Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate WP_011611668.1 TERY_RS09750 4Fe-4S dicluster domain-containing protein
Query= reanno::Smeli:SMc00926 (443 letters) >NCBI__GCF_000014265.1:WP_011611668.1 Length = 471 Score = 307 bits (787), Expect = 4e-88 Identities = 175/423 (41%), Positives = 242/423 (57%), Gaps = 24/423 (5%) Query: 31 SETILRKCVHCGFCTATCPTYVVLGDELDSPRGRIYLIKDMLENGRAADSETVT-HIDRC 89 S ++ CVHCGFC +TCP+Y V+G E+DSPRGRIY + D + NG A+ ++T + H D C Sbjct: 44 SPELIGACVHCGFCLSTCPSYRVIGKEMDSPRGRIY-VMDAINNGEASLNQTSSQHFDTC 102 Query: 90 LSCLSCLTTCPSGVDYMHLVDHARAHIEKTYKRPFKDRLARSVIAATLPYPSRFRLALGA 149 L CL+C+TTCPSGV Y L+ R +E+ R D+L RS+I PYP+R R L Sbjct: 103 LGCLACVTTCPSGVRYDKLIAATRPQVERNIPRSLPDKLIRSLIFNLFPYPNRLRPLLIP 162 Query: 150 AGLARPLA--GLLKRVPFLRTLGVMLDLAPSALP-----AARGAKPAVYAAKGTPRARVA 202 + + L L++ L + L S LP + P + A+G R RV Sbjct: 163 LFIYQKLGFNKLIRSSKLLDKISPRLAAMESILPEITVDSFSNNYPNIIPAEGEKRYRVG 222 Query: 203 LLTGCAQPVLRPEINDATIRLLTGQGVEVVVSAGEGCCGALVHHMGRDEQALQAGRHNID 262 L+ GC Q + +N ATIR+LT G EVV+ +GCC AL H G+ EQA + ID Sbjct: 223 LILGCVQRIFFSSVNMATIRVLTANGCEVVIPKSQGCCAALPEHQGQTEQAHALAKQMID 282 Query: 263 VWLKAAEEDGLDAIIITASGCGTTIKDYGHMLRLDPAYAEKAARVSALAKDVTEYLATLD 322 ++ G+DA+II A+GCG T+K+Y ++L+ D Y +KA S KDV E+LA + Sbjct: 283 SFVNT----GVDAVIINAAGCGHTLKEYDNILQDDSEYCDKAKEFSNKVKDVQEFLANVG 338 Query: 323 L-----PEQGARNLTVAYHSACSMQHGQKITSAP-KQLLKRAGFSVREPAEGHLCCGSAG 376 L P LT+ Y AC + HGQKI+ P K LLK G +REP + LCCGSAG Sbjct: 339 LTAKLYPLVEEEELTIVYQDACHLLHGQKISLEPRKLLLKIPGVKLREPIDAALCCGSAG 398 Query: 377 TYNILQPEISAKLKARKVRNIEATKPEVIATGNIGCITQI-----ASGTEIPILHTVELL 431 YN+LQPE + +L +KV N+ T E+IA+ N GC QI G + ++H +ELL Sbjct: 399 VYNMLQPETANELGEQKVENLLNTGAELIASPNPGCSLQIKKHLDLQGNNMSLMHPIELL 458 Query: 432 DWA 434 D++ Sbjct: 459 DYS 461 Lambda K H 0.320 0.135 0.409 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: 496 Number of extensions: 21 Number of successful extensions: 7 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: 443 Length of database: 471 Length adjustment: 33 Effective length of query: 410 Effective length of database: 438 Effective search space: 179580 Effective search space used: 179580 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 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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