Align glycolate oxidase subunit glcD (characterized)
to candidate WP_043745229.1 AMB_RS18795 FAD-binding oxidoreductase
Query= CharProtDB::CH_024646 (499 letters) >NCBI__GCF_000009985.1:WP_043745229.1 Length = 469 Score = 161 bits (407), Expect = 5e-44 Identities = 139/473 (29%), Positives = 219/473 (46%), Gaps = 32/473 (6%) Query: 20 SVLMALREHVPGLEILHTDEEIIPYECDGLSAYRTRPLLVVLPKQMEQVTAILAVCHRLR 79 S+L AL V ++ ++ PY + Y+ L VV P +V ++ +C Sbjct: 2 SILHALSAIVGPGNVITEASDLAPYLVEERGLYQGAALGVVRPGSTAEVAEVVRLCAAAG 61 Query: 80 VPVVTRGAGTGLSGGALPLEKGVLLVMA--RFKEILDINPVGRRARVQPGVRNLAISQAV 137 +P+V +G TGL GG +P E G +V++ R I ++PV + G + QA Sbjct: 62 IPMVPQGGNTGLCGGGVPSEDGQSVVISTERLTRIRAVDPVDFTLTAEAGCVLANLQQAA 121 Query: 138 APHNLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLLKIEVQTLDGEALT-LGS 196 + ++ +C IGGN++ NAGG + L+YG T +L +EV DG L Sbjct: 122 EEAGCLFPLSLGAEGSCRIGGNISTNAGGTNVLRYGNTRDLVLGLEVVLPDGRVWNGLKR 181 Query: 197 DALDSPGFDLLALFTGSEGMLGVTTEVTVKLLPKP---PVARVLLASFDSV----EKAGL 249 D+ G+ L LF G+EG LG+ T +KL P+P A V LA ++ +A Sbjct: 182 LRKDNTGYALQHLFIGAEGTLGIVTACVLKLFPRPREIATAFVALADLEAALPLFSRART 241 Query: 250 AVGD-IIANGIIPG-GLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVE-SDVQEDC 306 A GD + A ++P GLE L +R + A + + +LL EL ++E Sbjct: 242 ASGDSVTACELVPRRGLE----LGMRHVPG-VRAPFAAFHDWMLLLELSSSRPGGLREAL 296 Query: 307 ERVNDILLKAG-ATDVRLAQDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPRRALPG 365 E + + G A D +A+ +A+R FW R+ A P + D + +P Sbjct: 297 EEMLGQAFEDGLAVDAVIAESDAQRADFWRIRE-AIPEAQKKEGGSIKHDVAVATSRVPE 355 Query: 366 VLEGIARLSQQY--DLRVANVFHAGDGNMHPLILFDANEP------GEFARAEELGGKIL 417 ++ R + +RV H GDGN H F+ +P AR EE+ + Sbjct: 356 MIRRCTRAVEAAMPGVRVVPFGHLGDGNTH----FNLTQPEGADKAAFLARWEEMNRIVH 411 Query: 418 ELCVEVGGSISGEHGIGREKINQMCAQFNSDEITTFHAVKAAFDPDGLLNPGK 470 ++ VE+ GSIS EHGIGR K++++ ++ +K A DP G +NPGK Sbjct: 412 DIVVEMEGSISAEHGIGRLKVDELAHYKPGVDLDLMARIKGALDPLGQMNPGK 464 Lambda K H 0.320 0.140 0.415 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: 633 Number of extensions: 29 Number of successful extensions: 6 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: 499 Length of database: 469 Length adjustment: 34 Effective length of query: 465 Effective length of database: 435 Effective search space: 202275 Effective search space used: 202275 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 (21.8 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