Align Uncharacterized lactate 2-monooxygenase PB1A11.03; EC 1.13.12.4 (characterized)
to candidate WP_005455145.1 SACCYDRAFT_RS07750 alpha-hydroxyacid dehydrogenase
Query= SwissProt::Q9HDX2 (407 letters) >NCBI__GCF_000244975.1:WP_005455145.1 Length = 387 Score = 370 bits (951), Expect = e-107 Identities = 195/374 (52%), Positives = 247/374 (66%), Gaps = 9/374 (2%) Query: 16 YESEIYAKGLKFQRPQITVDGRHWEQLAVERMTKDAAGYVYGCAGKRETYDKNMESFKKW 75 Y+SEIY G P T D E +A + YV G AG T N E+F +W Sbjct: 8 YQSEIYLSGYGGTTPAFTTDLTRLEAVAERVLEPGPFAYVAGGAGSGATSRANREAFDRW 67 Query: 76 SIIPNRLIKSGFPDLSTTVFGQKYPFPIALAPVGVQKIFNPEGESGSCAAATREHIPYII 135 +++P L + +L+TTV G+ P P+ LAPVGVQ I +PE E + AA +P ++ Sbjct: 68 ALVPRMLTDATERELATTVLGETLPAPVVLAPVGVQSIVHPEAERATAKAAAGLGLPMVM 127 Query: 136 STASATSFEDIEKASGPGERWYQLYWPSNDHQDITISLLNRAKKTGCRVLIVTLDTFILG 195 STAS+TS ED+ ASGPG RW+QLYWP++ D+ S+L R + G VL+VTLDT+ LG Sbjct: 128 STASSTSIEDVASASGPGPRWFQLYWPNDP--DVCGSILARVRAAGFSVLVVTLDTWSLG 185 Query: 196 WRPSDMDNGYDPFLNPDSIGVEHGFSDPVFRKQFKEKHGVEVEENMLEAAKEFAGIVFPG 255 WRP D+DNGY PFL + V F+DPVFR + + +E++ A + ++ G Sbjct: 186 WRPCDLDNGYLPFLKGEGTAVP--FTDPVFRSRLESAP----DEDLAMAVLRWISMI-TG 238 Query: 256 ISHDWEDLKFLRKHWDGPIVLKGIMNVPDAKKAVEYGMQGIVVSNHGGRQQDGGVASLTM 315 DW+ L FLR+HWDGPIVLKGI +V DA++A G+ GIVVSNHGGRQ DG VASL M Sbjct: 239 TDRDWDALPFLREHWDGPIVLKGIQHVDDARRAAAAGVDGIVVSNHGGRQVDGAVASLDM 298 Query: 316 LPKIVDAVGDKLDVLFDSGVRSGADIAKALALGAKMVLIGRPYVYGLALEGSSGVSHVIR 375 LP+I AVGD+LDVLFDSGVR+GAD+ KALALGAK VL+GRPYVYGLAL G GV HV+R Sbjct: 299 LPEIATAVGDRLDVLFDSGVRTGADVVKALALGAKAVLVGRPYVYGLALGGEDGVRHVLR 358 Query: 376 CLLGDLELTLHLSG 389 LL DL+LTL LSG Sbjct: 359 SLLADLDLTLALSG 372 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: 458 Number of extensions: 21 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: 407 Length of database: 387 Length adjustment: 31 Effective length of query: 376 Effective length of database: 356 Effective search space: 133856 Effective search space used: 133856 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