSAIDNLSAQKAQGFVICTPDVKLGPGIVAKAKADGLKMMTVDDRLVDGAGKPIA 127 Query: 125 TVPLVMMAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKA 184 +VP + ++A IG++ G L E++KRGWD+K+ + +T +L TA RT+G+ DAL A Sbjct: 128 SVPHMGISAYNIGKQVGDGLAAEIKKRGWDMKDVGAIDVTYEQLPTAHDRTSGATDALIA 187 Query: 185 AGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQGF 244 AGFP+ I P D AF+AAN L ++P+ KHW+ +ND VLG VRA EG+GF Sbjct: 188 AGFPKANIVMAPQAKTDTENAFNAANIALTKNPQFKHWVAYALNDEGVLGAVRAAEGRGF 247 Query: 245 KAADIIGIGINGVD-AVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKF 303 KA ++IGIGI G D A++E K TGFYG+++ SP HG ++S ++Y+W+ + PP Sbjct: 248 KADNMIGIGIGGSDSALNEFKKPSPTGFYGTVIISPKRHGEETSTLMYDWITQGKAPPPL 307 Query: 304 TEVTDVVLITRDNFKEELEKKGL 326 T +T +L TRDN + +K GL Sbjct: 308 T-LTTGMLATRDNVADVRQKMGL 329 Lambda K H 0.315 0.132 0.381 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: 329 Length of database: 332 Length adjustment: 28 Effective length of query: 301 Effective length of database: 304 Effective search space: 91504 Effective search space used: 91504 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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