Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate GFF1416 Psest_1453 Glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__psRCH2:GFF1416 Length = 514 Score = 167 bits (424), Expect = 8e-46 Identities = 165/552 (29%), Positives = 241/552 (43%), Gaps = 91/552 (16%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 YD+ ++GGGI GAG+A A G+ L E D AE TSS S+KLVHGG+RYL+ +++ + Sbjct: 13 YDLAVVGGGINGAGIAADAAGRGLSVFLCEQGDLAEHTSSASSKLVHGGLRYLEHYELRL 72 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139 V + + ER ++ APHI P +LP + + ++ + LYD L K E Sbjct: 73 VREALAEREVLLAKAPHIVTPLRFVLPYRPHLRPS---WMIRTGLFLYDHL-----GKRE 124 Query: 140 NYLLTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKAKVVG 199 ++ + L+ E + G Y D +DARLV+ N A+ GA + + + V Sbjct: 125 KLGGSRSLRFGADSPLKDE-ITHGFEYADCWVDDARLVVLNAMAARELGAHIHPRTRCVS 183 Query: 200 ILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPW--SDIVRQLDKNDELPPQMRPTK 257 + +E +D RF + A+ ++N TGPW S I QL + P MR + Sbjct: 184 ARSSKALWHLHLERQD---GSRFSIRARALVNATGPWVASFIEEQLRQTS--PHGMRLIQ 238 Query: 258 GVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGDFAHPTVTQE 316 G H+VV KL Y D R+VF+ P + + GTTD +Y GD +T Sbjct: 239 GSHIVV--PKLYEGDHAYI-LQNEDRRIVFITPYLGQFSLIGTTDHEYHGDPTQVRITDA 295 Query: 317 DVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESFEQIVE 376 ++DYLL IVN F H Q++ DI S+AG+RPL DES + Sbjct: 296 EIDYLLAIVNAHFKH-QLSRADIRYSYAGVRPL----------------CDDESDQ---- 334 Query: 377 SVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDG----LLTLAGGK 432 PS ++R +L S LL++ GGK Sbjct: 335 --------------------------------PSAITRDYTLTLSDSAGEGPLLSVFGGK 362 Query: 433 ITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGE-LDAANVEEELAKLADQAQT 491 +T YR +AE A+ ++ L E + + + GGE LD E A A Sbjct: 363 LTTYRKLAEAALAQLAPLFPEMKRPW----THDAALPGGEHLD----EPSALAHALCASY 414 Query: 492 AGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDE-----KESTALNYSLHEEMVLTPVDY 546 A A YGS +L + L E + ++Y + EE T D Sbjct: 415 PWLPGPIARRWARTYGSRSWLLLKGTDSLQDLGECFGAGLHAREVDYLMVEEWAQTAEDI 474 Query: 547 LLRRTNHILFMR 558 L RRT LFM+ Sbjct: 475 LWRRTKLGLFMQ 486 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: 597 Number of extensions: 31 Number of successful extensions: 7 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: 514 Length adjustment: 36 Effective length of query: 573 Effective length of database: 478 Effective search space: 273894 Effective search space used: 273894 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