Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_043916933.1 jaqu_RS00200 sugar ABC transporter permease
Query= uniprot:A8LLL5 (334 letters) >NCBI__GCF_000877395.1:WP_043916933.1 Length = 329 Score = 413 bits (1062), Expect = e-120 Identities = 206/333 (61%), Positives = 258/333 (77%), Gaps = 10/333 (3%) Query: 3 PAFQGLITIIIGVGGCVGYFYFANQFLDKVLYPAKGPKAGRNINRANQIRPWIFLFPALF 62 P QG++TI++GVGGC+GYF+ +N LDKV++PAKG AG+NINRAN +RPW+F+FPA Sbjct: 6 PILQGVLTIVLGVGGCIGYFWASNIVLDKVIFPAKGANAGKNINRANMVRPWLFIFPAFA 65 Query: 63 VLLLYLGYPVVETLRLSLLERVPGGGYQWVGLDNYAQMASEPKFWEAMRNNMFWLIVVPA 122 L LYL YPVV + SL +R G ++G NYA + + +F +A+ NN+ W +VVPA Sbjct: 66 ALGLYLAYPVVGSFIRSLYDR---SGDTFIGFGNYAWLMQDSEFQQAVFNNILWALVVPA 122 Query: 123 LSTAFGLLAAQLTDRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDGRPIEQEQIGILNA 182 ST FGL+AAQLTDR+ WGN+AKS+IFMPMAISFVGAS+IWK VY IGI+NA Sbjct: 123 GSTFFGLVAAQLTDRLSWGNIAKSLIFMPMAISFVGASLIWKFVY----ANDADIGIVNA 178 Query: 183 IIVGL-GGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRGIPEETIEAAIIDGA 241 + G D V L + FWNNFFLM +L+W+QTGFAMVILSAALRGIPEET+EAAI+DGA Sbjct: 179 FREWVFGADSVDPLQVSFWNNFFLMFILIWIQTGFAMVILSAALRGIPEETVEAAIVDGA 238 Query: 242 SPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWETQVLANYMFDKLFRA 301 SPLQ+FFKIKVPQIM T+VVVWTTIT++VLKVFDIV+ MT G + TQ+L +YMF+ +FR Sbjct: 239 SPLQVFFKIKVPQIMGTIVVVWTTITILVLKVFDIVYTMTGGNFGTQILPSYMFEFMFR- 297 Query: 302 NDWGVGSASAMVIMLLVTPILIWNIHSARKEMR 334 D G +A A VIML+VTP+++WNI ARKEMR Sbjct: 298 -DDGRATAVAFVIMLIVTPVMVWNIIQARKEMR 329 Lambda K H 0.329 0.143 0.455 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: 390 Number of extensions: 17 Number of successful extensions: 4 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: 334 Length of database: 329 Length adjustment: 28 Effective length of query: 306 Effective length of database: 301 Effective search space: 92106 Effective search space used: 92106 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