Align L-ribulose-5-phosphate 4-epimerase UlaF; L-ascorbate utilization protein F; Phosphoribulose isomerase; EC 5.1.3.4 (characterized)
to candidate 349881 BT0353 putative sugar epimerase/aldolase (NCBI ptt file)
Query= SwissProt::P39306 (228 letters) >FitnessBrowser__Btheta:349881 Length = 227 Score = 320 bits (821), Expect = 1e-92 Identities = 150/227 (66%), Positives = 183/227 (80%), Gaps = 1/227 (0%) Query: 1 MQKLKQQVFEANMELPRYGLVTFTWGNVSAIDRERGLVVIKPSGVAYETMKAADMVVVDM 60 +++LK++VF AN+EL ++GLV FTWGNVSAIDRE LVVIKPSGV+Y+ MKA DMVVVD+ Sbjct: 2 LEELKEKVFHANLELVKHGLVIFTWGNVSAIDRETELVVIKPSGVSYDDMKAEDMVVVDL 61 Query: 61 SGKVVEGEYRPSSDTATHLELYRRYPSLGGIVHTHSTHATAWAQAGLAIPALGTTHADYF 120 GKVVEG +PSSDT TH+ LY+ +P +GG+VHTHST+ATAWAQAG IP +GTTHADYF Sbjct: 62 DGKVVEGRLKPSSDTPTHVVLYKAFPEIGGVVHTHSTYATAWAQAGCDIPNIGTTHADYF 121 Query: 121 FGDIPCTRGLSEEEVQGEYELNTGKVIIETLGNAEPLHTPGIVVYQHGPFAWGKDAHDAV 180 IPCT ++E EV+G YEL TG VI++ P+HTPG++V HGPF+WGKDAHDAV Sbjct: 122 HDAIPCTADMTEAEVKGAYELETGNVIVKRFEGLNPVHTPGVLVKNHGPFSWGKDAHDAV 181 Query: 181 HNAVVMEEVAKMAWIARGINPQLNHIDSFLMNKHFMRKHGPNAYYGQ 227 HNAVVME+VAKMA IA +NP L ++ L+ KHF RKHGPNAYYGQ Sbjct: 182 HNAVVMEQVAKMASIAYAVNPNLT-MNPLLVEKHFSRKHGPNAYYGQ 227 Lambda K H 0.318 0.134 0.411 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: 278 Number of extensions: 7 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: 228 Length of database: 227 Length adjustment: 22 Effective length of query: 206 Effective length of database: 205 Effective search space: 42230 Effective search space used: 42230 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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