Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate H281DRAFT_04681 H281DRAFT_04681 glycolate oxidase iron-sulfur subunit
Query= reanno::Cup4G11:RR42_RS17315 (421 letters) >FitnessBrowser__Burk376:H281DRAFT_04681 Length = 408 Score = 536 bits (1380), Expect = e-157 Identities = 261/420 (62%), Positives = 316/420 (75%), Gaps = 14/420 (3%) Query: 1 MQTTLAEFLRDTPDGEEAKSIVGKCVHCGFCTATCPTYQLLGDELDGPRGRIYLMKQVLE 60 MQT LA+F+R+TPDG+EA +I+ CVHCGFCTATCPTYQLLGDELDGPRGRIYL+KQ++E Sbjct: 1 MQTNLADFIRNTPDGDEADAILRNCVHCGFCTATCPTYQLLGDELDGPRGRIYLIKQMVE 60 Query: 61 GQPVTQSTRLHLDRCLTCRNCESTCPSGVKYGRLVDIGRKVVDDRLEAQGIQRPARERFA 120 G VT+ST++HLDRCLTCRNCESTCPSGV+YG+LV+IGRK+ + + + RP +R Sbjct: 61 GAEVTRSTQVHLDRCLTCRNCESTCPSGVQYGKLVEIGRKITEKK-----VTRPLGQRLT 115 Query: 121 RWALRETMTRPALFGTAMRMGQRVRPLLPQALRNKVPQAVDAGAWPRTTHARKMLLLDGC 180 R L + ALF AMR+GQ R LLP+ LR+KVP WP H RKML+L GC Sbjct: 116 RRFLASFVPNSALFTPAMRLGQHFRALLPRKLRDKVPARQRPLEWPTARHTRKMLMLAGC 175 Query: 181 VQPSMSPNINAATARVFDRLGVQLVMAREAGCCGAVRYHTGDHDGGLDNMRRNIDAWWPA 240 VQPSM PN+N ATARV D LGV+ ++A +AGCCGAVR H G +D L +MR NIDAWWP Sbjct: 176 VQPSMMPNVNVATARVLDALGVETLVAPDAGCCGAVRLHLGYNDEALVDMRANIDAWWPY 235 Query: 241 VQAGAEAIVMTASGCGVMVKEYGHLLRNDAHYADRARQISALTKDLSELLPNFADALQDA 300 V+ G EAIVM ASGCG VKEY HLLR+D YA++AR+I LT+D++E+LP+F + L Sbjct: 236 VEQGVEAIVMNASGCGATVKEYAHLLRHDPAYAEKARRIVELTRDIAEILPDFEEQLASI 295 Query: 301 AAEAGSSKGTNGTDGQRVAYHPPCTLQHGQQIRGKVEALLTGLGVDVKLCADSHLCCGSA 360 T VA+HPPCTLQHGQQ+RG VE LLT LGV+V+L AD+HLCCGSA Sbjct: 296 ---------TRRRAIHTVAFHPPCTLQHGQQVRGTVEHLLTRLGVEVRLPADNHLCCGSA 346 Query: 361 GTYSVLQPALSYRLRDEKLANLQALKPEAIVSANIGCITHLQSGTGTPVMHWIELVDRML 420 GTYS+ QP LSY LRD+KL L A +P+ IVSAN+GCI+HLQSGT TPV HWIELV+ ML Sbjct: 347 GTYSLTQPRLSYALRDQKLERLHAQEPQMIVSANVGCISHLQSGTSTPVAHWIELVEHML 406 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: 609 Number of extensions: 22 Number of successful extensions: 4 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: 408 Length adjustment: 31 Effective length of query: 390 Effective length of database: 377 Effective search space: 147030 Effective search space used: 147030 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