Align Fructose import permease protein FruG (characterized)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 160 bits (404), Expect = 6e-44 Identities = 101/307 (32%), Positives = 165/307 (53%), Gaps = 14/307 (4%) Query: 24 PTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVG 83 P + +V+ I+M+ + ++ I ++ + I+AV MT ILTGGIDLSVG Sbjct: 39 PFIGLLVVCIVMVFASDS----FLSGANIENVLRQVSINAIIAVGMTCVILTGGIDLSVG 94 Query: 84 AIVAITAVVGLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLA 143 +++A+ + L AG+ A + I + +G FG G + M P I TL+TM +A Sbjct: 95 SVMALAGTLAAGLMVAGMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVTLATMGIA 154 Query: 144 RGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFGYVFLH 203 RGLA L + G + + + + KI L V+I V+ V +V L Sbjct: 155 RGLA-------LIYTGGYPIDGLPDWVSFFGSGKI---LGVQAPVVIMAVIYVIAWVLLE 204 Query: 204 HTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAKNTVGV 263 GR +YAIGG+ + L G+ V R + I+Y + +A A+IV TA + S + GV Sbjct: 205 RMPFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPNAGV 264 Query: 264 GWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVIGLMIL 323 G+ELDA+A+VV+GGT I+GG G ++G+++G+L+ +L+ + GV ++ G +IL Sbjct: 265 GFELDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIIL 324 Query: 324 VFVVLQR 330 + + + R Sbjct: 325 LAIYISR 331 Lambda K H 0.327 0.142 0.400 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: 296 Number of extensions: 8 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: 340 Length of database: 335 Length adjustment: 28 Effective length of query: 312 Effective length of database: 307 Effective search space: 95784 Effective search space used: 95784 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 (21.7 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