Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate WP_035704441.1 BA79_RS18275 (Fe-S)-binding protein
Query= reanno::Smeli:SMc00926 (443 letters) >NCBI__GCF_000691145.1:WP_035704441.1 Length = 446 Score = 228 bits (582), Expect = 2e-64 Identities = 146/423 (34%), Positives = 212/423 (50%), Gaps = 31/423 (7%) Query: 32 ETILRKCVHCGFCTATCPTYVVLGD-ELDSPRGRIYLIKDMLENGRAADSETVTHIDRCL 90 E L C+ CGFC +CPTY+ G E SPRGRI L+K + + D + ++ CL Sbjct: 20 EKELLNCMRCGFCLPSCPTYIESGQQETHSPRGRIALMKAVRDGVIEPDEDVEHSLNLCL 79 Query: 91 SCLSCLTTCPSGVDYMHLVDHARAHIEKTYKRPFKDRLARSVIAATLPYPSRFRLALGAA 150 C +C CPSGV Y L++ AR I++ K+ F +L R V+ L +PS+ R+ A+ Sbjct: 80 GCRACEPVCPSGVKYGQLLEDARDIIQQHKKQSFPVKLMRRVVFKGL-FPSQSRMRQAAS 138 Query: 151 GL----ARPLAGLLKRVPFLRTLGVMLDLAPSALPAARGAKPA---VYAAKGTPRARVAL 203 L L ++ L+ L L L ALP K Y A G + RVA Sbjct: 139 FLRFYQTSGLQTAARKTRILKVLPSHLQLMEQALPKVPPQKKKRLNEYKAIGQAKKRVAF 198 Query: 204 LTGCAQPVLRPEINDATIRLLTGQGVEVVVSAGEGCCGALVHHMGRDEQALQAGRHNIDV 263 TGC + N ATI LL G +V+V + CCGAL H G +QA Q + NI+ Sbjct: 199 FTGCLMDTVFSNTNKATIHLLQLAGCDVIVPPIQTCCGALHGHSGEKDQAKQLAKRNIE- 257 Query: 264 WLKAAEEDGLDAIIITASGCGTTIKDYGHMLRLDPAYAEKAARVSALAKDVTEYLATLD- 322 A EE DAII+ A GCG + DYGH+L+ DP + +++ S D++ L L+ Sbjct: 258 ---AFEETDADAIIMNAGGCGAFLSDYGHLLQDDPDFQKRSKAFSQKITDISSILVELEF 314 Query: 323 -------LPEQGARNLTVAYHSACSMQHGQKITSAPKQLLKR-AGFSVREPAEGHLCCGS 374 LP Q + Y +C +++G + AP+ L+K G + +E + CCGS Sbjct: 315 HCRVPLALPAQ-----VITYQDSCHLRNGMNVQQAPRVLMKAIQGVTFKEMKDAGRCCGS 369 Query: 375 AGTYNILQPEISAKLKARKVRNIEATKPEVIATGNIGCITQIASGTE----IPILHTVEL 430 AG YNILQP++S ++ K+ T I T N GC Q+A+G + +P + + L Sbjct: 370 AGIYNILQPDMSMQILDHKMTEASNTAAAAIVTSNPGCQLQMAAGVKKAGHMPSMRAIHL 429 Query: 431 LDW 433 D+ Sbjct: 430 ADF 432 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: 450 Number of extensions: 28 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: 446 Length adjustment: 32 Effective length of query: 411 Effective length of database: 414 Effective search space: 170154 Effective search space used: 170154 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