Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate WP_013089823.1 BC1002_RS09455 lactate utilization protein
Query= uniprot:Q8EGS5 (464 letters) >NCBI__GCF_000092885.1:WP_013089823.1 Length = 471 Score = 261 bits (666), Expect = 5e-74 Identities = 156/417 (37%), Positives = 225/417 (53%), Gaps = 17/417 (4%) Query: 62 EIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSML 121 E + L NL +LETFE+ G+ V +A+ E R+V +I H VKK++K+KSM+ Sbjct: 54 ERRNRALENLDVWLETFEREATRRGVTVLFAETTQEAARLVGDIARKHDVKKVIKTKSMV 113 Query: 122 TEECHLNPYLEQRGIEVIDTDLGERIIQLA-KMPPSHIVVPAIHMKKEEVGDLFHDKLGT 180 TEE LN L Q G++ I+TDLGE I+Q+ PPSHI+ P +H K+E+ DLF G Sbjct: 114 TEEMRLNEVLGQMGVQSIETDLGEYILQINDNEPPSHIIAPVVHKDKDEIADLFAKTHGR 173 Query: 181 KAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKL 240 P +TR AR LR FLSAD +TG N IA+ G+V V TNEGN M +P++ Sbjct: 174 PRLTEIP-DMTREAREMLRPHFLSADMGVTGGNFVIAETGSVAVVTNEGNEGMCTVMPRV 232 Query: 241 QLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGE------MHVIIV 294 + GI+KV+P ++ A +R L R+ATGQ + Y + GP+ G+ M+V++V Sbjct: 233 HVAVTGIEKVLPTLEDLATAMRLLPRSATGQATSNYFSMLTGPRGAGDQDGPEHMYVVLV 292 Query: 295 DNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGATH---D 351 D GRT ++ E L+CIRCG C+N CPVY++ GG++Y + PGP+G + ++ D Sbjct: 293 DGGRTGLIGGD-FQEMLRCIRCGACMNHCPVYQKVGGHAYGWVYPGPMGSVLTPSYVGID 351 Query: 352 NTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKLPYGKNAYMPLVGKFMAST 411 + A TLCG C VCP +PL ++ R + E P+ + A + L G Sbjct: 352 KALDLPQAATLCGECNSVCPVGIPLSDLLRKLREKQTERHLRPWKERAGLALWGWLALHP 411 Query: 412 TLLNCSMGAARTALRILPG---SLLK-PFSGA-WGKYRELPVAPNSSFEAWFKKHRS 463 A L + G S+ K P GA W R++P +F + RS Sbjct: 412 DAYALVTKLAVRVLERMGGHNRSIAKLPLGGAGWTDTRDMPAPVGRTFRELYAAQRS 468 Lambda K H 0.320 0.134 0.413 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: 505 Number of extensions: 25 Number of successful extensions: 8 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: 464 Length of database: 471 Length adjustment: 33 Effective length of query: 431 Effective length of database: 438 Effective search space: 188778 Effective search space used: 188778 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