Align LOR/SDH bifunctional enzyme conserved domain-containing protein (characterized, see rationale)
to candidate WP_011868143.1 MMARC5_RS01900 TIGR00300 family protein
Query= uniprot:Q6LXX7 (415 letters) >NCBI__GCF_000016125.1:WP_011868143.1 Length = 415 Score = 780 bits (2013), Expect = 0.0 Identities = 394/415 (94%), Positives = 407/415 (98%) Query: 1 MFMREIELKGHIIDSFILAKVFDRTLELGGDYKVLEFDIGKKKIDTSYAKLLISGDTQQH 60 MFMREIELKGHIIDSFILAKVFDRTLELGGDY VLEFDIGKKK D SYAKLLISG ++QH Sbjct: 1 MFMREIELKGHIIDSFILAKVFDRTLELGGDYNVLEFDIGKKKTDVSYAKLLISGTSEQH 60 Query: 61 LDQILEELQNVGANIPEIENANLKPALKDSVLPDGFYSTTNHPTHVKVNDEWIEVANPKM 120 LDQILEELQNVGANIPEIENANLKPALKDSVLPDGFYSTTNHPTHVKVNDEWIEVANPKM Sbjct: 61 LDQILEELQNVGANIPEIENANLKPALKDSVLPDGFYSTTNHPTHVKVNDEWIEVANPKM 120 Query: 121 DAVIVVYPEEKRAETKVIRKVKKGDFVLIGHNGIRVMPPEKSREAGQLFEFMNSEVSSEK 180 DAVIVVYPEEKRAETKV+RKVKKGDFV+IGHNGIRVMPPEKSREAGQLFEFMNSEVSSEK Sbjct: 121 DAVIVVYPEEKRAETKVMRKVKKGDFVVIGHNGIRVMPPEKSREAGQLFEFMNSEVSSEK 180 Query: 181 PKEAIIKRIAKEMHEIREEYKKTGTGGIAIVGGPAIIHTGGGPALAKMVELGYIQAILAG 240 PKEAIIKRIA+EM+EIRE YKKTGTGGIAIVGGPAIIHTGGGPALAKMVELGYIQAILAG Sbjct: 181 PKEAIIKRIAQEMYEIRENYKKTGTGGIAIVGGPAIIHTGGGPALAKMVELGYIQAILAG 240 Query: 241 NALATHDIESALYGTSLGVNIKTAKPVTGGHKHHIYAINAINDAGNIKNAVESGVLKEGI 300 NALATHDIESAL+GTSLGV+IKTAKPVTGGHKHHIYAIN I DAGNIKNAVESGVLKEGI Sbjct: 241 NALATHDIESALFGTSLGVDIKTAKPVTGGHKHHIYAINTIIDAGNIKNAVESGVLKEGI 300 Query: 301 MYQCIKNNIPYVLAGSIRDDGPIPDVITDSMVAQDKMRTTVMDKKMVIMLSTLLHSVATG 360 MYQC+KN+IPYVLAGSIRDDGP+PDVITD+MVAQD+MRT VMDKKMVIMLSTLLHSVATG Sbjct: 301 MYQCVKNDIPYVLAGSIRDDGPLPDVITDAMVAQDQMRTMVMDKKMVIMLSTLLHSVATG 360 Query: 361 NLMPSYIKTVCVDIQPSTVTKLMDRGTSQAIGVVTDVGVFLVLLLKELERLELQE 415 NLMPSYIKTVCVDIQPSTVTKLMDRGTSQAIGVVTDVGVFLVLLLKELERLELQE Sbjct: 361 NLMPSYIKTVCVDIQPSTVTKLMDRGTSQAIGVVTDVGVFLVLLLKELERLELQE 415 Lambda K H 0.317 0.136 0.380 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: 682 Number of extensions: 16 Number of successful extensions: 1 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: 415 Length of database: 415 Length adjustment: 31 Effective length of query: 384 Effective length of database: 384 Effective search space: 147456 Effective search space used: 147456 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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