Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate 8500048 DvMF_0811 FAD dependent oxidoreductase (RefSeq)
Query= curated2:P35596 (608 letters) >FitnessBrowser__Miya:8500048 Length = 542 Score = 200 bits (509), Expect = 1e-55 Identities = 161/560 (28%), Positives = 258/560 (46%), Gaps = 106/560 (18%) Query: 18 RTLDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLK---- 73 R DLL+IGGG TG GVA+ AA GL+ L++ DFA+GTSSRSTKLVHGG+RYL+ Sbjct: 14 REFDLLVIGGGATGCGVAVDAATRGLDVALVDRADFAQGTSSRSTKLVHGGVRYLEKAVL 73 Query: 74 QFDVE---VVSDTVSERAVVQQIAPHIPKSDPMLLPV--YDEDGATFSLFRLKVAMDLYD 128 Q D E +V + + ER + APH+ + +L PV + + G F+ + LYD Sbjct: 74 QCDREQFGLVREGLRERGFLLANAPHLAHAVRLLTPVPTWKDAGYMFA------GLTLYD 127 Query: 129 LLAGVSNTPAANKVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDG 188 LLAG +K + K P L+ Y D + NDAR+ + + AN G Sbjct: 128 LLAGRLGL-GHSKFVGKRAAERMFPTLRMGDYKAAVTYWDGQFNDARMAVALARTANAHG 186 Query: 189 ALIANHVKAEGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKVRNLSNKGT 248 A NHV+ L E G++ G RD+LT + + ++AR +IN TGP +D VR + + G Sbjct: 187 ATCCNHVEVT-HLIKEGGRLRGAELRDMLTGETWTLRARGIINATGPMADTVRRMDDPGA 245 Query: 249 QFSQMRPTKGVHLVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTTDTDYTGDL 308 ++ + G+H+V+++ + DGR++F++P +N FGTTD ++ Sbjct: 246 D-EILKVSSGIHIVLEAGFTPPDLSLMIPK-TEDGRVLFMIPWQNHVVFGTTD-EHANPE 302 Query: 309 EHPKVTQEDVDYLLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGTISD 368 P D+DYLL +++ +T D+ + W+GLRPL+ Sbjct: 303 HDPVPDVADIDYLLRYA-SKYLSRPVTRGDVRAVWSGLRPLVFAPG-------------- 347 Query: 369 ESFDNLIATVESYLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNGLLTL 428 + ST E ++R ++ GLLT+ Sbjct: 348 ------------------------------KGSTQE-------LARTHVIEVSPAGLLTI 370 Query: 429 AGGKITDYRKMAEGAMERV-----VDILKAEFDRSFKLINSKTYPVSGGELNPANVDSEI 483 AGGK T YR MA+ ++R +++ + R K++ ++ + + GG Sbjct: 371 AGGKWTSYRMMAQDTVDRADVAFGLNLTRPCVTRHLKVVGARGF-IPGG----------- 418 Query: 484 EAFAQLGVSRGLDSKEAHYLANLYGSNAPKVFALAHSLEQAPGLSLADTL---------S 534 + ++ G+ + A L YG +V +A +L D + Sbjct: 419 --YTEIAREYGVPVELAKALHGTYGDETGQVLTIARD------ENLGDRVHPDHPHIMAE 470 Query: 535 LHYAMRNELTLSPVDFLLRR 554 + + +RNE+ + VD L+RR Sbjct: 471 VAFIVRNEMAMRLVDVLVRR 490 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: 705 Number of extensions: 30 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: 542 Length adjustment: 36 Effective length of query: 572 Effective length of database: 506 Effective search space: 289432 Effective search space used: 289432 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