Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate SMc02520 SMc02520 glycerol-3-phosphate dehydrogenase
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__Smeli:SMc02520 Length = 503 Score = 192 bits (489), Expect = 2e-53 Identities = 154/545 (28%), Positives = 256/545 (46%), Gaps = 81/545 (14%) Query: 17 KTTYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFD 76 +T +DV +IGGGI G G+A A G L EM DFA GTSS STKL+HGG+RYL+ ++ Sbjct: 4 QTIFDVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLEHYE 63 Query: 77 VEVVADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGS 136 +V + + ER ++ +APH+ P +LP + G + +++ + LYD ++ G Sbjct: 64 FRLVREALMEREVLWAMAPHVIWPMRFVLPFH--KGGPRPAWLIRLGLFLYD---HIGGR 118 Query: 137 KYENYLLTKEEVLAREPQLQAENLVG----GGVYLDFRNNDARLVIENIKRAQADGAAMI 192 K TK + R+P L G Y D +DARLV+ N + A GA ++ Sbjct: 119 KL--LPATKTLDMTRDP--AGAPLKGLFTKAFEYSDGWVDDARLVVLNARDAADRGARIM 174 Query: 193 SKAKVVGILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQ 252 ++ +VV +G +E+E T R + A++++N GPW D V + Sbjct: 175 ARTRVVSA--RREGGRWAIEIESTETGARETMRARMLVNAAGPWVDRVLSEAVGNNDVRN 232 Query: 253 MRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGDFAHP 311 +R +G H+VV ++K P+ +F DGR++F +P +++ T GTTD D+TG+ A Sbjct: 233 VRLVQGSHIVV-KKKFDDPRAYFFQ--NPDGRIMFAIPYQDEFTLIGTTDRDFTGNPADV 289 Query: 312 TVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLSDESF 371 ++ ++DYL +E F + +DI +++ +RPL D+ Sbjct: 290 RISDAEIDYLCRAASEYFSD-PVGREDIVWTYSAVRPLF-----------------DDGA 331 Query: 372 EQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKDGLLTLAGG 431 + E+ ++Y+ +E LL + GG Sbjct: 332 SKAQEATRDYVL---------------------------------RVENGDAPLLNVFGG 358 Query: 432 KITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELAKLADQAQT 491 K+T YR +AE A+++I E + E G + V + GG+ AA ++E+AKL + + Sbjct: 359 KLTTYRRLAESALEKIGETIGEKGRKWTAVSH----LPGGDFPAAGYDDEVAKL--RTRY 412 Query: 492 AGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLD-----EKESTALNYSLHEEMVLTPVDY 546 + A L LYG+ Q+L L + + +++ + +E L D Sbjct: 413 PFLTASHARRLVRLYGTRAAQLLGNAASEADLGKHFGADLYAAEVDWLIVQEWALRAEDV 472 Query: 547 LLRRT 551 L RRT Sbjct: 473 LWRRT 477 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: 567 Number of extensions: 32 Number of successful extensions: 5 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: 503 Length adjustment: 36 Effective length of query: 573 Effective length of database: 467 Effective search space: 267591 Effective search space used: 267591 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