Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate 208651 DVU3132 glycerol-3-phosphate dehydrogenase, FAD-dependent
Query= curated2:P35596 (608 letters) >MicrobesOnline__882:208651 Length = 546 Score = 216 bits (549), Expect = 3e-60 Identities = 179/616 (29%), Positives = 289/616 (46%), Gaps = 111/616 (18%) Query: 8 RELSIKKMQERTLDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHG 67 R++ + ++T DLLI+GGG TG GVAL AA GL+ L+E DFA+GTSS+STKLVHG Sbjct: 4 RQILERLQADKTFDLLIVGGGATGCGVALDAATRGLDVALVERDDFAQGTSSKSTKLVHG 63 Query: 68 GLRYLKQFDVE-------VVSDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRL 120 G+RYL++ ++ +V + + ER + + APH+ ++ PV A + L Sbjct: 64 GVRYLEKAILKADKEQFALVHEGLRERGYLLRNAPHLAHPVQLMTPVDSWKDAGY----L 119 Query: 121 KVAMDLYDLLAGVSNTPAANKVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIEN 180 + +YDLLAG ++ +++ + P L+ G +Y D + NDAR+ + Sbjct: 120 FAGLTMYDLLAGRLGL-GHSRFVTRSKAQRLFPTLRLGKAKGAVLYYDGQFNDARMAVTL 178 Query: 181 IKRANQDGALIANHVKAEGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKV 240 + A GA ANHV+ L E+G++ G V RD+ + + ++++AR +IN TGP+SD + Sbjct: 179 ARTAALHGATCANHVEVID-LVRENGRLCGAVLRDVNSGETWQVRARGIINATGPFSDGL 237 Query: 241 RNLSNKGTQFSQMRPTKGVHLVVDSSKIKVSQPVYFDTGLG-------DGRMVFVLPREN 293 R + ++ ++ + G+HLV+D P + LG DGR++F++P + Sbjct: 238 RRMDDQNA-CDILKVSSGIHLVID--------PGHTPPHLGLMVPRTDDGRVLFMIPWQG 288 Query: 294 KTYFGTTD--TDYTGDLEHPKVTQEDVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIA 351 FGTTD D + D P TQED+DYLL R+ ++ DD+ ++W GLRPL+ Sbjct: 289 HVVFGTTDEPVDISRD---PVPTQEDIDYLLNYA-GRYLSRPLSRDDVRAAWCGLRPLV- 343 Query: 352 GNSASDYNGGNNGTISDESFDNLIATVESYLSKEKTREDVESAVSKLESSTSEKHLDPSA 411 F+ K T+E Sbjct: 344 -------------------FE---------ADKSCTQE---------------------- 353 Query: 412 VSRGSSLDRDDNGLLTLAGGKITDYRKMAEGAMERV-----VDILKAEFDRSFKLINSKT 466 ++R ++ GLLT+ GGK T YR+MAE ++R + + + R ++I S+ Sbjct: 354 LARTHVIEVSPGGLLTITGGKWTSYRRMAEDTIDRADAAFELGLQRPCVTRDLRVIGSRG 413 Query: 467 YPVSGGELNPANVDSEIEAFAQLGVSRGLDSKEAHYLANLYGSNAPKVFALAHSLEQAPG 526 + V G A A++ G+D A L L+G P + LA Sbjct: 414 F-VRG-------------AHAEMARDFGVDPALARGLFELHGDETPLILTLAREEGLMDR 459 Query: 527 LSLADT---LSLHYAMRNELTLSPVDFLLRRTNHMLFMRDSLDSIVEPILDEMGRFYDWT 583 L A + +A+R+E+ + D ++RR L P D M + W Sbjct: 460 LHPAHNYIGAQVAFAVRHEMAVHLTDVMVRRLPLGLVDVQHTLEASAPAADIMAQELGW- 518 Query: 584 EEEKATYRADVEAALA 599 + AT + ++EA A Sbjct: 519 --DAATRQREMEALAA 532 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: 740 Number of extensions: 36 Number of successful extensions: 8 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: 546 Length adjustment: 36 Effective length of query: 572 Effective length of database: 510 Effective search space: 291720 Effective search space used: 291720 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