Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate 6936441 Sama_0629 glycerol-3-phosphate dehydrogenase (RefSeq)
Query= curated2:P35596 (608 letters) >FitnessBrowser__SB2B:6936441 Length = 404 Score = 135 bits (339), Expect = 4e-36 Identities = 107/338 (31%), Positives = 168/338 (49%), Gaps = 20/338 (5%) Query: 18 RTLDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDV 77 + +D+L++GGGI G G+A AAA+G LIE Q E TS S+KL+HGGLRYL+ + Sbjct: 2 KRVDVLVVGGGIAGVGIAQFAAAAGYSVALIERQRIGEATSGNSSKLIHGGLRYLETMQL 61 Query: 78 EVVSDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYDLLAGVSNTP 137 ++V ++ ER + Q+AP + + P PVY + ++ + LY LL+ + Sbjct: 62 DLVRKSLKERRALLQLAPSLVTAVPFYFPVY--RNSRRGALTIRAGLSLYGLLSEF-DAL 118 Query: 138 AANKVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHV-- 195 K LSK Q R L GL Y D + +D RL+ E + + L+ V Sbjct: 119 GRFKTLSKSQ-WSRLQGLNSAGLETVFQYWDAQTDD-RLLCEAVAHS---AILLGTDVFE 173 Query: 196 KAEGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKVRNLSNKGTQFSQMRP 255 AE SG G Q +I+A +VIN GPW +++ ++ Sbjct: 174 WAEVEHIQHSG--DGCQVSFTQQGQQHDIQAGVVINACGPWVNQLLERVTPTVSALEIDW 231 Query: 256 TKGVHLVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTTDTDYTGDLEHPKVTQ 315 +G HL++D V +Y ++ + D R+VFV+P KT GTT+T T P VT+ Sbjct: 232 VQGAHLLLDIP--PVDGVLYLESPI-DQRVVFVMPWYGKTLVGTTETRLTHLDNKPAVTE 288 Query: 316 EDVDYLLGIVNNRFPESNITIDDIE----SSWAGLRPL 349 + YLL + + FP++ +D++E ++ G+R L Sbjct: 289 AEKRYLLALYAHYFPDAG-KVDELEKKVTDTFCGVRVL 325 Lambda K H 0.314 0.133 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: 468 Number of extensions: 25 Number of successful extensions: 3 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: 608 Length of database: 404 Length adjustment: 34 Effective length of query: 574 Effective length of database: 370 Effective search space: 212380 Effective search space used: 212380 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