Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate WP_086509596.1 BZY95_RS08920 glycerol-3-phosphate dehydrogenase
Query= curated2:P35596 (608 letters) >NCBI__GCF_002151265.1:WP_086509596.1 Length = 500 Score = 183 bits (465), Expect = 1e-50 Identities = 169/548 (30%), Positives = 252/548 (45%), Gaps = 95/548 (17%) Query: 20 LDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDVEV 79 LDL IIGGGI G G+A AA GL L E D A TSS S+KL+HGGLRYL+ + + Sbjct: 9 LDLFIIGGGINGTGIANDAAGRGLSVSLCEQGDLAGATSSASSKLIHGGLRYLEHHEFRL 68 Query: 80 VSDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYDLLAGVSNTPAA 139 V + + ER V+ + APHI +LP + ++ + LYD L P + Sbjct: 69 VGEALREREVLLRKAPHIIWPLRFILP---HRSHLRPAWMIRAGLFLYDHLGKRKMLPGS 125 Query: 140 NKV-LSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHVKAE 198 V + D L+ EG+ G Y D +DARLV+ N +A + GA I + Sbjct: 126 RSVRFAADSPLQ-------EGIKRGFEYSDCWVDDARLVVLNALQAREGGAEILVRTRCI 178 Query: 199 GFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDK-VRNLSNKGTQFSQMRPTK 257 G E I + D+ + + FE +AR ++N GPW ++ VR + + +++S +R + Sbjct: 179 G--AKEENGIWRIELEDVRSGERFERQARTLVNAAGPWVERVVREQAARSSRYS-IRMIQ 235 Query: 258 GVHLVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENK-TYFGTTDTDYTGDLEHPKVTQE 316 G HL+V ++ Y D R+VFVLP E+ + GTTD Y GD +++E Sbjct: 236 GSHLIV--PRLNGDDRAYILQN-SDRRIVFVLPYEDDFSLIGTTDRRYQGDPTQAAISEE 292 Query: 317 DVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGTISDESFDNLIA 376 ++DYLLG+VN F + D+ SS++G+RPL SA Sbjct: 293 EIDYLLGVVNAHF-RRQLQRSDVISSFSGVRPLCDDESA--------------------- 330 Query: 377 TVESYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNG--LLTLAGGKIT 434 +PSA++R +L DD G LL++ GGKIT Sbjct: 331 -------------------------------EPSAMTRDYTLAFDDQGAPLLSVFGGKIT 359 Query: 435 DYRKMAEGAMERVVDILKAEFDRSFKLINSKTYPVSGGEL-NPANVDSE-IEAFAQLGVS 492 YRK+AE A++++ +L A S+ + + GGE+ N N + + + LG + Sbjct: 360 TYRKLAEAALKQLKPVLPA-MGPSW----TAEAALPGGEIGNQENFMARLLHDYPWLGEA 414 Query: 493 RGLDSKEAHYLANLYGSNAPKVFALAHSLEQ-----APGLSLADTLSLHYAMRNELTLSP 547 R A A YGS + A E GL+ A+ Y + +E + Sbjct: 415 R------ARRFARSYGSLCLRFLAGTQCAEDLGEHFGAGLTAAEA---DYLVDHEWATTV 465 Query: 548 VDFLLRRT 555 D L RRT Sbjct: 466 EDILWRRT 473 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: 568 Number of extensions: 25 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: 608 Length of database: 500 Length adjustment: 36 Effective length of query: 572 Effective length of database: 464 Effective search space: 265408 Effective search space used: 265408 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 Apr 09 2024. 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