Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate PfGW456L13_5129 Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5129 Length = 531 Score = 198 bits (504), Expect = 4e-55 Identities = 168/582 (28%), Positives = 272/582 (46%), Gaps = 92/582 (15%) Query: 8 RKETIQETAKTTYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHG 67 R+ + A T+D+++IGGGI+GAG+ + A G + +LLE +DFA GTSSRS+K+VHG Sbjct: 10 RQRVLPTLADETWDLIVIGGGISGAGILREAARRGWRCLLLEQRDFAWGTSSRSSKMVHG 69 Query: 68 GIRYLKTFDVEVVADTVRERAIVQQIAPHIPKPDPMLLPIY--DEPGATFSLFSVKVAMD 125 G+RY+ + D+VRER + AP + +P ++P Y PG + + Sbjct: 70 GLRYIAKGQWRLTRDSVRERQRLLDEAPGLVEPMSFMMPHYRGGFPGPRV----LGGLLS 125 Query: 126 LYDRLANVTGSKYENYLLTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQ 185 +YD LA + ++ +++ P ++ ++L+GG ++D +DARLV+ + A+ Sbjct: 126 IYDALA----GRRSHHFHDAQQLRYLAPGVKEDDLLGGTCFVDALTDDARLVMRVLGEAR 181 Query: 186 ADGAAMISKAKVVGILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDK 245 ADGA +++ +V +L E+G + GV+VED + + TG W++ +R D Sbjct: 182 ADGAVVLNGVRVQQLLR-EEGRVCGVQVEDCEGGGLLTLRCGALAVATGAWAERLRLPD- 239 Query: 246 NDELPPQMRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENKTYFGTTDTDYT 305 P Q+RP +G HL++ +L V Q F + D R VFV P E T GTTD D+ Sbjct: 240 ---APRQLRPLRGSHLLLPGWRLPVAQAFTF-LHERDRRPVFVFPWEGATVVGTTDLDHH 295 Query: 306 GDF-AHPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKG 364 GD +++ +++DYLL +++FP A++ D+ ++W+G+RP++ + G + Sbjct: 296 GDLDQSASISFDELDYLLAACSQQFPQAEVVAADVLSTWSGVRPVVGSAAGEH-----QD 350 Query: 365 KLSDESFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDG 424 K S+E+ E ++ Q P G Sbjct: 351 KPSNETREHVL----------WQEP----------------------------------G 366 Query: 425 LLTLAGGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELAK 484 +TLAGGK+T +R A +K +L VD DA V + Sbjct: 367 CVTLAGGKLTTFRPQAIEVLKACATMLDR-----PFVD-----------DATPVFAAVPP 410 Query: 485 LADQAQTAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKEST-----ALNYSLHEEM 539 LA G + LA +G +LP++ + G D T L + EM Sbjct: 411 LA----IPGLSANRWRRLAGRHGRDLPRLAQLIAEL-GHDTVGGTDTLWAELAVACDGEM 465 Query: 540 VLTPVDYLLRRTNHILFMRDTLDDVKAGVVAAMTDFFGWSEE 581 VL D LLRRT L + +D A + GW +E Sbjct: 466 VLHLDDLLLRRTRLGLLLPRGGEDYFAAIRQLCQPRLGWDDE 507 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: 661 Number of extensions: 33 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: 531 Length adjustment: 36 Effective length of query: 573 Effective length of database: 495 Effective search space: 283635 Effective search space used: 283635 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