Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate Pf1N1B4_769 Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_769 Length = 486 Score = 146 bits (369), Expect = 2e-39 Identities = 156/534 (29%), Positives = 229/534 (42%), Gaps = 85/534 (15%) Query: 33 GVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEVVADTVRERAIVQQ 92 G+A A G+ L E D A TSS S+KL+HGG+RYL+ ++ +V + + ER ++ Sbjct: 2 GIAADAAGRGLSVFLCEKDDLASHTSSASSKLIHGGLRYLEHYEFRLVREALAEREVLLA 61 Query: 93 IAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYENYLLTKEEVLARE 152 APHI K +LP P + ++ + LYD L K E +K + Sbjct: 62 KAPHIVKQMRFVLP--HRPHLR-PAWMIRAGLFLYDNL-----GKREKLEGSKSLKFGPD 113 Query: 153 PQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKAKVVGILHDEQGIINGVE 212 L++E + G Y D +DARLV+ N A+ GA + ++ + V + +E Sbjct: 114 SALKSE-ITKGFEYSDCWVDDARLVVLNAMAAREKGAHVHTQTRCVSARRTKGLWHLNLE 172 Query: 213 VEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQMRPTKGVHLVVDREKLKVPQ 272 D F + AK ++N GPW + D E P +R +G HL+V KL + Sbjct: 173 RAD---GSLFSIRAKALVNAAGPWVAKFIRDDLKMESPYGIRLIQGSHLIV--PKLYEGE 227 Query: 273 PTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGDFAHPTVTQEDVDYLLTIVNERFPH 331 + D R+VF +P N T GTTD +YTGD A +T+ + DYLL +VN F Sbjct: 228 HAHI-LQNEDQRIVFTIPYLNHFTLIGTTDREYTGDPAAVAITEGETDYLLKVVNAHF-K 285 Query: 332 AQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESFEQIVESVKEYLADERQRPVV 391 QI+ DDI S++G+RPL +DES Sbjct: 286 KQISRDDILHSYSGVRPL----------------CNDES--------------------- 308 Query: 392 EKAVKQAQERVEASKVDPSQVSRGSSLERSKDG----LLTLAGGKITDYRLMAEGAVKRI 447 +PS V+R +L S LL++ GGK+T YR +AE A+ ++ Sbjct: 309 ---------------DNPSAVTRDYTLALSGSAEEAPLLSVFGGKLTTYRKLAESALAQL 353 Query: 448 NELLQESGASFELVDSTTYPVSGGELDAANVEEELAKLADQAQTAGFNEAAATYLAHLYG 507 S+ S T P GGE D + +++ D+ E A + A YG Sbjct: 354 APYFAHIKPSW--TASATLP--GGE-DMTTPQALSSRIRDKFDWVP-TEIARRW-ATTYG 406 Query: 508 SNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEEMVLTPVDYLLRRTNHILF 556 S ++L L E L +Y EE T D L RRT LF Sbjct: 407 SRTWRMLEGVESLNDLGEHIGGGLYTREVDYLCSEEWATTAHDILWRRTKLGLF 460 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: 561 Number of extensions: 32 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: 486 Length adjustment: 35 Effective length of query: 574 Effective length of database: 451 Effective search space: 258874 Effective search space used: 258874 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: 52 (24.6 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