Align glycerol-3-phosphate oxidase (EC 1.1.3.21) (characterized)
to candidate GFF810 PGA1_c08240 aerobic glycerol-3-phosphate dehydrogenase GlpD
Query= BRENDA::Q833L7 (609 letters) >FitnessBrowser__Phaeo:GFF810 Length = 529 Score = 155 bits (391), Expect = 5e-42 Identities = 156/567 (27%), Positives = 240/567 (42%), Gaps = 102/567 (17%) Query: 18 QHLDVLIIGGGITGAGVALQASAAKMKTGLIEMQDFAEGTSSRSTKLVHGGIRYLKTFDV 77 Q D+ IIGGGI G G+A A+ + L EM D A TSS STKL HGG+RYL+ F+ Sbjct: 9 QITDLFIIGGGINGCGIARDAAGRGLSVALAEMNDLASATSSASTKLFHGGLRYLEYFEF 68 Query: 78 EVVADTVKERAVVQSIAPHIPKADPMLLPI-----YDEPNATFNLFS------------- 119 +V + + ER V+ PHI +LP +D T L + Sbjct: 69 RLVREALIEREVLLKAMPHISWPMRFVLPFHKDMRFDNTTPTSKLLTTIMPWMKGRRPAW 128 Query: 120 -VKIAMDLYDQLAD---VTGTKYANYLLTKDEVLAREPQLKSEGLQGGGVYLDYRNNDAR 175 +++ + +YD L + GT + L + +P+ K+ Y D DAR Sbjct: 129 LIRLGLFMYDSLGKRGILPGTSKLD-LASDPAGRPLDPKFKT-----AFEYSDCWIEDAR 182 Query: 176 LVIENIKQAVADGAHAVSRVQAVGFLYNDEGKITGIQAKDLLTDEQFEIHADVVINTTGP 235 LV+ N + A A GA ++R + G N + + I +D+ T E + A +++N GP Sbjct: 183 LVVLNARDAEARGAEIMTRTKVTGATRNADHWV--IDLEDITTGETSQRRAKMLVNAGGP 240 Query: 236 WSDKLRGLDKNDSFTPQMRPTKGVHLVVDKSRLNVPQPTYFDTGKQDGRMVFVVPREEK- 294 W + + +R +G H+VV K L YF G DGR++F +P EE Sbjct: 241 WVADVLRQKLGQNSRESVRLVRGSHIVVPK--LYDHGRCYFFQG-TDGRIIFAIPYEEDY 297 Query: 295 TYFGTTDTDYHGDFQHPTVEQSDVDYLLEVVNNRYPEVQLTIDDIEASWAGLRPLISANG 354 T GTTD D+ PT + DYL+ ++Y L+ DDI +++G+RPL Sbjct: 298 TLIGTTDADHPDPQTAPTCTPEEQDYLINFA-SQYFANPLSRDDIVWTYSGVRPL----- 351 Query: 355 GSDYNGGNNGKLSDKSIDEVIDVVDRYQKNQTDKREIEEVLNHLEDSLVENKVNPSAVSR 414 Y+ G + + RE LN Sbjct: 352 ---YDDGASSATA-------------------ATREYVLTLND----------------- 372 Query: 415 GSSLERSADGLLTLAGGKLTDYRKMAEGAMKMIQTILAEEYQKEFT---LIDSKNYPVSG 471 SA LL + GGK+T YRK+AE A++ I T+ + ++T + ++PV Sbjct: 373 ------SAAPLLNVFGGKITTYRKLAEAALEKIATVF-PDLPADWTAGVALPGGDFPVGD 425 Query: 472 GKLNPATVDEELEALAKHGVSKGLSEKDALYLAHLYGSNVPTVFEMIDDAKVIP---GLT 528 A + ++ L+ + + L YG+ V A + G T Sbjct: 426 VAKLTAKLAQDYPFLSPYATRR---------LIRAYGTEAWEVLGKATTAADLGEAFGAT 476 Query: 529 LTETVSLNYAMEEEMALTPVDFLLRRT 555 +T L++ + E T D+LLRRT Sbjct: 477 VTAR-ELDWTIAHEWVRTGEDYLLRRT 502 Lambda K H 0.314 0.133 0.372 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: 634 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 609 Length of database: 529 Length adjustment: 36 Effective length of query: 573 Effective length of database: 493 Effective search space: 282489 Effective search space used: 282489 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: 42 (22.0 bits) S2: 53 (25.0 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