Align glycerol-3-phosphate oxidase (EC 1.1.3.21) (characterized)
to candidate 17488 b3426 sn-glycerol-3-phosphate dehydrogenase, aerobic, FAD/NAD(P)-binding (NCBI)
Query= BRENDA::Q833L7 (609 letters) >FitnessBrowser__Keio:17488 Length = 501 Score = 171 bits (432), Expect = 9e-47 Identities = 159/572 (27%), Positives = 262/572 (45%), Gaps = 95/572 (16%) Query: 21 DVLIIGGGITGAGVALQASAAKMKTGLIEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEVV 80 D+++IGGGI GAG+A A+ + ++E QD A TSS S+KL+HGG+RYL+ ++ +V Sbjct: 5 DLIVIGGGINGAGIAADAAGRGLSVLMLEAQDLACATSSASSKLIHGGLRYLEHYEFRLV 64 Query: 81 ADTVKERAVVQSIAPHIPKADPMLLPIYDEPNATFNLFSVKIAMDLYDQLADVTGTKYAN 140 ++ + ER V+ +APHI A PM + P+ + ++I + +YD L T + Sbjct: 65 SEALAEREVLLKMAPHI--AFPMRFRLPHRPHLR-PAWMIRIGLFMYDHLGKRTSLPGST 121 Query: 141 YL-LTKDEVLAREPQLKSEGLQGGGVYLDYRNNDARLVIENIKQAVADGAHAVSRVQAVG 199 L + VL +P++K G Y D +DARLV+ N + V G ++R +A Sbjct: 122 GLRFGANSVL--KPEIKR-----GFEYSDCWVDDARLVLANAQMVVRKGGEVLTRTRATS 174 Query: 200 FLYNDEGKITGIQAKDLLTDEQFEIHADVVINTTGPWSDKLRGLDKNDSFTPQMRPTKGV 259 E + ++A+D+ T +++ A ++N TGPW + + +R KG Sbjct: 175 --ARRENGLWIVEAEDIDTGKKYSWQARGLVNATGPWVKQFFDDGMHLPSPYGIRLIKGS 232 Query: 260 HLVVDKSRLNVPQPTYFDTGKQDGRMVFVVP-REEKTYFGTTDTDYHGDFQHPTVEQSDV 318 H+VV R++ + Y +D R+VFV+P +E + GTTD +Y GD + +E+S++ Sbjct: 233 HIVV--PRVHTQKQAYI-LQNEDKRIVFVIPWMDEFSIIGTTDVEYKGDPKAVKIEESEI 289 Query: 319 DYLLEVVNNRYPEVQLTIDDIEASWAGLRPLISANGGSDYNGGNNGKLSDKSIDEVIDVV 378 +YLL V N + + QL+ DDI +++G+RPL S Sbjct: 290 NYLLNVYNTHFKK-QLSRDDIVWTYSGVRPLCDDESDS---------------------- 326 Query: 379 DRYQKNQTDKREIEEVLNHLEDSLVENKVNPSAVSRGSSL----ERSADGLLTLAGGKLT 434 P A++R +L E LL++ GGKLT Sbjct: 327 ------------------------------PQAITRDYTLDIHDENGKAPLLSVFGGKLT 356 Query: 435 DYRKMAEGAMKMIQTILAEEYQKEFTLIDSKNYPVSGGKLNPATVDEELEALAKHGVSKG 494 YRK+AE A++ + Y + +K + GG + D ++ Sbjct: 357 TYRKLAEHALEKL-----TPYYQGIGPAWTKESVLPGGAIEGDRDDYAARLRRRYPF--- 408 Query: 495 LSEKDALYLAHLYGS-------NVPTVFEMIDDAKVIPGLTLTETVSLNYAMEEEMALTP 547 L+E A + A YGS N TV ++ +D G E L Y ++ E Sbjct: 409 LTESLARHYARTYGSNSELLLGNAGTVSDLGEDF----GHEFYE-AELKYLVDHEWVRRA 463 Query: 548 VDFLLRRTNHLLFMR-DRLDQVKAGVIEEMAQ 578 D L RRT +++ D+ +V ++E Q Sbjct: 464 DDALWRRTKQGMWLNADQQSRVSQWLVEYTQQ 495 Lambda K H 0.314 0.133 0.372 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: 623 Number of extensions: 28 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: 501 Length adjustment: 36 Effective length of query: 573 Effective length of database: 465 Effective search space: 266445 Effective search space used: 266445 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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