Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate AZOBR_RS25870 AZOBR_RS25870 glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__azobra:AZOBR_RS25870 Length = 513 Score = 168 bits (426), Expect = 4e-46 Identities = 157/548 (28%), Positives = 243/548 (44%), Gaps = 88/548 (16%) Query: 20 YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79 YD+ I+GGGI G G+A A G L E +D A GTSS STKL+HGG+RYL+ ++ + Sbjct: 5 YDLAIVGGGINGCGIARDAAGRGCSVYLCEQKDLASGTSSASTKLIHGGLRYLEYYEFRL 64 Query: 80 VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139 V + +RER ++ ++APHI P +LP PG S F +++ + LYD L E Sbjct: 65 VREALREREVLWRMAPHIIWPLRFVLP--HLPGLRPSWF-LRLGLFLYDHLGG-----RE 116 Query: 140 NYLLTKEEVLAREPQLQAENLVGGGV--YLDFRNNDARLVIENIKRAQADGAAMISKAKV 197 T+ L +P + G Y D +DARLV+ N + A GA + ++ + Sbjct: 117 KLPGTRGLDLRNDPAGKPLKPGFGRAFEYSDCWVDDARLVVLNAQDAARMGATIRTRTRF 176 Query: 198 VGILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQMRPTK 257 + + E G+ V VED + +R + A+ ++N GPW V + + ++R + Sbjct: 177 LNAVR-EDGLWT-VTVEDTRSGQRSSIRARALVNAAGPWVSEVMRQGARSTVDARIRLVQ 234 Query: 258 GVHLVVDREKLKVPQPTYFDTGK------NDGRMVFVVPRENK-TYFGTTDTDYTGDFAH 310 G H+VV P FD + D R+VF +P E T GTTD DY GD A Sbjct: 235 GSHIVV---------PKLFDHDRCYIFQNADKRIVFAIPYERDFTLIGTTDNDYQGDPAD 285 Query: 311 PTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDES 370 ++ ++ YL + F +T D+ +++G+RPL Y+ G Sbjct: 286 VRASEAEIAYLCAAAGDYFA-KPVTPADVVWTYSGVRPL--------YDDGA-------- 328 Query: 371 FEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDGLLTLAG 430 + QA R +D + K LL + G Sbjct: 329 -----------------------STAQAATRDYVLALD--------APGDGKAALLNIFG 357 Query: 431 GKITDYRLMAEGAVKRINELLQE--SGASFELVDSTTYPVSGGELDAANVEEELAKLADQ 488 GKIT YR +A+ A+ ++ L + GAS + + T P GG+ A V +++L + Sbjct: 358 GKITTYRRLADAAIAKLAPFLPKLAPGAS-DWSSAGTLP--GGDFPADGVATLISELRGR 414 Query: 489 AQTAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEK-----ESTALNYSLHEEMVLTP 543 A + LA YG+ ++L+ + E L + Y + EE T Sbjct: 415 APF--LTQPHLERLARTYGTRARRILDSAARTEDLGRDFGGTLTEAEVRYLMTEEWAETA 472 Query: 544 VDYLLRRT 551 D L RRT Sbjct: 473 EDVLWRRT 480 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: 25 Number of successful extensions: 4 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: 513 Length adjustment: 36 Effective length of query: 573 Effective length of database: 477 Effective search space: 273321 Effective search space used: 273321 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