Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate HSERO_RS04840 HSERO_RS04840 glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__HerbieS:HSERO_RS04840 Length = 510 Score = 171 bits (433), Expect = 7e-47 Identities = 153/549 (27%), Positives = 242/549 (44%), Gaps = 87/549 (15%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 YD+L++GGGI GAG+A A G++ +L E D A+ TSS STKL+HGG+RYL+ ++ ++ Sbjct: 5 YDLLVVGGGINGAGIARDAAGRGLRVLLCEQHDLAQHTSSASTKLIHGGLRYLEYYEFKL 64 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139 V ++ER ++ + APHI P ++P + ++ + +YD LA K E Sbjct: 65 VRKALQEREVLLRSAPHIIWPLRFVMP---HDANQRPAWMIRAGLFMYDHLA-----KRE 116 Query: 140 NYLLTKEEVLAREP--QLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKAKV 197 ++ LAR Q + G VY D +DARLV+ N AQ GA ++++ K Sbjct: 117 ILPPSEGANLARHDAGQPLKGDYRKGFVYSDGWVDDARLVVLNAMDAQERGARILTRTKC 176 Query: 198 VGILHDEQGIINGVEVEDQLTN--ERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQMRP 255 + +G I +E Q ++ EV A+ ++N GPW+ Q + +R Sbjct: 177 ISA--RREGDIWHAVLEHQREGGVQQEEVRARAIVNAAGPWAARFAQAVPQAKSGRSLRL 234 Query: 256 TKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVP-RENKTYFGTTDTDYTGDFAHPTVT 314 KG H+VV R P + D R++F +P +E T GTTD +Y GD + Sbjct: 235 IKGSHIVVKR---MFDHPYAYIFQNPDKRIIFAIPYQEEFTLIGTTDLEYHGDAGKVEID 291 Query: 315 QEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESFEQI 374 ++DYL + N F QI +D+ +++G+RPL+ D+S E Sbjct: 292 AAEIDYLCDMANRYFKR-QIGKEDVVWTYSGVRPLL-----------------DDSAENA 333 Query: 375 VESVKEYL--ADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDGLLTLAGGK 432 ++YL D+ P +L + GGK Sbjct: 334 SAITRDYLLECDDAGAP-----------------------------------MLNVWGGK 358 Query: 433 ITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELD-----AANVEEELAKLAD 487 IT YR +AE A+ + L S S+ + P+ GG+L+ A + + Sbjct: 359 ITTYRKLAEEALAMLAPHLGASSQSW----TAGAPLPGGDLEQPGKMVARYDFDAYLRKF 414 Query: 488 QAQTAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEEMVLT 542 QA+ A A YGS + Q++ L E+ S L Y + E + Sbjct: 415 QARHPWLPAELAHRYARSYGSRVEQIIGQADSLAALGEELSPGLYEAEARYLVQHEWARS 474 Query: 543 PVDYLLRRT 551 D L RR+ Sbjct: 475 ADDILWRRS 483 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: 575 Number of extensions: 25 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: 510 Length adjustment: 36 Effective length of query: 573 Effective length of database: 474 Effective search space: 271602 Effective search space used: 271602 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