Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate GFF773 PGA1_c07870 alpha-glucoside transport system permease protein AglF
Query= uniprot:A8LLL5 (334 letters) >FitnessBrowser__Phaeo:GFF773 Length = 335 Score = 543 bits (1398), Expect = e-159 Identities = 259/335 (77%), Positives = 296/335 (88%), Gaps = 1/335 (0%) Query: 1 MHPAFQGLITIIIGVGGCVGYFYFANQFLDKVLYPAKGPKAGRNINRANQIRPWIFLFPA 60 MHPA QGL TI GVGGCVGYFYF+N LD+V++PA+G RNI RAN IRPW+FLFPA Sbjct: 1 MHPAIQGLFTIAFGVGGCVGYFYFSNLVLDRVIFPARGAHIARNIRRANMIRPWLFLFPA 60 Query: 61 LFVLLLYLGYPVVETLRLSLLERVPGGGYQWVGLDNYAQMASEPKFWEAMRNNMFWLIVV 120 L L LYL YPVVETLRLS+ ERVPGGG ++VGL NY QM +E KFWEA++NN WL+VV Sbjct: 61 LLALGLYLAYPVVETLRLSVTERVPGGGSEFVGLANYQQMLAEAKFWEALQNNFLWLLVV 120 Query: 121 PALSTAFGLLAAQLTDRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDGRPIEQEQIGIL 180 PA STAFGLLAAQLTDR+ WGN+AKS+IFMPMAISFVGA+VIWKLVYD RP +QIG+L Sbjct: 121 PAASTAFGLLAAQLTDRLAWGNIAKSLIFMPMAISFVGAAVIWKLVYDARPEGTDQIGVL 180 Query: 181 NAIIVGLGGD-PVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRGIPEETIEAAIID 239 NA+ + GGD P+ +LTIPFWN+FFLM+VL+W+QTGFAMVILSAALRGIPEET+EAAI+D Sbjct: 181 NALYIYFGGDGPMQWLTIPFWNSFFLMMVLIWIQTGFAMVILSAALRGIPEETVEAAIVD 240 Query: 240 GASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWETQVLANYMFDKLF 299 GA P QIFFKIKVPQIM T+VVVWTTIT+VVLKVFDIVFAMTNGQWETQVLANYM+DKLF Sbjct: 241 GAGPFQIFFKIKVPQIMDTIVVVWTTITIVVLKVFDIVFAMTNGQWETQVLANYMYDKLF 300 Query: 300 RANDWGVGSASAMVIMLLVTPILIWNIHSARKEMR 334 RANDWGVGSASAMVIMLLV PIL+WN+++AR+EMR Sbjct: 301 RANDWGVGSASAMVIMLLVLPILVWNVYNARREMR 335 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: 458 Number of extensions: 12 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: 334 Length of database: 335 Length adjustment: 28 Effective length of query: 306 Effective length of database: 307 Effective search space: 93942 Effective search space used: 93942 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