Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate HSERO_RS19095 HSERO_RS19095 glycolate oxidase
Query= reanno::Cup4G11:RR42_RS17315 (421 letters) >FitnessBrowser__HerbieS:HSERO_RS19095 Length = 414 Score = 576 bits (1485), Expect = e-169 Identities = 277/424 (65%), Positives = 335/424 (79%), Gaps = 18/424 (4%) Query: 1 MQTTLAEFLRDTPDGEEAKSIVGKCVHCGFCTATCPTYQLLGDELDGPRGRIYLMKQVLE 60 MQT LA+F+R+T G+EA SI+ CVHCGFCTATCPTYQLLGDELDGPRGRIYL+KQVLE Sbjct: 1 MQTNLADFIRNTQAGQEADSILRSCVHCGFCTATCPTYQLLGDELDGPRGRIYLIKQVLE 60 Query: 61 GQPVTQSTRLHLDRCLTCRNCESTCPSGVKYGRLVDIGRKVVDDRLEAQGIQRPARERFA 120 G+P T +T+ HLDRCLTCRNCESTCPSGV+YGRLVDIGRKVV+++ + RP +R Sbjct: 61 GKPATAATQSHLDRCLTCRNCESTCPSGVQYGRLVDIGRKVVEEQ-----VPRPLSQRVM 115 Query: 121 RWALRETMTRPALFGTAMRMGQRVRPLLPQALRNKVPQAVDAGAWPRTTHARKMLLLDGC 180 R AL+E + R +F AM+ GQ +RPLLP+ L+NKVP +AGAWP THAR+ML L+GC Sbjct: 116 RTALKELVPRKWIFRPAMKAGQMLRPLLPKLLQNKVPLPQEAGAWPTRTHARQMLYLEGC 175 Query: 181 VQPSMSPNINAATARVFDRLGVQLVMAREAGCCGAVRYHTGDHDGGLDNMRRNIDAWWPA 240 VQPSMSPNIN+ATARV D LGVQL +AGCCGA+RYH D +GGL++MRRNIDAWWP Sbjct: 176 VQPSMSPNINSATARVLDALGVQLFAPPKAGCCGAIRYHMNDQEGGLEDMRRNIDAWWPY 235 Query: 241 VQA----GAEAIVMTASGCGVMVKEYGHLLRNDAHYADRARQISALTKDLSELLPNFADA 296 ++ A+ IVM ASGCG VKEYGHLL++D YA++AR+IS +T+D+SE+LP F +A Sbjct: 236 IEGRDGIRADTIVMNASGCGSTVKEYGHLLQHDPVYAEKARRISHMTRDISEILPEFEEA 295 Query: 297 LQDAAAEAGSSKGTNGTDGQRVAYHPPCTLQHGQQIRGKVEALLTGLGVDVKLCADSHLC 356 L+ + +G+RVAYHPPCTLQHGQ+IRGKVE +L GVDV+LCADSHLC Sbjct: 296 LKHKLKD---------FNGKRVAYHPPCTLQHGQKIRGKVEGILRAAGVDVQLCADSHLC 346 Query: 357 CGSAGTYSVLQPALSYRLRDEKLANLQALKPEAIVSANIGCITHLQSGTGTPVMHWIELV 416 CGSAGTYS+LQP LSYRLRD K++ LQA P+ IV+ NIGC+THLQSGT TPV HWIEL+ Sbjct: 347 CGSAGTYSILQPELSYRLRDNKISKLQATDPDMIVTGNIGCVTHLQSGTDTPVRHWIELL 406 Query: 417 DRML 420 D L Sbjct: 407 DAAL 410 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: 641 Number of extensions: 24 Number of successful extensions: 5 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: 414 Length adjustment: 32 Effective length of query: 389 Effective length of database: 382 Effective search space: 148598 Effective search space used: 148598 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