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) >FitnessBrowser__WCS417:GFF1097 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:
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