Align Uncharacterized protein (characterized, see rationale)
to candidate Echvi_1569 Echvi_1569 Fe-S oxidoreductase
Query= uniprot:B2TBW0 (256 letters) >FitnessBrowser__Cola:Echvi_1569 Length = 245 Score = 247 bits (631), Expect = 1e-70 Identities = 124/244 (50%), Positives = 158/244 (64%), Gaps = 7/244 (2%) Query: 10 MKVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTER 69 M+V LFIPC++D FYP ATLELLE++G+ V YP QTCCGQPMANSG + Sbjct: 1 MRVGLFIPCYVDQFYPGAAQATLELLEKYGMDVVYPLSQTCCGQPMANSGYERYGKASSE 60 Query: 70 VFARNFAGYDYIVGPSASCIHHVREHLTALEQTDEVKKVRANAYELVEFLHDVVGAREFP 129 +F NF ++YIV PS SC HV++H+ L +T E K+ YEL EFL D++ Sbjct: 61 LFLENFGEFEYIVAPSGSCTLHVKDHV--LPKTAEAPKI----YELCEFLTDILKVDHVD 114 Query: 130 WAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDECCGF 189 A FP++VG H+SC LR L+ A SE F+KP +LL VKGIE V+ R DECCGF Sbjct: 115 -ASFPYKVGFHSSCHGLRGLRLAKCSERMDEEFNKPLSLLSKVKGIEMVELDRKDECCGF 173 Query: 190 GGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFIHIAQ 249 GGTF+V EE VSV MG D++ DH G E + DMSCLMH QG +R K+ + +HIA+ Sbjct: 174 GGTFAVAEEAVSVTMGNDRIADHQRNGVEVLTGADMSCLMHMQGLLKRQKSPIKVMHIAE 233 Query: 250 VLNG 253 +LNG Sbjct: 234 ILNG 237 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: 219 Number of extensions: 8 Number of successful extensions: 2 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: 245 Length adjustment: 24 Effective length of query: 232 Effective length of database: 221 Effective search space: 51272 Effective search space used: 51272 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: 46 (22.3 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