Align Fructose import permease protein FrcC (characterized)
to candidate PP_2456 PP_2456 D-ribose ABC transporter - permease subunit
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Putida:PP_2456 Length = 331 Score = 158 bits (399), Expect = 2e-43 Identities = 91/299 (30%), Positives = 156/299 (52%), Gaps = 9/299 (3%) Query: 56 VLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSSV 115 +L++I L F+S T + + Q+ + ++ T V++ GIDLSVG+++ L++ Sbjct: 33 LLAMIVLFSFLSSHFWSYGTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVLALAAS 92 Query: 116 IMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASNFLY 175 + +G+ S + G+ V AL G I G + ++P FIV+LG+ ++ + + Sbjct: 93 TVSVAILGWGWGVLPSALLGMAVAALAGSITGGVTVAWRIPSFIVSLGVLEMARGLAYQF 152 Query: 176 SANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAWGRYVY 235 + + T D A S FG + ++ +L++ L VL RT +GRY+ Sbjct: 153 TDSRTAYIGDAYAWFSNPVAFG---------VSPAFIIALLVIVLAQLVLTRTVFGRYLI 203 Query: 236 AVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIESITA 295 +G + EA +LAG++ + ++ L GL+ LA I R+ + P AG ++ I A Sbjct: 204 GIGTNEEAVRLAGIDPRPYKVLVFALMGLLAGLAALFQISRLEAADPNAGSGLELQVIAA 263 Query: 296 VVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAIDQW 354 VVIGG SL GGRGS++ FG LI+ V + GL +G ++ G +I+IAV +D + Sbjct: 264 VVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGASEPTKRIITGAVIVIAVVLDTY 322 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: 363 Number of extensions: 23 Number of successful extensions: 2 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: 360 Length of database: 331 Length adjustment: 29 Effective length of query: 331 Effective length of database: 302 Effective search space: 99962 Effective search space used: 99962 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