Align D-lactate oxidase and glycolate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate WP_086511790.1 BZY95_RS20755 glycolate oxidase iron-sulfur subunit
Query= reanno::psRCH2:GFF3770 (405 letters) >NCBI__GCF_002151265.1:WP_086511790.1 Length = 415 Score = 588 bits (1516), Expect = e-172 Identities = 291/409 (71%), Positives = 327/409 (79%), Gaps = 5/409 (1%) Query: 1 MQTNLSEAAKKLPRAEEAESILRSCVHCGFCNATCPTYQLLGDELDGPRGRIYLMKQMFE 60 MQT+ +E A K P +EA+ +LRSCVHCGFCNATCPTYQLLGDE DGPRGRIYLMKQM E Sbjct: 1 MQTHFTEEALKQPHIQEADRVLRSCVHCGFCNATCPTYQLLGDERDGPRGRIYLMKQMLE 60 Query: 61 GGE----VTESTQLHLDRCLTCRNCETTCPSGVKYHNLLDIGRDFIEQQVQRPLGERVVR 116 + VTE T+LHLDRCLTCRNCETTCPSGV+YH LLDIGR IE++V R ER R Sbjct: 61 NPDDSENVTEQTRLHLDRCLTCRNCETTCPSGVEYHKLLDIGRAEIERRVPRSTAERAQR 120 Query: 117 GGLRTVIPRPGLFKALLGAGNALKPLMPASLKDHLPREIRPAKPRPQ-VMHSRRVLILEG 175 LR + P F+ALL G KPL+P LKD LP + A RP H+R++LILEG Sbjct: 121 YALRKALVEPKRFQALLKLGQTFKPLVPGKLKDKLPPKPVDAGTRPDHKRHARQMLILEG 180 Query: 176 CVQPSLSPSTNAAAARVLDRLGISVSPAREAGCCGAVDYHLNAQDAGLDRARRNIDAWWP 235 CVQP LSP+TNAA ARVLDRLGI ++P EAGCCGAVD+HLNAQD G RAR NIDAWWP Sbjct: 181 CVQPGLSPNTNAATARVLDRLGIGLTPVAEAGCCGAVDFHLNAQDDGRARARANIDAWWP 240 Query: 236 AIEAGAEAIVQTASGCGAFVKEYGHLLKDDPAYAAKAARVSELAKDLVEVLRSAELEKLN 295 IEAGAEAIVQTAS CGAFVKEY +LKDDPAYA KA RVSELAKDLVEVLR EL L Sbjct: 241 HIEAGAEAIVQTASACGAFVKEYRDILKDDPAYADKARRVSELAKDLVEVLRDEELASLE 300 Query: 296 VRADKRMAFHCPCTLQHAQKLGGAVEDVLTRLGYQLTAVPDAHLCCGSAGSYSITQPEIS 355 V +R+AFHCPCTLQHAQKLGGAVE VL +LG+ LT V DAHLCCGSAG+YSITQPE++ Sbjct: 301 VNEGRRLAFHCPCTLQHAQKLGGAVEGVLVKLGFTLTPVQDAHLCCGSAGTYSITQPELA 360 Query: 356 HQLRDNKLNALESGKPEVIVTANIGCQTHLDGAGRTPVKHWIEVVEESM 404 QLRDNKLNALE+G PE IVTANIGCQTHL+GAGRTPV+HWIE+V+E++ Sbjct: 361 TQLRDNKLNALEAGNPETIVTANIGCQTHLNGAGRTPVRHWIEIVDEAL 409 Lambda K H 0.319 0.135 0.410 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: 630 Number of extensions: 18 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: 405 Length of database: 415 Length adjustment: 31 Effective length of query: 374 Effective length of database: 384 Effective search space: 143616 Effective search space used: 143616 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: 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