Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate RR42_RS29875 RR42_RS29875 glycolate oxidase
Query= reanno::Cup4G11:RR42_RS17315 (421 letters) >FitnessBrowser__Cup4G11:RR42_RS29875 Length = 419 Score = 509 bits (1310), Expect = e-149 Identities = 254/419 (60%), Positives = 309/419 (73%), Gaps = 17/419 (4%) Query: 1 MQTTLAEFLRDTPDGEEAKSIVGKCVHCGFCTATCPTYQLLGDELDGPRGRIYLMKQVLE 60 MQT L+ +TP+G EA+ I+ KCVHCGFCTATCPTY LLGDE +GPRGRIYLMKQ+LE Sbjct: 1 MQTKLSHEFANTPEGAEAEEILRKCVHCGFCTATCPTYLLLGDERNGPRGRIYLMKQLLE 60 Query: 61 GQPVTQSTRLHLDRCLTCRNCESTCPSGVKYGRLVDIGRKVVDDRLEAQGIQRPARERFA 120 G+ VT ST+ +LDRCLTCRNCESTCPSGV+YG+LV IGRK+VD+R I RP ++R Sbjct: 61 GEEVTASTQQNLDRCLTCRNCESTCPSGVEYGKLVHIGRKLVDER-----IPRPPKDRAV 115 Query: 121 RWALRETMTRPALFGTAMRMGQRVRPLLPQALRNKVPQAVDAGAWPRTTHARKMLLLDGC 180 RW LRE +T P LF AM++G+ VRPLLP L NK+ + AG P HARK+L+L+GC Sbjct: 116 RWLLREGLTSP-LFLPAMKIGRMVRPLLPSKLANKLTPSRPAGQRPTRRHARKVLMLEGC 174 Query: 181 VQPSMSPNINAATARVFDRLGVQLVMAREAGCCGAVRYHTGDHDGGLDNMRRNIDAWWPA 240 VQP+M PNIN+ATARV D Q+V AGCCGA+R HTGDH GGLD+MRRNIDAWWPA Sbjct: 175 VQPAMMPNINSATARVLDAADFQVVSVPRAGCCGAIRLHTGDHKGGLDDMRRNIDAWWPA 234 Query: 241 VQAG-AEAIVMTASGCGVMVKEYGHLLRNDAHYADRARQISALTKDLSELLPNFADALQD 299 + +G EAIVM ASGCG VK+Y LL++DA YA++A ++S LT+DLSELLP L+ Sbjct: 235 ISSGEVEAIVMNASGCGATVKDYADLLKHDAEYAEKAARVSELTRDLSELLPELLPRLRG 294 Query: 300 AAAEAGSSKGTNGTDGQRVAYHPPCTLQHGQQIRGKVEALLTGLGVDV-KLCADSHLCCG 358 D +A+HPPCTLQHGQ++RG VE L LG V + +SHLCCG Sbjct: 295 K---------VKACDKPALAFHPPCTLQHGQKLRGVVEEHLGQLGFSVHRASVESHLCCG 345 Query: 359 SAGTYSVLQPALSYRLRDEKLANLQALKPEAIVSANIGCITHLQSGTGTPVMHWIELVD 417 SAGTYSVLQP +S +LRD K+ +L +P+ IVSANIGCI HLQSGT TPV HWIE++D Sbjct: 346 SAGTYSVLQPEISLQLRDRKIEHLSEKQPDCIVSANIGCIQHLQSGTPTPVKHWIEVLD 404 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: 642 Number of extensions: 29 Number of successful extensions: 8 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: 419 Length adjustment: 32 Effective length of query: 389 Effective length of database: 387 Effective search space: 150543 Effective search space used: 150543 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