Align Fructose import permease protein FruF (characterized)
to candidate Pf6N2E2_524 Inositol transport system permease protein
Query= SwissProt::Q8G846 (356 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_524 Length = 340 Score = 143 bits (360), Expect = 8e-39 Identities = 91/286 (31%), Positives = 157/286 (54%), Gaps = 26/286 (9%) Query: 58 LITMLQESARYLMIATGMTLVISTAGIDLSVGSVMAVAG--AAAMQTLSN---------- 105 L+ M+ + + ++A G+T VI T GIDLS GSV+A++ AA++ S+ Sbjct: 56 LVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLT 115 Query: 106 GMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDAS 165 + VW+ ++ L VGL G +NG++++ G+ PFI TL MM++ RG+A+ T G Sbjct: 116 DLPVWIPVVAGLGVGLLAGAINGSIIAITGIPPFIATLGMMVSARGLARYYTEG------ 169 Query: 166 AVAGNEPLKWFANGF-ILGIPA-NFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRM 223 +P+ ++ + +G A +I +++ ++ + R T G A+G N +A+R Sbjct: 170 -----QPVSMLSDSYTAIGHGAMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAART 224 Query: 224 TGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLG 283 +GI K+ L +VY+I+G LA +AG+ A+A G E+ AI A VIGGTSL G Sbjct: 225 SGINVKRHLVIVYSIAGLLAGLAGVVASARA-ATGQAGMGMSYELDAIAAAVIGGTSLAG 283 Query: 284 GKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVVVIVICVM 329 G + G+ +GA+I+ ++ +GV+A ++++V V+ Sbjct: 284 GVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVI 329 Lambda K H 0.325 0.136 0.384 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: 325 Number of extensions: 18 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: 356 Length of database: 340 Length adjustment: 29 Effective length of query: 327 Effective length of database: 311 Effective search space: 101697 Effective search space used: 101697 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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