Align glycolate oxidase subunit glcD (characterized)
to candidate WP_011840607.1 RSPH17029_RS04045 FAD-binding protein
Query= CharProtDB::CH_024646 (499 letters) >NCBI__GCF_000015985.1:WP_011840607.1 Length = 457 Score = 215 bits (548), Expect = 2e-60 Identities = 143/425 (33%), Positives = 210/425 (49%), Gaps = 18/425 (4%) Query: 56 PLLVVLPKQMEQVTAILAVCHRLRVPVVTRGAGTGLSGGALPLEKGVLLVMARFKEILDI 115 P V P+ +V I +C RVP+V GAGT L G AL L+ GV + A+ IL++ Sbjct: 40 PDAVAFPRSTAEVARIAEICTAHRVPMVGWGAGTSLEGHALALKGGVTIDFAQMDRILEL 99 Query: 116 NPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLT 175 P RVQPG+ ++ A+ L++ DP + S+GG A A G ++YG Sbjct: 100 RPEDMIVRVQPGLTREGLNAALRDTGLFFPVDPGAD--ASLGGMAATRASGTTAVRYGTM 157 Query: 176 VHNLLKIEVQTLDGEALTLGSDA-LDSPGFDLLALFTGSEGMLGVTTEVTVKLLPKPPVA 234 N+L +EV DG + G+ A S G+DL AL GSEG LG+ TE+T++L +P Sbjct: 158 RDNVLGLEVVLSDGRVIRTGTAAPKSSAGYDLTALMVGSEGTLGLITELTLRLHGQPEAV 217 Query: 235 RVLLASFDSVEKAGLAVGDIIANGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCE 294 + +F + A V + I +GI +E +D S+ A + P A LL E Sbjct: 218 SAAVCAFPDMGAAVGCVIETIQHGIPMARIEFLDAASVTACNAYAQMEMP--AVPHLLIE 275 Query: 295 LDGVESDVQEDCERVNDILLKAGATDVRLAQDEAERVRFWAGRKNAFPAVGRISP--DYY 352 G E+ V E ER +I + G+ D + A +R R W R A+ A + P + + Sbjct: 276 FHGTEAGVAEQAERFGEIAAEHGSADFQWATRTEDRARLWKMRHAAYRACLALRPGAEGW 335 Query: 353 CMDGTIPRRALPGVLEGIARLSQQYDLRVANV-----FHAGDGNMHPLILFDANEPGEFA 407 D +P L +E Q DL + V H GDGN H ++L D E A Sbjct: 336 VTDVCVPISRLAEAVE-----ETQADLAASPVPGPILGHVGDGNFHAILLVDPQSAEELA 390 Query: 408 RAEELGGKILELCVEVGGSISGEHGIGREKINQMCAQFNSDEITTFHAVKAAFDPDGLLN 467 A+ L G++ E + +GG+++GEHGIG K+ M A+ + A+K A DP GL+N Sbjct: 391 EAQRLSGRMAERALRLGGTVTGEHGIGFGKLGYMEAEHGAG-WAVMGAIKQALDPFGLMN 449 Query: 468 PGKNI 472 PGK + Sbjct: 450 PGKMV 454 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: 603 Number of extensions: 33 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: 457 Length adjustment: 34 Effective length of query: 465 Effective length of database: 423 Effective search space: 196695 Effective search space used: 196695 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. 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