Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate GFF4163 PS417_21325 arabinose ABC transporter permease
Query= CharProtDB::CH_014278 (328 letters) >FitnessBrowser__WCS417:GFF4163 Length = 321 Score = 380 bits (977), Expect = e-110 Identities = 200/323 (61%), Positives = 242/323 (74%), Gaps = 2/323 (0%) Query: 1 MSSVSTSGSGAPKSSFSFGRIWDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISM 60 MS V T+ P F+ + D + ML+ +F+ A+F+ NF + +NM+GLGLAIS Sbjct: 1 MSEVKTAKGFWP--GFNQRKFLDDWVMLLAALSIFVLSALFIDNFLSPLNMRGLGLAIST 58 Query: 61 SGMVACGMLFCLASGDFDLSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVN 120 G+ AC MLFCLASG FDLSV SVIACAGV +VI T+S+ +GV+A L +G++ GL+N Sbjct: 59 VGIAACTMLFCLASGHFDLSVGSVIACAGVVAGIVIRDTDSVVLGVSAALAMGLVVGLIN 118 Query: 121 GFVIAKLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLT 180 G VIAKL+INALI TLATMQIVRGLAYI S+GKAVG+ DE FF G G+P PI +T Sbjct: 119 GIVIAKLRINALIATLATMQIVRGLAYIFSNGKAVGVMDEGFFVFGNGQLLGVPVPIIIT 178 Query: 181 VACLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILA 240 V C + FG LLN TT+GRNT+AIGGN+EAA LAGV V RTKIIIF + GL+ A+AG+ILA Sbjct: 179 VLCFVFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGLIGALAGVILA 238 Query: 241 SRMTSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISP 300 SRMTSGQPM G+EL VISACVLGGVSL GGIG I +V+AG+LIL +ENAMNL NI Sbjct: 239 SRMTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDT 298 Query: 301 FAQYVVRGLILLAAVIFDRYKQK 323 F QYV+RG ILL AVI DR KQ+ Sbjct: 299 FYQYVIRGSILLLAVIIDRMKQR 321 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: 418 Number of extensions: 13 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: 321 Length adjustment: 28 Effective length of query: 300 Effective length of database: 293 Effective search space: 87900 Effective search space used: 87900 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