Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate PP_1073 PP_1073 glycerol-3-phosphate dehydrogenase (aerobic)
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__Putida:PP_1073 Length = 514 Score = 157 bits (398), Expect = 8e-43 Identities = 154/552 (27%), Positives = 247/552 (44%), Gaps = 91/552 (16%) Query: 13 QETAKTTYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYL 72 Q YD+ +IGGGI G G+A A G+K L E D A+ TSS S+KL+HGG+RYL Sbjct: 10 QPPTANCYDLAVIGGGINGVGIAADAAGRGLKVFLCEKDDLAQHTSSASSKLIHGGLRYL 69 Query: 73 KTFDVEVVADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLAN 132 + ++ +V + + ER ++ APHI KP +LP P + ++ + LYD L Sbjct: 70 EHYEFRLVREALAEREVLLAKAPHIVKPMRFVLP--HRPHLR-PAWMIRAGLFLYDHLG- 125 Query: 133 VTGSKYENYLLTKEEVLAREPQLQAENLVGGGV-YLDFRNNDARLVIENIKRAQADGAAM 191 + L L P + + G Y D +DARLV+ N A+ GA + Sbjct: 126 ------KRKRLGASRSLRFGPGYPLKPAITRGFEYADCAVDDARLVVLNAMAARELGAHI 179 Query: 192 ISKAKVVGILHDEQGIINGV-EVEDQLTNERFE-VHAKVVINTTGPWSDIVRQLDKNDEL 249 ++ + L E+ + G+ +VE Q + + +HA+ ++N GPW + D + Sbjct: 180 RTRTR---CLRAER--VEGLWQVELQHADGSLQTIHARALVNAAGPWVASFIKDDLKLDA 234 Query: 250 PPQMRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGDF 308 P +R +G H++V R L + Y D R+VF +P ++ T GTTD +Y+GD Sbjct: 235 PYGIRLIQGSHIIVPR--LYEGEHAYI-LQNEDQRIVFCIPYLDRFTLIGTTDREYSGDP 291 Query: 309 AHPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSD 368 A +T+++ YLL +VNE F H Q++ DI +++G+RPL +D Sbjct: 292 AAVAITEQETHYLLKVVNEHFNH-QLSQADILHTYSGVRPL----------------CND 334 Query: 369 ESFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKD----G 424 ES +PS V+R +L S + Sbjct: 335 ES------------------------------------DNPSAVTRDYTLALSAEVGQAP 358 Query: 425 LLTLAGGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELAK 484 LL++ GGK+T YR +AE A+ + + A + + + P+ G E V+ + Sbjct: 359 LLSVFGGKLTTYRKLAESAMAELKPFFTQMRAPW----TASAPLPGAE-GMTTVQALIDA 413 Query: 485 LADQAQTAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEEM 539 + + + A L YGS + ++L+ E L + L +Y L EE Sbjct: 414 VLARCGWLPVDLAKRWVLT--YGSRVWRLLDGVHGPEDLGQAIGAGLFTREVDYLLEEEW 471 Query: 540 VLTPVDYLLRRT 551 D + RRT Sbjct: 472 AEQTADIIWRRT 483 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: 535 Number of extensions: 25 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: 609 Length of database: 514 Length adjustment: 36 Effective length of query: 573 Effective length of database: 478 Effective search space: 273894 Effective search space used: 273894 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