Align Uncharacterized protein (characterized, see rationale)
to candidate GFF2942 HP15_2886 protein of unknown function cysteine-rich region domain protein
Query= uniprot:E4PLR5 (279 letters) >FitnessBrowser__Marino:GFF2942 Length = 259 Score = 286 bits (731), Expect = 4e-82 Identities = 137/248 (55%), Positives = 175/248 (70%), Gaps = 2/248 (0%) Query: 25 YPEKPEAVTLFGTCVVDLFFPEAGLDTIRLLEREGVRVHFPQEQSCCGQPAWTSGYRDEA 84 YP KP V +GTC+VD+F+P+AG+ + LLEREG+ V FPQ Q+CCGQPA+TSGY DEA Sbjct: 8 YPAKPAKVYFYGTCLVDMFYPDAGIAGVELLEREGIEVLFPQNQTCCGQPAYTSGYHDEA 67 Query: 85 KAVARAQLDILDRSGLPVVVPSGSCAGMFRHHYPALFADEPDTLKRVEALAERTFELTEF 144 ++VARAQLD+ P+VVPSGSC GM R HYP LF D D +K E +A R +ELT+F Sbjct: 68 RSVARAQLDLFP-GDWPIVVPSGSCGGMMRKHYPDLFEDTTDEVKAAE-VAGRVWELTDF 125 Query: 145 LLKVCRVQLADRGAPSKIALHTSCSARREMNTHLHARELLQQLEGVERIDHDHESECCGF 204 LL VC ++L D G P+ +A+HTSCSARREM +LL QL+ V ++ ECCGF Sbjct: 126 LLNVCHIKLEDLGEPTTVAMHTSCSARREMGVAEVGPKLLGQLKNVNLVEQIRPEECCGF 185 Query: 205 GGTFSVRMPEVSGAMVKDKTRSLIDSGAVEMVTADGGCLMNINGSLEKQKESFRGRHLAS 264 GGTF+VR PE+S AMV +K +L+D+G + VT D GCLMNI G EK ++ G+H+ S Sbjct: 186 GGTFAVRHPEISSAMVSEKVDALVDTGTRQFVTTDCGCLMNIAGYAEKNQKPVEGQHILS 245 Query: 265 FLWERTNG 272 FLW RT G Sbjct: 246 FLWSRTQG 253 Lambda K H 0.320 0.134 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: 282 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: 279 Length of database: 259 Length adjustment: 25 Effective length of query: 254 Effective length of database: 234 Effective search space: 59436 Effective search space used: 59436 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: 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