Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease
Query= uniprot:A0A161GM94 (322 letters) >NCBI__GCF_900177295.1:WP_085121058.1 Length = 335 Score = 161 bits (408), Expect = 2e-44 Identities = 101/294 (34%), Positives = 157/294 (53%), Gaps = 1/294 (0%) Query: 26 MLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIA 85 ML A+ I + +L+ FL+ N+ + GI + M + + +G DLSVGSV Sbjct: 36 MLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVILTGGIDLSVGSVAG 95 Query: 86 CAGVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGLA 145 +G+V + ++D + + I ++ G VGL++GI+I R+ A + TL M I R LA Sbjct: 96 LSGIVLGLALKDY-PIPVAILLGVLTGAGVGLVSGILIGYFRLAAFVVTLGMMAIGRSLA 154 Query: 146 YIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGGN 205 YIF+ A+ +FG+P +L +L L YT GR AIG N Sbjct: 155 YIFSGQTAISGFPSDLSSIVYTDVFGIPTNVLFLGFAYLLAWGYLTYTKGGRTIYAIGSN 214 Query: 206 QEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACVLGG 265 +EAA AG+ V I+ + V G + A+A +++ S P+ G G EL I+A V+GG Sbjct: 215 KEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPLTGNGMELDAIAAVVIGG 274 Query: 266 VSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRL 319 SL GG G I + GVLI+ +I N +NL + F+Q GSI+++A++++RL Sbjct: 275 ASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIIIMALLVERL 328 Lambda K H 0.330 0.144 0.420 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: 257 Number of extensions: 16 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: 322 Length of database: 335 Length adjustment: 28 Effective length of query: 294 Effective length of database: 307 Effective search space: 90258 Effective search space used: 90258 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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