Align Uncharacterized protein (characterized, see rationale)
to candidate Pf1N1B4_1187 Predicted L-lactate dehydrogenase, Fe-S oxidoreductase subunit YkgE
Query= uniprot:B2TBW0 (256 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1187 Length = 274 Score = 150 bits (380), Expect = 2e-41 Identities = 99/246 (40%), Positives = 129/246 (52%), Gaps = 16/246 (6%) Query: 11 KVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTERV 70 +V LF C +D FYPE G+ + LLER GI+VDYPQ Q+CCGQP SG +A R Sbjct: 32 RVYLFGTCVVDLFYPEAGMDAIHLLEREGIRVDYPQGQSCCGQPAYTSGYTEQARTVARS 91 Query: 71 FARNFAGYDYIVGPSASCIHHVREHLTAL--EQTDEVKKVRANA---YELVEFLHDVVGA 125 FAG +V PS SC +REH L ++ +K+V+A A YEL EFL V Sbjct: 92 QLALFAGNYPVVVPSGSCAGMLREHYADLFKDEPQTLKQVQALADRTYELAEFLLFVCKV 151 Query: 126 REFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDE 185 + E P +V LH SCSA R + + + G R LL + +E V + E Sbjct: 152 QLKDSGE-PVKVALHTSCSARREMN----THLHG------RELLAQLSNVERVDHSHESE 200 Query: 186 CCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFI 245 CCGFGGTFSV +S M DK R +GA ++S D CLM+ G E+ + R Sbjct: 201 CCGFGGTFSVRMPDISGAMVADKTRSLKESGAHKVLSADCGCLMNINGSLEKQQEALRGQ 260 Query: 246 HIAQVL 251 H+A L Sbjct: 261 HLASFL 266 Lambda K H 0.323 0.137 0.422 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: 242 Number of extensions: 13 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: 256 Length of database: 274 Length adjustment: 25 Effective length of query: 231 Effective length of database: 249 Effective search space: 57519 Effective search space used: 57519 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 47 (22.7 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