Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate N515DRAFT_3909 N515DRAFT_3909 homodimeric glycerol 3-phosphate dehydrogenase (quinone) (EC 1.1.5.3)
Query= curated2:P35596 (608 letters) >FitnessBrowser__Dyella79:N515DRAFT_3909 Length = 499 Score = 176 bits (446), Expect = 2e-48 Identities = 170/549 (30%), Positives = 256/549 (46%), Gaps = 92/549 (16%) Query: 20 LDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDVEV 79 +D+L++GGGI G G+A A GL L E D A TSS STKL+HGGLRYL+QF+ + Sbjct: 5 VDVLVVGGGINGTGIARDAVGRGLSVWLCEQDDLASHTSSASTKLIHGGLRYLEQFEFAL 64 Query: 80 VSDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYD-LLAGVSNTPA 138 V ++ER ++ ++APHI +LP + +++ + LYD L G + P Sbjct: 65 VGKALAEREILLRVAPHIIWPLRFVLP---HQSHLRPAWMIRLGLFLYDHLQRGRRSLPG 121 Query: 139 ANKV-LSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHVKA 197 + +V LS+ V QP L+ E + G VY D DARLV+ N A Q GA + H + Sbjct: 122 SRRVRLSRHAV--GQP-LRDEFPI-GFVYSDAWVQDARLVVLNAMDAVQRGARVMTHTRC 177 Query: 198 EGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWS-DKVRNLSNKGTQFSQMRPT 256 SG+ + QV E+ AR ++N TGPW+ D + ++ +G +R Sbjct: 178 VS--ARRSGE-RWLARLQSSNGQVTEVAARALVNATGPWAVDFLDEVAAEGHDHG-LRLV 233 Query: 257 KGVHLVVDSSKIKVSQPVYFDTGLG------DGRMVFVLPRENK-TYFGTTDTDYTGDLE 309 KG H+VV P +D D R+VF +P E + T GTTD +Y GD Sbjct: 234 KGSHIVV---------PRLYDHRYAYIFQQPDRRIVFAIPYEREFTLIGTTDVEYRGDPA 284 Query: 310 HPKVTQEDVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGTISDE 369 HP++ ++ YL V NR+ + I D+ S++G+RPL+ +S G S+ Sbjct: 285 HPRIDTQETAYLCDAV-NRYFKRGIVPADVVWSYSGVRPLLDDDS---------GKASEV 334 Query: 370 SFDNLIATVESYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNGLLTLA 429 + D L+ ++E A RG+ LL + Sbjct: 335 TRDYLL--------------ELEQA-------------------RGAP-------LLNVF 354 Query: 430 GGKITDYRKMAEGAMERVVDILKAEFDRSFKLINSKTYPVSGGEL-NPANVDSEIEAFAQ 488 GGK+T +RK+AE A++R+ +L K +P+ GG++ +P + ++ A Sbjct: 355 GGKLTTFRKLAEEAVDRLAPLL----GNREPAWTGKGHPLPGGDIQDPGRLAEQLRA--- 407 Query: 489 LGVSRGLDSKEAHYLANLYGSNAPKVFALAHSLEQAPGLSLADTLS--LHYAMRNELTLS 546 L A LA+ YGS + +V A SL AD + + Y R E S Sbjct: 408 --TRPWLGEAMAWRLAHTYGSQSVRVLGDAASLTGLGEHFGADLYASEVDYLRRYEWAGS 465 Query: 547 PVDFLLRRT 555 D L RRT Sbjct: 466 AEDVLWRRT 474 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: 554 Number of extensions: 26 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: 499 Length adjustment: 36 Effective length of query: 572 Effective length of database: 463 Effective search space: 264836 Effective search space used: 264836 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