Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate Pf6N2E2_5572 Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5572 Length = 512 Score = 162 bits (411), Expect = 2e-44 Identities = 138/458 (30%), Positives = 207/458 (45%), Gaps = 77/458 (16%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 YD+ +IGGGI G G+A A G+ L E D A TSS S+KL+HGG+RYL+ ++ + Sbjct: 15 YDIAVIGGGINGVGIAADAAGRGLSVFLCEKDDLASHTSSASSKLIHGGLRYLEHYEFRL 74 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139 V + + ER ++ APHI K +LP P + ++ + LYD L K E Sbjct: 75 VREALAEREVLLTKAPHIVKQMRFVLP--HRPHLR-PAWMIRAGLFLYDHL-----GKRE 126 Query: 140 NYLLTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKAKVVG 199 +K + L++E + G Y D +DARLV+ N A+ GA + ++ + V Sbjct: 127 QLAGSKSLKFGADSALKSE-ITKGFEYSDCWVDDARLVVLNAMAAREKGAHIHTRTRCVN 185 Query: 200 ILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQMRPTKGV 259 + +E D F + AK ++N GPW + D E P +R +G Sbjct: 186 ARRSKGLWHLHLERAD---GSLFSIRAKALVNAAGPWVAKFIRDDLKLESPYGIRLIQGS 242 Query: 260 HLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGDFAHPTVTQEDV 318 HL+V KL + + D R+VF +P N+ T GTTD +YTGD A +T+ + Sbjct: 243 HLIV--PKLYEGEHAHI-LQNEDQRIVFTIPYLNQFTLIGTTDREYTGDPAKVAITEGET 299 Query: 319 DYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESFEQIVESV 378 DYLL +VN F QI+ DDI S++G+RPL Sbjct: 300 DYLLKVVNAHF-KKQISRDDILHSYSGVRPLCN--------------------------- 331 Query: 379 KEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDG----LLTLAGGKIT 434 DE P S V+R +L S G LL++ GGK+T Sbjct: 332 -----DESDNP--------------------SAVTRDYTLALSGGGEEAPLLSVFGGKLT 366 Query: 435 DYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGE 472 YR +AE A+ ++ + + V++ + GGE Sbjct: 367 TYRKLAESAMAQLAPYFTQMRPGWTAVEA----LPGGE 400 Lambda K H 0.314 0.132 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: 587 Number of extensions: 27 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: 609 Length of database: 512 Length adjustment: 36 Effective length of query: 573 Effective length of database: 476 Effective search space: 272748 Effective search space used: 272748 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