Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate BWI76_RS26190 BWI76_RS26190 glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__Koxy:BWI76_RS26190 Length = 502 Score = 176 bits (446), Expect = 2e-48 Identities = 152/548 (27%), Positives = 249/548 (45%), Gaps = 82/548 (14%) Query: 19 TYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVE 78 T D+++IGGGI GAG+A A G+ ++LE D A TSS S+KL+HGG+RYL+ ++ Sbjct: 3 TKDLIVIGGGINGAGIAADAAGRGLSVLMLEANDLACATSSASSKLIHGGLRYLEHYEFR 62 Query: 79 VVADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKY 138 +V++ + ER ++ ++APHI P LP P + +++ + +YD L T Sbjct: 63 LVSEALAEREVLLKMAPHIAFPMRFRLP--HRPHLR-PAWMIRIGLFMYDHLGKRTSLPS 119 Query: 139 ENYL-LTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKAKV 197 L E VL E +V G Y D +DAR+V+ N + G + ++ + Sbjct: 120 STGLRFGTESVLKPE-------IVRGFEYSDCWVDDARMVLANAQMVVRKGGEVRTRTRA 172 Query: 198 VGILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDEL--PPQMRP 255 + + I VE ED + ERF A+ ++N TGPW + + D+ L P +R Sbjct: 173 ISAKRENGLWI--VEAEDIDSGERFTWQARGLVNATGPW--VKQFFDEGMHLRSPYGIRL 228 Query: 256 TKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVP-RENKTYFGTTDTDYTGDFAHPTVT 314 KG H+VV R Q + D R+VFV+P + + GTTD +Y GD + Sbjct: 229 IKGSHIVVPRVH---AQKQAYILQNEDKRIVFVIPWMDEFSIIGTTDVEYKGDPKAVAID 285 Query: 315 QEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESFEQI 374 ++++YLL + N F +T DDI +++G+RP L D+ + Sbjct: 286 GKEINYLLNVYNAHFKKT-LTRDDIVWTYSGVRP-----------------LCDDESDSP 327 Query: 375 VESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDGLLTLAGGKIT 434 ++Y D E + LL++ GGK+T Sbjct: 328 QAITRDYTLDIHD-------------------------------ENGQAPLLSVFGGKLT 356 Query: 435 DYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELAKLADQAQTAGF 494 YR +AE A++++ + G ++ + T + GG++ + ++ AKL + A Sbjct: 357 TYRKLAEHALEKLTPYYKGIGPAW----TKTAVLPGGDI-GGDRDDYAAKL--RRHFAFI 409 Query: 495 NEAAATYLAHLYGSNLPQVLNYKTKFEGLDEK-----ESTALNYSLHEEMVLTPVDYLLR 549 +E+ A + A YGSN +L T L E L Y + E V D + R Sbjct: 410 SESMARHYARTYGSNSEWILGEATSLADLGEDFGHEFYEAELRYLVEHEWVRRLDDAIWR 469 Query: 550 RTNHILFM 557 RT +++ Sbjct: 470 RTKQGMWL 477 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: 558 Number of extensions: 28 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: 502 Length adjustment: 36 Effective length of query: 573 Effective length of database: 466 Effective search space: 267018 Effective search space used: 267018 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