Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate Ac3H11_797 Glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
Query= curated2:P35596 (608 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_797 Length = 530 Score = 204 bits (518), Expect = 1e-56 Identities = 166/561 (29%), Positives = 254/561 (45%), Gaps = 93/561 (16%) Query: 9 ELSIKKMQERTLDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGG 68 +L + Q DL +IGGG TG GVAL AAA G L++ DFA+GTSSR+TKLVHGG Sbjct: 14 DLLARLAQPHHYDLAVIGGGATGLGVALDAAARGFSVVLVDSHDFAKGTSSRATKLVHGG 73 Query: 69 LRYLKQFDVEVVSDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYD 128 +RYL Q ++ +V + + ER + APH+ + P ++P Y F + + +YD Sbjct: 74 VRYLAQGNIALVREALHERTTLLHNAPHLAQPLPFVMPSYRFWETPF----YGIGLMMYD 129 Query: 129 LLAGVSNTPAANKVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDG 188 LAG + A + L + + L P + EGL GG Y D + +DARL + + A G Sbjct: 130 ALAGKAGL-GATQFLGRARTLACLPTARTEGLKGGVKYWDGQFDDARLALALARTAASLG 188 Query: 189 ALIANHVKAEGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKVRNLSNKGT 248 AL+ N+ A L E+GK+ G V D + Q F ++AR V+N TG W D +R + + Sbjct: 189 ALVVNYCPARA-LVHEAGKVAGFVCEDADSGQQFTVRARTVVNATGVWVDSLRQMDGEAI 247 Query: 249 QFSQ---MRPTKGVHLVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTTDTDYT 305 + P++GVH+VVD + S DGR++F +P K GTTD+ Sbjct: 248 GRPVKPIVAPSQGVHIVVDREFLP-SDHALMVPKTADGRVLFAVPWLGKLILGTTDSPRQ 306 Query: 306 GDLEHPKVTQEDVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGT 365 + P+ +E+V ++L + R+ +DI S W GLRPL+ D +G N Sbjct: 307 DIVREPEPFREEVRFILE-ESARYLTRAPKAEDIRSIWVGLRPLV---KPQDDDGDNTKK 362 Query: 366 ISDESFDNLIATVESYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNGL 425 I SR ++ +GL Sbjct: 363 I----------------------------------------------SREHTVLASRSGL 376 Query: 426 LTLAGGKITDYRKMAEGAMER-----VVDILKAEFDRSFKLINSKTYPVSGGELNPANVD 480 +T+ GGK T YR MAE +++ ++ A L+ + PV Sbjct: 377 ITVTGGKWTTYRAMAEDVLQKCFATGLLPTKPAGVTNQLPLVGTPQAPVQ---------- 426 Query: 481 SEIEAFAQLGVSRGLDSKEAHYLANLYGSNAPKVFALAHSLEQAPGLSLADTLSLHYAMR 540 ++ ++GL S YGS A V A+ + G L + + + +A R Sbjct: 427 ------HRISDAQGLHS---------YGSEAAAVLAIP-GAQTVLGGGLTEAM-VRFAAR 469 Query: 541 NELTLSPVDFLLRRTNHMLFM 561 +E + D L RR + +LF+ Sbjct: 470 HEYACTVEDVLARR-SRLLFL 489 Lambda K H 0.314 0.133 0.368 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: 642 Number of extensions: 33 Number of successful extensions: 7 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: 608 Length of database: 530 Length adjustment: 36 Effective length of query: 572 Effective length of database: 494 Effective search space: 282568 Effective search space used: 282568 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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