Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate WP_013091019.1 BC1002_RS15885 L-arabinose ABC transporter permease AraH
Query= CharProtDB::CH_014278 (328 letters) >NCBI__GCF_000092885.1:WP_013091019.1 Length = 334 Score = 319 bits (817), Expect = 7e-92 Identities = 161/309 (52%), Positives = 227/309 (73%), Gaps = 3/309 (0%) Query: 20 RIWD---QYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGD 76 R WD + G+++VF +LF + VP F + N++GL L++++ G ++ M+F LA G+ Sbjct: 24 RTWDLINKSGIVMVFVILFAVLSFTVPGFLSSRNIQGLLLSVTLIGSISVTMMFVLALGE 83 Query: 77 FDLSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTL 136 DLSVAS++A +GV +V+I T S+++GVAAG+L G GLVNG ++A+ KIN+LI TL Sbjct: 84 VDLSVASIVAFSGVVASVLITATHSVFVGVAAGVLAGGAVGLVNGTLVARYKINSLIVTL 143 Query: 137 ATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTF 196 A M++VRGLAYI S+G AV I +E FF LG ++ G+ PIW + ++FG LL KT F Sbjct: 144 AMMEVVRGLAYITSNGDAVMISEERFFDLGGGSFLGISYPIWSNIIGFVLFGFLLKKTVF 203 Query: 197 GRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYEL 256 G+N LA+GGN EAA LAG+PV R KI +FVL GLV+ AG++LASRM+ G P TS+G EL Sbjct: 204 GKNVLAVGGNSEAAVLAGLPVTRIKITVFVLQGLVTGFAGVMLASRMSLGDPKTSVGLEL 263 Query: 257 IVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVI 316 VISACVLGGVSL GG+ IS V+ G+LI+G+V++AM+LLN+ F QY++RG ILL AV+ Sbjct: 264 GVISACVLGGVSLTGGVATISGVLVGVLIMGSVQDAMSLLNVPTFYQYLIRGGILLLAVL 323 Query: 317 FDRYKQKAK 325 FD++++ + Sbjct: 324 FDQFRRSKR 332 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: 383 Number of extensions: 22 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: 334 Length adjustment: 28 Effective length of query: 300 Effective length of database: 306 Effective search space: 91800 Effective search space used: 91800 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 24 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