Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate WP_043529964.1 JH15_RS10345 L-arabinose ABC transporter permease AraH
Query= CharProtDB::CH_014278 (328 letters) >NCBI__GCF_000759345.1:WP_043529964.1 Length = 338 Score = 322 bits (825), Expect = 8e-93 Identities = 168/304 (55%), Positives = 218/304 (71%) Query: 23 DQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVA 82 D G++ +F +LFIA A+F+P+F T NM GL L+I++ G +A M+ LA G+ DLSVA Sbjct: 33 DTSGLIGIFLILFIALALFIPDFLTGRNMVGLLLSITVIGTIATTMMMVLALGEVDLSVA 92 Query: 83 SVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIV 142 S++A AGV AVV + + S++IGV G+ G G NGFV+AK IN+LI TLA M+ V Sbjct: 93 SIVAFAGVVAAVVTSTSGSVFIGVVGGVAAGGAVGAFNGFVVAKFGINSLIATLAAMEFV 152 Query: 143 RGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLA 202 RGLAYI S G AV I FF LG A++ GL P+W +AC +IFG+LLN T+FGRN LA Sbjct: 153 RGLAYITSGGDAVMITVPGFFDLGSASFLGLTLPVWTMIACFVIFGILLNMTSFGRNVLA 212 Query: 203 IGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISAC 262 GGN EAA LAGV V R KII+F L G+V+ IAG++L SRM G P T++G EL VISAC Sbjct: 213 TGGNAEAAALAGVNVKRLKIIVFGLQGVVAGIAGVLLTSRMGLGDPNTALGLELAVISAC 272 Query: 263 VLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQ 322 VLGGV+L GG+ I+ V+ G+LI+G V+NAM LLN+ F QY+VRG ILL AV+FDR+KQ Sbjct: 273 VLGGVALSGGVATITGVLVGVLIMGCVQNAMGLLNVPTFYQYLVRGAILLLAVMFDRWKQ 332 Query: 323 KAKR 326 ++ Sbjct: 333 TRRQ 336 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: 394 Number of extensions: 21 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: 338 Length adjustment: 28 Effective length of query: 300 Effective length of database: 310 Effective search space: 93000 Effective search space used: 93000 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