Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= uniprot:A0A161GM94 (322 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 205 bits (521), Expect = 1e-57 Identities = 112/295 (37%), Positives = 174/295 (58%), Gaps = 3/295 (1%) Query: 31 IGIFVLCTLMI---DNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIACA 87 IG+ V+C +M+ D+FLS N+ + +S I A M + +G DLSVGSV+A A Sbjct: 41 IGLLVVCIVMVFASDSFLSGANIENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMALA 100 Query: 88 GVVAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGLAYI 147 G +AA +M + ++ + +GL G NG +A + +I TLATM I RGLA I Sbjct: 101 GTLAAGLMVAGMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVTLATMGIARGLALI 160 Query: 148 FANGKAVGVSQESFFVFGNGQMFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGGNQE 207 + G + + FG+G++ GV P++I V ++ LL +GR AIGGN++ Sbjct: 161 YTGGYPIDGLPDWVSFFGSGKILGVQAPVVIMAVIYVIAWVLLERMPFGRYVYAIGGNEQ 220 Query: 208 AALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACVLGGVS 267 A L+GV V R K+I++ + G+ A A ++L +R+ SGQP G GFEL I+A V+GG S Sbjct: 221 ATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPNAGVGFELDAIAAVVMGGTS 280 Query: 268 LSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQR 322 +SGG G I + G L+L ++ N +N+ ++ + Q VI+G I+LLA+ I R +++ Sbjct: 281 ISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIILLAIYISRDRRK 335 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: 291 Number of extensions: 20 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 Sep 17 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