Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate BPHYT_RS03500 BPHYT_RS03500 glycolate oxidase
Query= reanno::Cup4G11:RR42_RS17315 (421 letters) >FitnessBrowser__BFirm:BPHYT_RS03500 Length = 408 Score = 552 bits (1423), Expect = e-162 Identities = 265/420 (63%), Positives = 320/420 (76%), Gaps = 14/420 (3%) Query: 1 MQTTLAEFLRDTPDGEEAKSIVGKCVHCGFCTATCPTYQLLGDELDGPRGRIYLMKQVLE 60 MQT LA+F+R+TPDG+EA I+ CVHCGFCTATCPTYQ+LGDELDGPRGRIYL+KQ++E Sbjct: 1 MQTNLADFIRNTPDGDEADGILRNCVHCGFCTATCPTYQILGDELDGPRGRIYLIKQMVE 60 Query: 61 GQPVTQSTRLHLDRCLTCRNCESTCPSGVKYGRLVDIGRKVVDDRLEAQGIQRPARERFA 120 G PVT+ST++HLDRCLTCRNCESTCPSGV+YGRLV+IGRK+ +++ + RP +R Sbjct: 61 GAPVTRSTQVHLDRCLTCRNCESTCPSGVQYGRLVEIGRKLTEEK-----VTRPLGQRLV 115 Query: 121 RWALRETMTRPALFGTAMRMGQRVRPLLPQALRNKVPQAVDAGAWPRTTHARKMLLLDGC 180 R L + ALF MR+GQ RPLLP+ LR+KVP WP H RKML+L GC Sbjct: 116 RRMLASFVPNSALFTPTMRIGQHFRPLLPKKLRDKVPARQRPLEWPTAKHPRKMLMLAGC 175 Query: 181 VQPSMSPNINAATARVFDRLGVQLVMAREAGCCGAVRYHTGDHDGGLDNMRRNIDAWWPA 240 VQPSM PN+N ATARVFD LGV+ ++A +AGCCGA+R H G +D LD++R NIDAWWP Sbjct: 176 VQPSMMPNVNIATARVFDALGVETLIAPDAGCCGAIRLHLGYNDDALDDLRANIDAWWPY 235 Query: 241 VQAGAEAIVMTASGCGVMVKEYGHLLRNDAHYADRARQISALTKDLSELLPNFADALQDA 300 ++ G EAIVM ASGCG VKEY HLLR+D YA++AR++ LT+D++E+LP F +AL Sbjct: 236 IEQGVEAIVMNASGCGATVKEYAHLLRHDPAYAEKARRVVELTRDVAEILPEFEEALVSV 295 Query: 301 AAEAGSSKGTNGTDGQRVAYHPPCTLQHGQQIRGKVEALLTGLGVDVKLCADSHLCCGSA 360 T VA+HPPCTLQHGQQIRGKVE LLT LGV+V+L ADSHLCCGSA Sbjct: 296 ---------TRRRSVHTVAFHPPCTLQHGQQIRGKVEHLLTALGVEVRLPADSHLCCGSA 346 Query: 361 GTYSVLQPALSYRLRDEKLANLQALKPEAIVSANIGCITHLQSGTGTPVMHWIELVDRML 420 GTYS+ QP LSY LRD+KL LQA +P+ IVSAN+GCI HLQSGT TPV HWIELV+ ML Sbjct: 347 GTYSLTQPKLSYALRDQKLDRLQAQEPQVIVSANVGCIAHLQSGTSTPVAHWIELVEHML 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: 618 Number of extensions: 21 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