Align Fructose import permease protein FruG (characterized)
to candidate Ac3H11_605 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_605 Length = 345 Score = 222 bits (565), Expect = 1e-62 Identities = 127/316 (40%), Positives = 190/316 (60%), Gaps = 8/316 (2%) Query: 17 KLDRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTG 76 + + + +P A + +F+ M +G L+ + +L ID+A+LII+AV MT IL+G Sbjct: 26 RFNPKYLPLAATISLFVAMATLGSVLYTGFFSAQVFLNLLIDNAFLIIVAVGMTFVILSG 85 Query: 77 GIDLSVGAIVAITAVVGLKLA-NAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIA 135 GIDLSVG++VA+T +V L + G + + ++LL+G FG G LIE F +QPFI Sbjct: 86 GIDLSVGSVVALTTMVLAALVEHRGWNPMVAIPLVLLMGTAFGAFMGFLIERFRLQPFIV 145 Query: 136 TLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVV 195 TL+ MFLARGL +IS DS++ + + + +S +G +IA+ V+ Sbjct: 146 TLAGMFLARGLCYLISIDSISITHEGYSELAQWRLPLWEGASLS------LGALIAIAVL 199 Query: 196 VFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIG 255 + H T GR++YA+GGS SA LMGLPV+RT +Y S +ALA +V+T + Sbjct: 200 LVALFVAHCTPFGRSVYAVGGSEHSAVLMGLPVRRTLIGVYTLSGFCSALAGVVFTFYML 259 Query: 256 SAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTS-DFGVPAEWT 314 S VG ELDA+A+VVIGGT++TGG GYV G++ G L+ I+ L S D + + WT Sbjct: 260 SGYGLHAVGMELDAIAAVVIGGTLLTGGVGYVAGTLFGVLMLGIIQTLISFDGTLSSWWT 319 Query: 315 TIVIGLMILVFVVLQR 330 IV+G+++ F +LQR Sbjct: 320 RIVVGVLLFAFCLLQR 335 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: 319 Number of extensions: 12 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: 340 Length of database: 345 Length adjustment: 29 Effective length of query: 311 Effective length of database: 316 Effective search space: 98276 Effective search space used: 98276 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