Align Uncharacterized lactate 2-monooxygenase PB1A11.03; EC 1.13.12.4 (characterized)
to candidate WP_011778563.1 MVAN_RS06560 alpha-hydroxy-acid oxidizing enzyme
Query= SwissProt::Q9HDX2 (407 letters) >NCBI__GCF_000015305.1:WP_011778563.1 Length = 391 Score = 187 bits (475), Expect = 5e-52 Identities = 121/360 (33%), Positives = 190/360 (52%), Gaps = 24/360 (6%) Query: 40 EQLAVERMTKDAAGYVYGCAGKRETYDKNMESFKKWSIIPNRLIKSGFPDLSTTVFGQKY 99 +Q A +R+ K A + + K T N+ESF + P+ + + D++T+V GQ Sbjct: 14 QQRAKKRLPKSAYSSLISASEKGVTVTDNVESFAELGFAPHVIGATEKRDMATSVLGQDI 73 Query: 100 PFPIALAPVGVQKIFNPEGESGSCAAATREHIPYIISTASATSFEDIEKASGPGERWYQL 159 P+ ++P GVQ I +P+GE AA +S+ ++ ED+ + + ++Q+ Sbjct: 74 SLPVIISPTGVQAI-DPDGEVAVARAAAARGTAMGLSSFASKPMEDVTAVND--KIFFQI 130 Query: 160 YWPSNDHQDITISLLNRAKKTGCRVLIVTLDTFILGWR-------PSDMDNGYDPFLNPD 212 YW + +D ++ + RA+ G + LI+T D R P MD ++P+ Sbjct: 131 YWLGS--RDDILARMERARAAGAKGLILTTDWSFAHGRDWGSPKIPERMDLKTMIRMSPE 188 Query: 213 SIGVEHGFSD-------PVFRKQFKEKHGVEVEENMLEAAKEFAGIVFPGISHDWEDLKF 265 I F P R + + G E EA ++ G P WED+ + Sbjct: 189 VITKPRWFFSFAKHLRPPDLRVPNQGRRG-EAGPTFFEAYGQWMGTPPP----TWEDVAW 243 Query: 266 LRKHWDGPIVLKGIMNVPDAKKAVEYGMQGIVVSNHGGRQQDGGVASLTMLPKIVDAVGD 325 LR+ W GP +LKG + V DAK+AV+ G+ I VSNHGG DG A++ LP I DAVGD Sbjct: 244 LREQWGGPFLLKGTVRVDDAKRAVDAGVSAITVSNHGGNNLDGTPAAIRCLPAIADAVGD 303 Query: 326 KLDVLFDSGVRSGADIAKALALGAKMVLIGRPYVYGLALEGSSGVSHVIRCLLGDLELTL 385 +++VL D G+R G+D+ KA+ALGA+ V+IGR Y++GLA G +GV +V+ L G ++ L Sbjct: 304 QVEVLLDGGIRRGSDVVKAVALGARAVMIGRAYLWGLAANGQAGVENVLDILRGGIDSAL 363 Lambda K H 0.319 0.138 0.421 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: 376 Number of extensions: 17 Number of successful extensions: 2 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: 407 Length of database: 391 Length adjustment: 31 Effective length of query: 376 Effective length of database: 360 Effective search space: 135360 Effective search space used: 135360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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