Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate Ac3H11_2880 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2880 Length = 350 Score = 140 bits (353), Expect = 5e-38 Identities = 98/293 (33%), Positives = 151/293 (51%), Gaps = 16/293 (5%) Query: 29 FASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAFTG----VFL---AKVIG 81 FA+ + N+LT AF+GIIAVGM FVI+SGGIDLSVGS+ A +F+ A V+G Sbjct: 61 FATYDNVMNVLTRTAFIGIIAVGMCFVIISGGIDLSVGSMAALIAGSVILFMNAMAPVLG 120 Query: 82 DFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLRG-VSYLVSEESIP 140 + ++ L +V+G FG GLLI +I FI+TL + R ++Y + +I Sbjct: 121 SPMAAVVVGMLLAVVLGAVFGLVHGLLITKGRIEPFIVTLGTLGIFRAYLTYFSNGGAIT 180 Query: 141 INHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHRTRFGNQVYAIGGNATSAN 200 + + + D S + + G + + L V ++G + +RT +G V AIG N A Sbjct: 181 LENDLSDIYSPVYYANLLGVPIPVW--IFLLVAIVGGVILNRTAYGRYVQAIGSNEQVAQ 238 Query: 201 LMGISTRSTTIRIYMLSTGLATLAGIVFSIYT-QAGYALAGVGV--ELDAIASVVIGGTL 257 + I YML L GI +Y + G A G+ EL+AIA+V++GGT+ Sbjct: 239 YAAVDVHKIKILTYML---LGVCVGIATLLYVPRLGSASPTTGLLWELEAIAAVIVGGTV 295 Query: 258 LSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFIFIALQRG 310 L GG G++ GT+ G + +I +N +S + G ++ +QRG Sbjct: 296 LKGGAGSITGTVVGAILLSVISNILNLTSIISVYLNAAVQGFVIIAVAFMQRG 348 Lambda K H 0.329 0.145 0.428 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: 340 Number of extensions: 21 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: 331 Length of database: 350 Length adjustment: 28 Effective length of query: 303 Effective length of database: 322 Effective search space: 97566 Effective search space used: 97566 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 (21.8 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