Align glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate BPHYT_RS28480 BPHYT_RS28480 hydroxyglutarate oxidase
Query= CharProtDB::CH_000554 (387 letters) >FitnessBrowser__BFirm:BPHYT_RS28480 Length = 398 Score = 127 bits (318), Expect = 7e-34 Identities = 106/399 (26%), Positives = 184/399 (46%), Gaps = 44/399 (11%) Query: 7 DICIIGGGIIGASVARELAKFDK--KIVVLEANPRLALETSSHNSGLVHGGFDPRPETLN 64 D CIIGGGI+G + A EL + + +++LE LA + HNSG++H G +P +L Sbjct: 4 DFCIIGGGIVGLATAMELLQREPTASLLLLEKETTLAKHQTGHNSGVIHAGIYYQPGSLK 63 Query: 65 AKLNVLGKKRYEDWIKEMDFPYLRIDSTIVAFNDEEMKHVHMLYDRGLINGLDPKEMQVI 124 A+L G + + + E P+ +VA N E+ + LY R NGL ++ + Sbjct: 64 AELCKRGAEATKQFCTEHAIPFDVCGKLLVASNPLELSRMEALYARSQQNGL---RVERL 120 Query: 125 DAKELQKREPNISKQAVGALVCNSSIAIDPVLLTTTLMRNAIKNGVELKVNSKVVDIKKV 184 DA ELQ+REPNI +G L +++ +D + + R K G E+++ ++V I +V Sbjct: 121 DAAELQRREPNI--VGLGGLFLDATGIVDYRQVCEAMARVIEKAGGEIRLGTQVTSIAEV 178 Query: 185 DNIFEIKTAKDEIIQAEVVVNVAGHYADVIANMAGYG-DFKLTTRRGEYRILDKSEAGIV 243 + + + ++ +A+ +V G +D +A +AG D ++ RGEY L S+ +V Sbjct: 179 GDYVTVGASDEQQWRAKKLVVCGGLQSDRLARLAGVKIDHQIVPFRGEYYRLPASKNDVV 238 Query: 244 NSVVFMV--PTIHGKGVIVAPMLDGRVMVGPTAL-----DGVPKEETLLVTQQQY----- 291 +++ + P + GV + M+DG V VGP A+ + PK L +Y Sbjct: 239 RHLIYPIPDPDLPFLGVHLTRMIDGSVTVGPNAVLGFGRENYPKFSVNLRDVAEYAAFPG 298 Query: 292 ----------DNIGKIGKHLI------------PNINMDKTCTVYAGSRPIDIETNDFII 329 +G++ L P++ +D AG R + + ++ Sbjct: 299 FWKTIWRNLGSGMGEMKNSLFKRGYLEQCRKYCPSLTVDDLLPYEAGIRAQAVMRDGTLV 358 Query: 330 RP--AKNDKKFINVAGMKSPAIASAPAIADMVCDLVKNA 366 + + ++V SPA SA I M+ D + A Sbjct: 359 HDFLFADTPRMVHVCNAPSPAATSAMPIGSMIADRILKA 397 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: 298 Number of extensions: 13 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: 387 Length of database: 398 Length adjustment: 31 Effective length of query: 356 Effective length of database: 367 Effective search space: 130652 Effective search space used: 130652 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