Align Putative L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF (characterized, see rationale)
to candidate RR42_RS21285 RR42_RS21285 (Fe-S)-binding protein
Query= uniprot:A0A0C4Y8G6 (489 letters) >FitnessBrowser__Cup4G11:RR42_RS21285 Length = 476 Score = 958 bits (2476), Expect = 0.0 Identities = 475/476 (99%), Positives = 476/476 (100%) Query: 14 LHFVPAADFKARSRAALDDPKLRSSFRGAMDFLQAKRAVQFPDGDELEQLRDLGEAIRQH 73 +HFVPAADFKARSRAALDDPKLRSSFRGAMDFLQAKRAVQFPDGDELEQLRDLGEAIRQH Sbjct: 1 MHFVPAADFKARSRAALDDPKLRSSFRGAMDFLQAKRAVQFPDGDELEQLRDLGEAIRQH 60 Query: 74 ALSQLPDLLVQLEDKLTAAGVQVHWAETADEANAIVHGIAQARQASRVIKGKSMASEEIE 133 ALSQLPDLLVQLEDKLTAAGVQVHWAETADEANAIVHGIAQARQASRVIKGKSMASEEIE Sbjct: 61 ALSQLPDLLVQLEDKLTAAGVQVHWAETADEANAIVHGIAQARQASRVIKGKSMASEEIE 120 Query: 134 LNHYLAERGIDCIESDMGEYIVQLAGEKPSHIVMPAIHKTRGDIAELFEQHIPGTPYTED 193 LNHYLAERGIDCIESDMGEYIVQLAGEKPSHIVMPAIHKTRGDIAELFEQHIPGTPYTED Sbjct: 121 LNHYLAERGIDCIESDMGEYIVQLAGEKPSHIVMPAIHKTRGDIAELFEQHIPGTPYTED 180 Query: 194 VDELIQTGRRALRQEFVNADIGLSGVNFAAADTGTLWLVENEGNGRLSTTVPDVHIAIMG 253 VDELIQTGRRALRQEFVNADIGLSGVNFAAADTGTLWLVENEGNGRLSTTVPDVHIAIMG Sbjct: 181 VDELIQTGRRALRQEFVNADIGLSGVNFAAADTGTLWLVENEGNGRLSTTVPDVHIAIMG 240 Query: 254 MEKVVARLEHIVPLASLLTRSATGQAITTYFNLISGPRRAGERDGPREVHLVLLDNGRSQ 313 MEKVVARLEHIVPLASLLTRSATGQAITTYFNLISGPRRAGERDGPREVHLVLLDNGRSQ Sbjct: 241 MEKVVARLEHIVPLASLLTRSATGQAITTYFNLISGPRRAGERDGPREVHLVLLDNGRSQ 300 Query: 314 AYADEQLRATLQCIRCGACMNHCPVYTRIGGHAYGTTYPGPIGKIISPHLLGLDATADLA 373 AYADEQLRATLQCIRCGACMNHCPVYTRIGGHAYGTTYPGPIGKIISPHLLGLDATADLA Sbjct: 301 AYADEQLRATLQCIRCGACMNHCPVYTRIGGHAYGTTYPGPIGKIISPHLLGLDATADLA 360 Query: 374 TASSLCGACGEVCPVRIPIPQLLIRLRTEANRDPSEQVAHPLRGQGTKFSRGEHLVWRFW 433 TASSLCGACGEVCPVRIPIPQLLIRLRTEANRDPSEQVAHPLRGQGTKFSRGEHLVWRFW Sbjct: 361 TASSLCGACGEVCPVRIPIPQLLIRLRTEANRDPSEQVAHPLRGQGTKFSRGEHLVWRFW 420 Query: 434 SGAFAHPLAYRLFRWAATRLRVLTPKHQLGWTRHRAPLTPAPRSLSDLLRERGQAE 489 SGAFAHPLAYRLFRWAATRLRVLTPKHQLGWTRHRAPLTPAPRSLSDLLRERGQAE Sbjct: 421 SGAFAHPLAYRLFRWAATRLRVLTPKHQLGWTRHRAPLTPAPRSLSDLLRERGQAE 476 Lambda K H 0.320 0.135 0.406 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: 897 Number of extensions: 17 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: 489 Length of database: 476 Length adjustment: 34 Effective length of query: 455 Effective length of database: 442 Effective search space: 201110 Effective search space used: 201110 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: 52 (24.6 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