Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate BPHYT_RS16490 BPHYT_RS16490 glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__BFirm:BPHYT_RS16490 Length = 509 Score = 167 bits (424), Expect = 8e-46 Identities = 161/576 (27%), Positives = 248/576 (43%), Gaps = 99/576 (17%) Query: 15 TAKTTYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKT 74 T + YD+L++GGGI GAG+A A G+ +L E D A TSS STKL+HGG+RYL+ Sbjct: 2 TQGSRYDLLVVGGGINGAGIARDAAGRGLSVLLCEQDDLAAHTSSASTKLIHGGLRYLEY 61 Query: 75 FDVEVVADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVT 134 + +V ++ER + + APHI P ++P + + ++ + LYD LA Sbjct: 62 REFGLVRKALQERETLLRAAPHIMWPLRFVMPHMPD---LRPAWLIRAGLFLYDHLAR-- 116 Query: 135 GSKYENYLLTKEEVLAREPQLQA---ENLVGGGVYLDFRNNDARLVIENIKRAQADGAAM 191 L ++ R A +++ G VY D NDARLV+ N AQ GA + Sbjct: 117 ----RELLPGSRGIVMRNHPAGAPLVDSIKRGFVYSDGWVNDARLVVLNALDAQEHGAKI 172 Query: 192 ISKAKVVGILHDEQGIINGVEVEDQL---TNERFEVHAKVVINTTGPWSDIVRQLDKNDE 248 +++ K++ + G E QL +V A + N GPW + Q Sbjct: 173 LTRTKLL------SAVRAGGEWRAQLKRADGTLLDVRAASIANAAGPWVGELLQGALGRA 226 Query: 249 LPPQMRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGD 307 +R KG H +V R + F D R++F +P E+ T GTTD +Y GD Sbjct: 227 ASHSVRLVKGSH-IVTRRLFEHDHAYIFQ--NPDKRIIFAIPYEHDYTLIGTTDLEYRGD 283 Query: 308 FAHPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLS 367 + + ++ YL +N F +I+ D+ +++G+RPL+ G Sbjct: 284 PSQVAINADETQYLCDSINRYFKQ-KISPADVRWTYSGVRPLLEEEGAD----------- 331 Query: 368 DESFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLE----RSKD 423 +PS V+R SLE + Sbjct: 332 ----------------------------------------NPSAVTRDYSLELDAPAGEA 351 Query: 424 GLLTLAGGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELA 483 LL++ GGKIT +R +AE AV ++ + LQ +S+ + P+ GG++ AN E L+ Sbjct: 352 PLLSVFGGKITTFRKLAEEAVDKLAQALQNGASSW----TAGAPLPGGDIPNANFERFLS 407 Query: 484 KLADQAQTAGFNEAAATYLAHLYGSNLPQVLNY--------KTKFEGLDEKESTALNYSL 535 + + Q A A LA YG+ + QVL + GL E E L Y Sbjct: 408 EF--KQQHAWLPADLAHRLARAYGTRVKQVLGNARSVADLGRAFAPGLYEAE---LTYLR 462 Query: 536 HEEMVLTPVDYLLRRTNHILFMR-DTLDDVKAGVVA 570 E + D L RR+ L + TLD + + A Sbjct: 463 DTEWARSAQDVLWRRSKLGLHVEPGTLDSITRDIDA 498 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: 548 Number of extensions: 31 Number of successful extensions: 4 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: 509 Length adjustment: 36 Effective length of query: 573 Effective length of database: 473 Effective search space: 271029 Effective search space used: 271029 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