Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate WP_083491969.1 ABB28_RS07835 glycerol-3-phosphate dehydrogenase
Query= curated2:P35596 (608 letters) >NCBI__GCF_001431535.1:WP_083491969.1 Length = 501 Score = 148 bits (373), Expect = 6e-40 Identities = 162/549 (29%), Positives = 232/549 (42%), Gaps = 94/549 (17%) Query: 20 LDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDVEV 79 LD+L++GGGI G G+A AA L L E D A TSS S+KLVHGGLRYL+ + Sbjct: 2 LDVLVVGGGINGTGIARDAAGRVLTVALCEQHDLASHTSSASSKLVHGGLRYLEHGQFGM 61 Query: 80 VSDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYDLLAGVS-NTPA 138 V ++ ERAV+ +IAPH+ + P +LP + + + + + LYD L G S P Sbjct: 62 VRKSLQERAVLMRIAPHLVQPLPFVLP---HEAHLRPAWLIHLGLWLYDHLGGRSPQLPR 118 Query: 139 ANKVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHVKAE 198 + + + L +E L G Y D + DARLV+ N A + GA I E Sbjct: 119 SRSLRLRGHPLGAP---LREDLRRGFTYTDAQAPDARLVVVNAIDAAERGAHIWTRTVCE 175 Query: 199 GFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDK-VRNLSNKGTQFSQMRPTK 257 G V RD Q ++ R+++N TG W+ + V N+S T+ +R + Sbjct: 176 QAWRQADG--WSVDLRDPDGTQ-RSVRTRMLVNATGAWAPRFVENISL--TRGVALRLVQ 230 Query: 258 GVHLVVDS-----SKIKVSQPVYFDTGLGDGRMVFVLPRENK-TYFGTTDTDYTGDLEHP 311 G H+VV + + QP DGR+VF LP E+ T GTTD D+ GD Sbjct: 231 GSHIVVPALYAHDHAYLLQQP--------DGRIVFALPFEDHYTLIGTTDVDFEGDPGAV 282 Query: 312 KVTQEDVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGTISDESF 371 V DYL N F + + DI ++G+R L+ Sbjct: 283 HVDDAQRDYLCAAANRSFRQQT-SPRDIVWEFSGVRALL--------------------- 320 Query: 372 DNLIATVESYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNG--LLTLA 429 +D E+ + SAV+R LD D G LL + Sbjct: 321 -----------------DDPEA--------------EASAVTRDYRLDLDAEGAPLLNVL 349 Query: 430 GGKITDYRKMAEGAMERVVDILKAEFDRSFKLINSKTYPVSGGELNPANVDSEIEAFAQL 489 GGK+T YR++AE A VD+L + + + +G +L A + + A L Sbjct: 350 GGKLTTYRRLAEEA----VDLLAGHAGTA-----APAWTATGAQLPGAERGTPAQCAAWL 400 Query: 490 GVS-RGLDSKEAHYLANLYGSNAPKVFALAHSLEQAPGLSLAD--TLSLHYAMRNELTLS 546 L K A + YG+ A + A SL AD + Y +E Sbjct: 401 ATQWPWLPPKLAARWSRTYGARATLILGQADSLAALGTHFGADLYEAEVRYLCTHEWARQ 460 Query: 547 PVDFLLRRT 555 D L RRT Sbjct: 461 ADDVLWRRT 469 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: 593 Number of extensions: 33 Number of successful extensions: 5 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: 501 Length adjustment: 36 Effective length of query: 572 Effective length of database: 465 Effective search space: 265980 Effective search space used: 265980 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 24 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