Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate Ac3H11_3398 Glycolate dehydrogenase (EC 1.1.99.14), iron-sulfur subunit GlcF
Query= reanno::Cup4G11:RR42_RS17315 (421 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3398 Length = 417 Score = 524 bits (1350), Expect = e-153 Identities = 267/426 (62%), Positives = 313/426 (73%), Gaps = 18/426 (4%) Query: 1 MQTTLAEFLRDTPDGEEAKSIVGKCVHCGFCTATCPTYQLLGDELDGPRGRIYLMKQVLE 60 MQT L+ R DG EA+SI+ KCVHCGFCTATCPTYQLLGDELDGPRGRIYL+KQVLE Sbjct: 1 MQTQLSPEYRARADGLEAESILRKCVHCGFCTATCPTYQLLGDELDGPRGRIYLIKQVLE 60 Query: 61 GQPVTQSTRLHLDRCLTCRNCESTCPSGVKYGRLVDIGRKVVDDRLEAQGIQRPARERFA 120 G+ T+ T++HLDRCLTCRNCESTCPSGV+YG LVDIGRK+VD++ + RP E+ Sbjct: 61 GETPTRKTQMHLDRCLTCRNCESTCPSGVQYGHLVDIGRKIVDEK-----VPRPVGEKAL 115 Query: 121 RWALRETMTRPALFGTAMRMGQRVRPLLPQALRNKVPQAVDAGAWPRTTHARKMLLLDGC 180 RWAL+E + P LF AM+ GQ VR LLP+AL+ KVP DAGAWP HARK+LLL GC Sbjct: 116 RWALKEGLPSP-LFAPAMKAGQLVRGLLPEALKAKVPAPQDAGAWPTREHARKVLLLAGC 174 Query: 181 VQPSMSPNINAATARVFDRLGVQLVMAREAGCCGAVRYHTGDHDGGLDNMRRNIDAWWPA 240 VQ +M PNIN ATARV D +G+Q V+A +AGCCGAV++H D GG+ MR NIDAWWP Sbjct: 175 VQLAMMPNINTATARVLDAVGIQTVIAPKAGCCGAVKFHLNDQAGGMAEMRANIDAWWPL 234 Query: 241 VQA-GAEAIVMTASGCGVMVKEYGHLLRNDAHYADRARQISALTKDLSELLPNFADALQD 299 V+A G EAIVM ASGCGV VKEYGH+L++DA YA +A +ISALT+DLSELLP L D Sbjct: 235 VEAGGVEAIVMNASGCGVTVKEYGHILKDDAQYAAKAERISALTRDLSELLPAMLPELAD 294 Query: 300 AAAEAGSSKGTNGTDGQRVAYHPPCTLQHGQQIRGKVEALLTGLGVDVKLCA-DSHLCCG 358 +G AYHPPCTLQHGQ++RG VEA L LG + D+HLCCG Sbjct: 295 ------KLQGRVNQPDTMYAYHPPCTLQHGQKLRGGVEAHLNQLGFQLSTARNDAHLCCG 348 Query: 359 SAGTYSVLQPALSYRLRDEKLANLQAL----KPEAIVSANIGCITHLQSGTGTPVMHWIE 414 SAGTYSVL P LSY+LRD KL L P+ I+SANIGCITHLQSGTGTPV HW+E Sbjct: 349 SAGTYSVLNPDLSYQLRDRKLGVLAEAFGEQPPDMILSANIGCITHLQSGTGTPVRHWVE 408 Query: 415 LVDRML 420 ++D L Sbjct: 409 VLDEAL 414 Lambda K H 0.321 0.135 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: 640 Number of extensions: 25 Number of successful extensions: 9 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: 421 Length of database: 417 Length adjustment: 32 Effective length of query: 389 Effective length of database: 385 Effective search space: 149765 Effective search space used: 149765 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 (21.9 bits) S2: 50 (23.9 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