Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate Ga0059261_3265 Ga0059261_3265 Glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__Korea:Ga0059261_3265 Length = 377 Score = 132 bits (331), Expect = 3e-35 Identities = 110/335 (32%), Positives = 163/335 (48%), Gaps = 29/335 (8%) Query: 19 TYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVE 78 TYD+LI GGGI G +A + + G+ +L+E D A TSS S+KL+HGG+RYL+T++ Sbjct: 2 TYDLLIAGGGINGCAIAREASLLGLSVLLVEKDDLAAHTSSASSKLIHGGLRYLETYEFR 61 Query: 79 VVADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKY 138 +V + + ER + APH+ P +LP + + V+ + LYD L GS Sbjct: 62 LVREALHERERMLAAAPHLIHPMAFVLP---HAHSVRPWWMVRAGLYLYDLLG--LGSS- 115 Query: 139 ENYLLTKEEVLAR-EPQLQ--AENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKA 195 L + L R +P+L A N VGG +Y D + +DA LV N A A+GA + + Sbjct: 116 ----LPRSRALRRDDPRLAPIAHN-VGGFLYWDAQVDDAALVRANAADAVANGAQVETGV 170 Query: 196 KVVGILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDK-NDELPPQMR 254 V G + G+ V + D+ T + + ++N TGPW + LD +R Sbjct: 171 AVTGA--ERGGMGWHVFLSDRRT-----IDTRAIVNATGPW--VKAFLDTIRIRTTSGLR 221 Query: 255 PTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENKTYFGTTDTDYTGDFAHPTVT 314 KG H+VV L Y + D R+VF P T GTTD +T Sbjct: 222 LIKGSHIVV--PALWEGDHAYI-LQQPDRRVVFATPWRGGTMIGTTDVPVERP-EDAGIT 277 Query: 315 QEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPL 349 ++DYL N R+ QI D+ +W+G+R L Sbjct: 278 SAEIDYLCAAAN-RYFRRQIAPADVTGTWSGIRAL 311 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: 479 Number of extensions: 23 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 609 Length of database: 377 Length adjustment: 34 Effective length of query: 575 Effective length of database: 343 Effective search space: 197225 Effective search space used: 197225 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: 51 (24.3 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