Align Putative L-lactate dehydrogenase, Fe-S oxidoreductase subunit YkgE (characterized, see rationale)
to candidate Synpcc7942_1717 Synpcc7942_1717 glycolate oxidase subunit (Fe-S) protein
Query= uniprot:A0A0C4YIN5 (262 letters) >FitnessBrowser__SynE:Synpcc7942_1717 Length = 433 Score = 107 bits (266), Expect = 6e-28 Identities = 77/251 (30%), Positives = 111/251 (44%), Gaps = 24/251 (9%) Query: 4 RRYPPAPAQVYLFATCLVDMFVPQAGLDAVRLLEREGLTVHFPRGQSCCGQPAYSSGNPE 63 RRY +V L C+ +F P+ A+R+L G V P Q CCG A+ G + Sbjct: 184 RRY-----RVGLLLGCVQRLFNPEVNAAAIRVLRANGCDVVIPPQQGCCGAVAHHQGEMQ 238 Query: 64 QARAVALAQLDLF-AEPWPVIVPSGSCAGMMRHHWPQLFAQDPVAGPKAALLAERVYELS 122 QA+ +A A + F AE I+ + S G H+ + A DP +A LA+RV ++ Sbjct: 239 QAQDLARAVIRSFEAENLDAILVTASGCGHTLKHYGAILADDPEWCDRAQQLADRVQDVQ 298 Query: 123 EFL--------LHVLKVRFDVSGVAGQPPETVVLHTSCAARREMGTRDHGVALVDALPGV 174 EFL LH L+ + P VV +C R+ L+ +PG+ Sbjct: 299 EFLATVGLTTPLHPLQ----------EQPLVVVYQDACHMLHGQKIRNQPRQLLQQIPGI 348 Query: 175 TRTEHQRESECCGFGGTFSLKHPDISGAMVQDKIASACATGCDRLVSADCGCLLNIGHAA 234 E CCG G ++L P I+ + Q K S TG + SA+ GC + I H Sbjct: 349 ELREPVDAQLCCGSAGIYNLLQPAIAAELGQQKARSLAETGAQMIASANIGCYVQIRHHL 408 Query: 235 RHQGAPLPVEH 245 + Q LPV H Sbjct: 409 QAQSKDLPVLH 419 Lambda K H 0.323 0.136 0.433 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: 355 Number of extensions: 24 Number of successful extensions: 4 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: 262 Length of database: 433 Length adjustment: 28 Effective length of query: 234 Effective length of database: 405 Effective search space: 94770 Effective search space used: 94770 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 (22.0 bits) S2: 49 (23.5 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