Align Fructose import permease protein FruG (characterized)
to candidate RR42_RS32895 RR42_RS32895 ABC transporter permease
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Cup4G11:RR42_RS32895 Length = 318 Score = 141 bits (355), Expect = 3e-38 Identities = 90/298 (30%), Positives = 163/298 (54%), Gaps = 11/298 (3%) Query: 33 ILMIIMGQALFGT-YIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGAIVAITAV 91 +L++ +G ++ G ++ + + ++ L+++A+ MTL I+T G+DLS+GA++ + V Sbjct: 25 LLLLSLGFSVTGPGFLSVENLLNIGAQSTILLLIALPMTLIIMTEGLDLSMGAVLTLCGV 84 Query: 92 VGLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMFLARGLASIIS 151 V + A L + LL G FGLL G L+ + PF+ATL T+ +A+GLA +++ Sbjct: 85 VLAMVMVATESLPLALGAALLTGLAFGLLNGALVSWLEIPPFVATLGTLGVAQGLA-LVA 143 Query: 152 TDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFGYVFLHHTRTGRTI 211 TD G + I I +I ++ L + + IA V + L+HTR G + Sbjct: 144 TD------GQSVTGIGEAIPLIYAGQL---LGVPLPIWIAAVFYGLFHWLLYHTRFGAYV 194 Query: 212 YAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAKNTVGVGWELDAVA 271 +A+GG+R + + G+ + +Y +A +A+++ TA + + T +G E DA+A Sbjct: 195 FALGGNREALKFSGVRINVYLIAVYALGGLMAGVAALLLTARMNAGHPTAAIGLEFDAIA 254 Query: 272 SVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVIGLMILVFVVLQ 329 +V +GGT G G++ G+VLG L +L + GVP+ IGL++LV ++++ Sbjct: 255 AVAVGGTTFDRGNGWLPGTVLGVLAVGVLRNGLNLVGVPSSVQVAAIGLLVLVVLLIE 312 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: 239 Number of extensions: 9 Number of successful extensions: 3 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: 318 Length adjustment: 28 Effective length of query: 312 Effective length of database: 290 Effective search space: 90480 Effective search space used: 90480 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