Align Fructose import permease protein FruG (characterized)
to candidate Pf6N2E2_524 Inositol transport system permease protein
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_524 Length = 340 Score = 150 bits (379), Expect = 5e-41 Identities = 101/330 (30%), Positives = 178/330 (53%), Gaps = 34/330 (10%) Query: 20 RQMIPTLAAVVIFILMIIMGQALFGTYIR-LGFISS------LFIDHAYLIILAVAMTLP 72 R+ +PT ++ + ++ I + +FG +R F+ + + + + + +LA+ +T Sbjct: 17 RRRLPTELSIFLVLIGIGLVFEMFGWIMRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQV 76 Query: 73 ILTGGIDLSVGAIVAITAVVGLKLANAG------------VPAFLVMIIMLLIGAVFGLL 120 I+T GIDLS G+++A++A++ LA +P ++ ++ L +G + G + Sbjct: 77 IITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVVAGLGVGLLAGAI 136 Query: 121 AGTLIEEFNMQPFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISN 180 G++I + PFIATL M ARGLA + +G S +S+ I + + Sbjct: 137 NGSIIAITGIPPFIATLGMMVSARGLARY-------YTEGQPVSMLSDSYTAIGHGAMP- 188 Query: 181 DLSFNVGVIIALVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSA 240 VII LVV V ++ L +T+ G+ YAIGG+ +A G+ VKR I+Y + Sbjct: 189 -------VIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAG 241 Query: 241 TLAALASIVYTANIGSAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSIL 300 LA LA +V +A + + +G+ +ELDA+A+ VIGGT + GG G + G+V+G+L+ ++ Sbjct: 242 LLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVM 301 Query: 301 DPLTSDFGVPAEWTTIVIGLMILVFVVLQR 330 + GV A I+ GL+I+V VV+ + Sbjct: 302 ASGFTFVGVDAYIQDIIKGLIIVVAVVIDQ 331 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: 262 Number of extensions: 12 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: 340 Length adjustment: 28 Effective length of query: 312 Effective length of database: 312 Effective search space: 97344 Effective search space used: 97344 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