Align Fructose import permease protein FruG (characterized)
to candidate BWI76_RS02810 BWI76_RS02810 sugar ABC transporter permease YjfF
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Koxy:BWI76_RS02810 Length = 328 Score = 181 bits (460), Expect = 2e-50 Identities = 108/315 (34%), Positives = 178/315 (56%), Gaps = 8/315 (2%) Query: 20 RQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGID 79 ++ +P + + +F+L + F + I ++ D+A+L I+AV MT IL+GGID Sbjct: 3 KRNLPLMITLAVFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGID 62 Query: 80 LSVGAIVAITAVVGLKLANA-GVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLS 138 LSVG+++A T V K G+ + ++L++G FG G LI+ + FI TL+ Sbjct: 63 LSVGSVIAFTGVFLAKAIGFWGISPLVAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLA 122 Query: 139 TMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFG 198 MF RG++ ++S +S+ + I ++S +G+++ L+VV+ G Sbjct: 123 GMFFLRGVSYLVSEESIPINHPVYDALSGLAWTIPGGGRLSA-----MGLLM-LLVVIGG 176 Query: 199 YVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAK 258 H TR G +YAIGG+ +SA LMG+ + T IY+ S LA LA IV++ + Sbjct: 177 IFMAHRTRFGNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGY 236 Query: 259 NTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDP-LTSDFGVPAEWTTIV 317 GVG ELDA+ASVVIGGT+++GG G VLG++ G ++ ++ + D + + WT I Sbjct: 237 ALAGVGVELDAIASVVIGGTLLSGGVGTVLGTLFGVGIQGLIQTYINFDGTLSSWWTKIA 296 Query: 318 IGLMILVFVVLQRAV 332 IG+++ +F+ LQR + Sbjct: 297 IGILLFIFIALQRGL 311 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: 15 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: 328 Length adjustment: 28 Effective length of query: 312 Effective length of database: 300 Effective search space: 93600 Effective search space used: 93600 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