Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate WP_012709582.1 NGR_RS26605 glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >NCBI__GCF_000018545.1:WP_012709582.1 Length = 505 Score = 189 bits (481), Expect = 2e-52 Identities = 157/553 (28%), Positives = 252/553 (45%), Gaps = 101/553 (18%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 +DV +IGGGI G G+A G L EM DFA GTSS STKL+HGG+RYL+ ++ + Sbjct: 7 FDVFVIGGGINGCGIARDAVGRGYSVALAEMDDFASGTSSGSTKLIHGGLRYLEHYEFRL 66 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139 V + + ER ++ +APH+ P +LP + G + +++ + LYD + Sbjct: 67 VREALMEREVLWAMAPHVIWPMRFVLPYH--KGGPRPAWLIRLGLFLYDHIGG------- 117 Query: 140 NYLLTKEEVLAREPQLQAENLVGGG----------VYLDFRNNDARLVIENIKRAQADGA 189 ++L L GG Y D +DARLV+ N + A GA Sbjct: 118 ------RKLLPATSTLDMTRDAAGGPLKRLFTKAFEYSDGWVDDARLVVLNARDAADRGA 171 Query: 190 AMISKAKVVGILHDEQGIING---VEVEDQLTNERFEVHAKVVINTTGPWSD--IVRQLD 244 ++++ +VV + NG +E ED T R + A++++N TGPW D + L Sbjct: 172 RIMARTRVVSARRE-----NGRWAIETEDAQTGARETLRARLLVNATGPWVDRVLADTLG 226 Query: 245 KNDELPPQMRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTD 303 KND +R +G H+VV R K P+ +F DGR++F +P +N T GTTD D Sbjct: 227 KND--VHNVRLVQGSHIVVKR-KFDDPRAYFFQ--NPDGRIMFAIPYQNDFTLIGTTDRD 281 Query: 304 YTGDFAHPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGK 363 +TG+ A ++ ++DYL +E F +T DDI +++ +RPL Sbjct: 282 FTGNPADVRISDAEIDYLCKSASEYFSD-PVTTDDIVWTYSAVRPLY------------- 327 Query: 364 GKLSDESFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKD 423 D+ + E+ ++Y+ RVE + + Sbjct: 328 ----DDGASKAQEATRDYVL-----------------RVEG--------------QNGQA 352 Query: 424 GLLTLAGGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELA 483 LL + GGK+T YR +AE A+++I E + G+ + + T + GG+ A + E+ Sbjct: 353 PLLNVFGGKLTTYRRLAESALEKIGEAIGTKGSKW----TATSHLPGGDFAATAYDTEVD 408 Query: 484 KLADQAQTAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEE 538 L +A+ + A L LYG+ +L + L + T L ++ + +E Sbjct: 409 ML--KARYPFLALSHARRLVRLYGTQAASLLGHAASQADLGKHFGTDLYEVEVDWLIGQE 466 Query: 539 MVLTPVDYLLRRT 551 D L RRT Sbjct: 467 WARRAEDVLWRRT 479 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: 606 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: 505 Length adjustment: 36 Effective length of query: 573 Effective length of database: 469 Effective search space: 268737 Effective search space used: 268737 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 Apr 09 2024. 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