Align Fructose import permease protein FruG (characterized)
to candidate 3607107 Dshi_0529 Monosaccharide-transporting ATPase (RefSeq)
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Dino:3607107 Length = 333 Score = 124 bits (310), Expect = 4e-33 Identities = 93/306 (30%), Positives = 149/306 (48%), Gaps = 10/306 (3%) Query: 25 TLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSVGA 84 TL A VI +L + ++ + +S L + ILAV L +++GGID+S A Sbjct: 15 TLVAGVI-MLFCFVATVSDPRFLTITTVSDLLRASIVIGILAVGAMLVLVSGGIDVSFTA 73 Query: 85 IVAITAVVGLKLANA---GVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQPFIATLSTMF 141 I L+ +P ++ +I ++ GA G + G I + I TL T+ Sbjct: 74 IAVFAMYSSTVLSLTIWPEIPWPVIFVISVVFGAALGAINGFFIAFLGLPTLIVTLGTLS 133 Query: 142 LARG-LASIISTDSLTF--PQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIALVVVVFG 198 + RG L + I + ++ P DFS + + N S + L V+V Sbjct: 134 IFRGFLLTFIGSQRISDLPPSMRDFS---RGVIARGTTEAGNFYSIPWAALALLFVIVLT 190 Query: 199 YVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYTANIGSAK 258 + L T GR+IYAIGGS SA +G+ VK TQ+ +Y+ LA LA I++ + A Sbjct: 191 WFILKKTMLGRSIYAIGGSVESARRIGINVKWTQFFVYVYVGALAGLAGIIHGSVGRMAD 250 Query: 259 NTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPAEWTTIVI 318 VG EL +A+VV+GG + GG+G + G++LG + I+ G+P W ++ I Sbjct: 251 PFSLVGLELSVIAAVVLGGARLIGGYGTLTGTMLGVALIVIVQNSLIVIGIPTTWQSVTI 310 Query: 319 GLMILV 324 G++IL+ Sbjct: 311 GILILL 316 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: 282 Number of extensions: 16 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: 333 Length adjustment: 28 Effective length of query: 312 Effective length of database: 305 Effective search space: 95160 Effective search space used: 95160 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