Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate AO353_04190 AO353_04190 glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04190 Length = 512 Score = 165 bits (417), Expect = 5e-45 Identities = 162/548 (29%), Positives = 243/548 (44%), Gaps = 87/548 (15%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 YD+ +IGGGI G G+A A G+ L E D A TSS S+KL+HGG+RYL+ ++ + Sbjct: 15 YDIAVIGGGINGVGIAADAAGRGLSVFLCEKDDLASHTSSASSKLIHGGLRYLEHYEFRL 74 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139 V + + ER ++ APHI KP +LP P + ++ + LYD L K E Sbjct: 75 VREALAEREVLLAKAPHIVKPMRFVLP--HRPHLR-PAWMIRAGLFLYDHL-----GKRE 126 Query: 140 NYLLTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKAKVVG 199 +K + L++E + G Y D +DARLV+ N A+ GA + ++ + V Sbjct: 127 KLAGSKSLKFGADSALKSE-ITKGFEYSDCWVDDARLVVLNAMAAREKGAHVHTQTRCVS 185 Query: 200 ILHDEQGIINGVEVEDQLTNER-FEVHAKVVINTTGPWSDIVRQLDKNDELPPQMRPTKG 258 +G+ E+ + T+ R F + AK ++N GPW + D E P +R +G Sbjct: 186 -ARRSKGL---WELNLERTDGRLFSIRAKALVNAAGPWVAKFIRDDLKMESPYGIRLIQG 241 Query: 259 VHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGDFAHPTVTQED 317 HL+V KL + + D R+VF +P N+ T GTTD +YTGD A T+T+ + Sbjct: 242 SHLIV--PKLYEGEHAHI-LQNEDQRIVFTIPYLNQFTLIGTTDREYTGDPAKVTITEGE 298 Query: 318 VDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESFEQIVES 377 DYLL +VN F QI+ DI +++G+RPL +DES Sbjct: 299 TDYLLKVVNAHF-KKQISRSDILHTYSGVRPL----------------CNDES------- 334 Query: 378 VKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDG----LLTLAGGKI 433 +PS V+R +L S LL++ GGK+ Sbjct: 335 -----------------------------DNPSAVTRDYTLALSGSAEEAPLLSVFGGKL 365 Query: 434 TDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELAKLADQAQTAG 493 T YR +AE A+ ++ + G T P GGE D + A + D+ Sbjct: 366 TTYRKLAESAMAQLAPYFK--GMKPSWTAQATLP--GGE-DMTTPQALSALIRDKFD--W 418 Query: 494 FNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEEMVLTPVDYLL 548 A A YGS ++L + + E L +Y EE + D L Sbjct: 419 LPTEIARRWATTYGSRTWRLLEGVQSLKDMGEHLGGGLYTREVDYLCSEEWATSAHDILW 478 Query: 549 RRTNHILF 556 RR+ LF Sbjct: 479 RRSKLGLF 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: 572 Number of extensions: 30 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: 512 Length adjustment: 36 Effective length of query: 573 Effective length of database: 476 Effective search space: 272748 Effective search space used: 272748 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