Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate 7025757 Shewana3_2907 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein (RefSeq)
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__ANA3:7025757 Length = 464 Score = 934 bits (2414), Expect = 0.0 Identities = 453/464 (97%), Positives = 460/464 (99%) Query: 1 MAYQHNHEAMGSQVHAYKADIFCRDETRVDWHSKALWLLREKRDRAAGSLPEWEQLRQLG 60 MAYQHNHEA GSQVHA+KADIFCRDETRVDWHSKALW+LREKRDRAAGSLPEWEQLRQLG Sbjct: 1 MAYQHNHEATGSQVHAHKADIFCRDETRVDWHSKALWVLREKRDRAAGSLPEWEQLRQLG 60 Query: 61 SEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSM 120 SEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVH+ILASHKVKKLVKSKSM Sbjct: 61 SEIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHDILASHKVKKLVKSKSM 120 Query: 121 LTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGT 180 LTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGT Sbjct: 121 LTEECHLNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGT 180 Query: 181 KAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKL 240 KAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKL Sbjct: 181 KAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKL 240 Query: 241 QLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGEMHVIIVDNGRTE 300 QLHSMGIDK+VPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGEMHVIIVDNGRTE Sbjct: 241 QLHSMGIDKIVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGEMHVIIVDNGRTE 300 Query: 301 MMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGATHDNTNSIAWAC 360 M+KDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGA HD+TNSIAWAC Sbjct: 301 MLKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGAKHDDTNSIAWAC 360 Query: 361 TLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKLPYGKNAYMPLVGKFMASTTLLNCSMGA 420 TLCGSCTYVCPTKVPLDKII HHRRLKAEAG+LPYGKN YMPLVGKFMASTTLLNCSMGA Sbjct: 361 TLCGSCTYVCPTKVPLDKIIFHHRRLKAEAGQLPYGKNGYMPLVGKFMASTTLLNCSMGA 420 Query: 421 ARTALRILPGSLLKPFSGAWGKYRELPVAPNSSFEAWFKKHRSL 464 ARTALRILPGSLLKPFSGAWGKYRELPVAPNSSFEAWFKKHRSL Sbjct: 421 ARTALRILPGSLLKPFSGAWGKYRELPVAPNSSFEAWFKKHRSL 464 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: 869 Number of extensions: 11 Number of successful extensions: 3 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: 464 Length adjustment: 33 Effective length of query: 431 Effective length of database: 431 Effective search space: 185761 Effective search space used: 185761 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 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