Align glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate 16750 b2660 orf, hypothetical protein (VIMSS)
Query= CharProtDB::CH_000554 (387 letters) >FitnessBrowser__Keio:16750 Length = 422 Score = 112 bits (280), Expect = 2e-29 Identities = 84/280 (30%), Positives = 139/280 (49%), Gaps = 10/280 (3%) Query: 7 DICIIGGGIIGASVARELAKF--DKKIVVLEANPRLALETSSHNSGLVHGGFDPRPETLN 64 D IIGGGIIG S A +L D +I +LE A + HNSG++H G P +L Sbjct: 3 DFVIIGGGIIGMSTAMQLIDVYPDARIALLEKESAPACHQTGHNSGVIHAGVYYTPGSLK 62 Query: 65 AKLNVLGKKRYEDWIKEMDFPYLRIDSTIVAFNDEEMKHVHMLYDRGLINGLDPKEMQVI 124 A+ + G + + + + Y +VA +D EM+ + L++R NG+ E + + Sbjct: 63 AQFCLAGNRATKAFCDQNGIRYDNCGKMLVATSDLEMERMRALWERTAANGI---EREWL 119 Query: 125 DAKELQKREPNISKQAVGALVCNSSIAIDPVLLTTTLMRNAIKNGVELKVNSKVVDIKKV 184 +A EL++REPNI+ +G + SS + +T + + G E+ N++V + + Sbjct: 120 NADELREREPNIT--GLGGIFVPSSGIVSYRDVTAAMAKIFQSRGGEIIYNAEVSGLNEH 177 Query: 185 DNIFEIKTAKDEIIQAEVVVNVAGHYADVIANMAGY-GDFKLTTRRGEYRILDKSEAGIV 243 N I+T + +A +++ +G AD + M G F + RGEY L IV Sbjct: 178 KNGVVIRTRQGGEYEASTLISCSGLMADRLVKMLGLEPGFIICPFRGEYFRLAPEHNQIV 237 Query: 244 NSVVFMV--PTIHGKGVIVAPMLDGRVMVGPTALDGVPKE 281 N +++ + P + GV + M+DG V VGP A+ +E Sbjct: 238 NHLIYPIPDPAMPFLGVHLTRMIDGSVTVGPNAVLAFKRE 277 Lambda K H 0.318 0.136 0.391 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: 324 Number of extensions: 16 Number of successful extensions: 4 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: 387 Length of database: 422 Length adjustment: 31 Effective length of query: 356 Effective length of database: 391 Effective search space: 139196 Effective search space used: 139196 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: 50 (23.9 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