Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate GFF1097 PS417_05565 glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >lcl|FitnessBrowser__WCS417:GFF1097 PS417_05565 glycerol-3-phosphate dehydrogenase Length = 512 Score = 160 bits (405), Expect = 1e-43 Identities = 157/550 (28%), Positives = 244/550 (44%), Gaps = 91/550 (16%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 YDV +IGGGI G G+A A G+ L E D A TSS S+KL+HGG+RYL+ ++ + Sbjct: 15 YDVAVIGGGINGVGIAADAAGRGLSVFLCEKDDLASHTSSASSKLIHGGLRYLEHYEFRL 74 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139 V + + ER ++ APHI K +LP P + ++ + LYD L K E Sbjct: 75 VREALAEREVLLAKAPHIVKQMRFVLP--HRPHLR-PAWMIRAGLFLYDNL-----GKRE 126 Query: 140 NYLLTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKAKVVG 199 +K + L++E + G Y D +DARLV+ N A+ GA + ++ + + Sbjct: 127 KLEGSKSLKFGPDSPLKSE-ITKGFEYSDCWVDDARLVVLNAMAAREKGAHIHTQTRCIS 185 Query: 200 ILHDEQGI--INGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQMRPTK 257 H G+ +N + L F + A+ ++N GPW + D + P +R + Sbjct: 186 -AHRSNGMWEMNMERADGSL----FSIRARALVNAAGPWVAKFIKDDLKLDSPYGIRLIQ 240 Query: 258 GVHLVVDREKLKVPQPTYFDTGKN-DGRMVFVVPRENK-TYFGTTDTDYTGDFAHPTVTQ 315 G HL+V K+ + + +N D R+VF +P N T GTTD +YTGD A +T+ Sbjct: 241 GSHLIVP----KLYEGAHAHILQNEDQRIVFTIPYLNHLTIIGTTDREYTGDPAKVAITE 296 Query: 316 EDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESFEQIV 375 + DY+L +VN F Q++ DDI +++G+RPL +DES Sbjct: 297 GETDYMLKVVNAHF-KKQLSRDDIVHTYSGVRPL----------------CNDES----- 334 Query: 376 ESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERS----KDGLLTLAGG 431 +PS ++R +L S + +L++ GG Sbjct: 335 -------------------------------DNPSAITRDYTLALSGGTGEAPILSVFGG 363 Query: 432 KITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELAKLADQAQT 491 K+T YR +AE A+ ++ + S+ S + GGE E LA+ A +++ Sbjct: 364 KLTTYRKLAESAMAQLAPYFTQMRPSWTAKAS----LPGGE--DMTTPEALAE-AIRSKF 416 Query: 492 AGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEEMVLTPVDY 546 A + YGS ++L L E L +Y EE P D Sbjct: 417 DWVPSEIARRWSTTYGSRTWRLLEGVQSLADLGEHLGGGLYTREVDYLCAEEWATQPQDV 476 Query: 547 LLRRTNHILF 556 L RRT LF Sbjct: 477 LWRRTKLGLF 486 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: 603 Number of extensions: 34 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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