Align Inositol transport system permease protein (characterized)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Keio:17810 Length = 321 Score = 213 bits (542), Expect = 5e-60 Identities = 137/335 (40%), Positives = 194/335 (57%), Gaps = 34/335 (10%) Query: 11 TVPTKSRRR------LPTELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVS 64 T T S RR L + S+ +L+ I +V L F +N+ L ++ Q S Sbjct: 2 TTQTVSGRRYFTKAWLMEQKSLIALLVLIAIVSTL-----SPNFFTINN--LFNILQQTS 54 Query: 65 IIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVA 124 + ++A+G+T VI+T+GIDLS GS+LAL+ +AAS+ ++ + VA Sbjct: 55 VNAIMAVGMTLVILTSGIDLSVGSLLALTGAVAASIVGI------------EVNALVAVA 102 Query: 125 MGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSM----LSDSYT 180 L +G GA+ G I+A + FIATL MM+ RG+ YT G PV+ +D + Sbjct: 103 AALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFG 162 Query: 181 AIGHGA-----MPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLII 235 G G PV I +V + L +T+ G+Y YA+GGN A R SGINV + II Sbjct: 163 WFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKII 222 Query: 236 VYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGA 295 VYS+ GLLA LAG++ AR ++ Q G YELDAIAA V+GGTSLAGG GRI GT+IGA Sbjct: 223 VYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGA 282 Query: 296 LILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVID 330 LILG + +G +GV +Y Q I+K ++I++AV++D Sbjct: 283 LILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVD 317 Lambda K H 0.325 0.140 0.394 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: 270 Number of extensions: 11 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: 340 Length of database: 321 Length adjustment: 28 Effective length of query: 312 Effective length of database: 293 Effective search space: 91416 Effective search space used: 91416 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