Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate WP_011653625.1 RL_RS21800 L-arabinose ABC transporter permease AraH
Query= CharProtDB::CH_014278 (328 letters) >NCBI__GCF_000009265.1:WP_011653625.1 Length = 316 Score = 336 bits (861), Expect = 5e-97 Identities = 173/301 (57%), Positives = 219/301 (72%) Query: 24 QYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVAS 83 + G++V+FA F+ ++FVPNF T NM GL ++ G+VAC M+FCLAS DFDLSV S Sbjct: 11 EQGLVVIFAAAFVIVSLFVPNFLTERNMLGLLQSVVTIGIVACTMMFCLASRDFDLSVGS 70 Query: 84 VIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIVR 143 ++A +G+ +V N T S+ +G+ A LL G + G VNG VIA+ +INALITTLATMQIVR Sbjct: 71 IVAFSGMIAVMVSNATGSIPVGLLAALLCGAVVGFVNGIVIARFRINALITTLATMQIVR 130 Query: 144 GLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLAI 203 GLA I SDG+AVGI D +F+ L + + +P PIW+ + I+FG +LN+T FG+NTLAI Sbjct: 131 GLALIASDGRAVGINDPAFYQLALSRFLTVPTPIWIMLILFILFGFVLNRTVFGKNTLAI 190 Query: 204 GGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISACV 263 GGN EA+RLAGV VV ++ IF L GLV IAGI+LASR+TSGQP + G EL VISACV Sbjct: 191 GGNPEASRLAGVNVVNMRVWIFALQGLVCGIAGILLASRITSGQPNAATGLELSVISACV 250 Query: 264 LGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQK 323 LGGVSL GG +S V+ G+LI+G EN MNLLNI F QYVVRGLILL AV+ D + Sbjct: 251 LGGVSLAGGRAAMSGVIVGVLIMGIAENVMNLLNIQAFYQYVVRGLILLIAVLLDNLRSS 310 Query: 324 A 324 A Sbjct: 311 A 311 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: 395 Number of extensions: 20 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: 316 Length adjustment: 28 Effective length of query: 300 Effective length of database: 288 Effective search space: 86400 Effective search space used: 86400 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 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