Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate WP_011651405.1 RL_RS09080 sugar ABC transporter permease
Query= uniprot:A0A161GM94 (322 letters) >NCBI__GCF_000009265.1:WP_011651405.1 Length = 334 Score = 195 bits (495), Expect = 1e-54 Identities = 101/313 (32%), Positives = 181/313 (57%), Gaps = 10/313 (3%) Query: 16 DLRRFL-DDWVMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASG 74 D RR L ++ + LA + + V+ + + FL+ N+ + L S G+ A M + + + Sbjct: 16 DRRRLLIQEYGIFLAFLLLVVVLSFSNEFFLTGGNISNVLLQTSINGVLAIGMTFVILTR 75 Query: 75 HFDLSVGSVIACAGVVAAVVMRDTNS---------VFLGISAALVMGLIVGLINGIVIAK 125 DLSVGSV+A AG+V+A + + V +G++ +++G+ G I+G ++++ Sbjct: 76 GIDLSVGSVVALAGIVSASFSTTSATAAIAGAPYPVAIGLAVGILVGVACGAISGAIVSR 135 Query: 126 LRVNALITTLATMQIVRGLAYIFANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLF 185 V A + TL + RGL I+ G+ V +F G G +FG+P P++I V F Sbjct: 136 FSVPAFVATLGMLSAARGLTLIYGGGRPVPALTPAFRWIGTGDVFGIPAPVIILAVVFAA 195 Query: 186 FGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSG 245 W+L+ T +GR A+GGN AA +G+++ R + ++ + G + LAG++L++R S Sbjct: 196 SWWILSRTRFGRYIYAVGGNPHAAKTSGIDIGRIRFTVYVISGGLAGLAGMLLSARTGSA 255 Query: 246 QPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVI 305 P G +EL I+A V+GG SLSGG+G + + G LI+ ++ N ++L I ++YQ V+ Sbjct: 256 LPQAGIAYELDAIAAVVIGGTSLSGGVGRVTGTLIGALIIGVMNNGLDLMGIQSYYQQVL 315 Query: 306 RGSILLLAVVIDR 318 +G++++ AV++D+ Sbjct: 316 KGALIVGAVMLDQ 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: 271 Number of extensions: 12 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: 322 Length of database: 334 Length adjustment: 28 Effective length of query: 294 Effective length of database: 306 Effective search space: 89964 Effective search space used: 89964 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 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