Align Fructose import permease protein FrcC (characterized)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 165 bits (418), Expect = 4e-45 Identities = 96/301 (31%), Positives = 159/301 (52%), Gaps = 9/301 (2%) Query: 52 LIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMV 111 L+ ++ ++A L F+SA T I ++ + ++ T V++ AGIDLSVG++M Sbjct: 592 LLAVLAGMVALFSSLSEYFWSAETFITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVMA 651 Query: 112 LSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLAS 171 L++ ++G+ + L G +CG I G + +LP FIV+LGM + V S Sbjct: 652 LAAATSAAAILQWGWTVPAAAALALATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGS 711 Query: 172 NFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAWG 231 ++ + + T D + S FFG ++ ++ V+LV + VL+RT +G Sbjct: 712 AYVVTDSRTQYVGDAISWLSA-PFFGG--------ISFAFLLAVVLVVVAQLVLSRTVFG 762 Query: 232 RYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIE 291 R V +G + EA +LAGV+ + + ++ ++GL+ LAG R+ + P AG ++ Sbjct: 763 RCVVGIGTNEEAMRLAGVDPRPIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQ 822 Query: 292 SITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAI 351 I AVVIGG SL GGRGS++ FG LI+ V GL +G ++ G +I+ AV + Sbjct: 823 VIAAVVIGGTSLMGGRGSVVNTAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIV 882 Query: 352 D 352 D Sbjct: 883 D 883 Lambda K H 0.327 0.141 0.420 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: 680 Number of extensions: 32 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 360 Length of database: 892 Length adjustment: 36 Effective length of query: 324 Effective length of database: 856 Effective search space: 277344 Effective search space used: 277344 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: 53 (25.0 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