Align Glucose/galactose transporter (characterized, see rationale)
to candidate 351634 BT2106 putative transmembrane hexose transporter (NCBI ptt file)
Query= uniprot:Q8A6W8 (389 letters) >FitnessBrowser__Btheta:351634 Length = 386 Score = 284 bits (727), Expect = 3e-81 Identities = 147/376 (39%), Positives = 236/376 (62%), Gaps = 5/376 (1%) Query: 10 SKLVPVMLCFFAMGFVDLVGIASNYVKADLGLTDSQANIFPSLVFFWFLIFSVPTGMLMS 69 SK++PV+ FF MGF DLVG++ Y K +++QA PS+VF WFL+ S+P + M Sbjct: 5 SKILPVLFGFFIMGFCDLVGVSVTYAKDYFSWSETQAGFLPSMVFIWFLLISIPISIWMD 64 Query: 70 RIGQKKTVLLSLIVTFASLLLPVFGDSYALMLISFSLLGIGNALMQTSLNPLLSNIVRGD 129 + G+K L+ L+ TF +LLP+ + I+F+LLGIGN ++Q SLNPLL+N++ Sbjct: 65 KKGRKTISLIGLLSTFIGMLLPLLTFTQTACYIAFALLGIGNTILQVSLNPLLTNVIAEG 124 Query: 130 RLASSLTFGQFVKAIASFLAPYIAMWGATQAIPSFDLGWRVLFPIYMVIAILAILLLNAT 189 +L+S +T GQF+KA++SF+ P +A + + + W ++FPI+ I +++ + L T Sbjct: 125 KLSSIMTAGQFIKALSSFVGPIVAGFCSV-----YFNNWILMFPIFAAITLISGIWLFFT 179 Query: 190 QIEEEKEEGKPSTFGQCLALLGKPFILLCFIGIMCHVGIDVGTNTTAPKILMERIGMTLD 249 I E+ ++ S+F Q ++LL I L F GI+C VG+DVG N PK+L+E +T + Sbjct: 180 PINEKDDKRLTSSFYQVISLLKNKTICLLFGGIICIVGLDVGMNVFTPKLLIENAELTKE 239 Query: 250 DAAFATSLYFIFRTAGCFLGSFILRQMSPKSFFGISVVMMLAAMVGLFIFHDKAVIYACI 309 A++ TS YF RT G G +L + S ++ I++ ++L A+ ++ H + +I + Sbjct: 240 IASYGTSWYFAARTLGTLCGVILLAKFSEIYYYRINMFIVLIALSCIYWIHSQYIILLLV 299 Query: 310 ALIGFGNSNVFSVIFSQALLYLPGKKNEVSGLMIMGLFGGTVFPLAMGVASDTSMGQNGA 369 +I F S++F+VI+S AL LP K NE+SGLMI G+ GG++ P MGV +D + Q+G+ Sbjct: 300 CIIAFAMSSIFAVIYSLALHTLPYKTNEISGLMITGISGGSIIPPLMGVCADYTESQSGS 359 Query: 370 IAVMTVGVLYLLFYTF 385 I VM + V+YL+ +F Sbjct: 360 ILVMLICVIYLILCSF 375 Lambda K H 0.330 0.143 0.423 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: 476 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: 389 Length of database: 386 Length adjustment: 30 Effective length of query: 359 Effective length of database: 356 Effective search space: 127804 Effective search space used: 127804 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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