Align Uncharacterized protein (characterized, see rationale)
to candidate GFF2942 HP15_2886 protein of unknown function cysteine-rich region domain protein
Query= uniprot:B2TBW0 (256 letters) >FitnessBrowser__Marino:GFF2942 Length = 259 Score = 153 bits (387), Expect = 3e-42 Identities = 100/245 (40%), Positives = 131/245 (53%), Gaps = 15/245 (6%) Query: 11 KVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTERV 70 KV + C +D FYP+ GIA +ELLER GI+V +PQ QTCCGQP SG H EA R Sbjct: 14 KVYFYGTCLVDMFYPDAGIAGVELLEREGIEVLFPQNQTCCGQPAYTSGYHDEARSVARA 73 Query: 71 FARNFAGYDYIVGPSASCIHHVREHLTAL--EQTDEVK--KVRANAYELVEFLHDVVGAR 126 F G IV PS SC +R+H L + TDEVK +V +EL +FL +V + Sbjct: 74 QLDLFPGDWPIVVPSGSCGGMMRKHYPDLFEDTTDEVKAAEVAGRVWELTDFLLNVCHIK 133 Query: 127 EFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDEC 186 E P V +H SCSA R E ++EV P+ LL +K + V+ RP+EC Sbjct: 134 LEDLGE-PTTVAMHTSCSARR---EMGVAEVG------PK-LLGQLKNVNLVEQIRPEEC 182 Query: 187 CGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFIH 246 CGFGGTF+V +S M +KV ++ G V+ D CLM+ G AE+ + H Sbjct: 183 CGFGGTFAVRHPEISSAMVSEKVDALVDTGTRQFVTTDCGCLMNIAGYAEKNQKPVEGQH 242 Query: 247 IAQVL 251 I L Sbjct: 243 ILSFL 247 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: 221 Number of extensions: 9 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: 259 Length adjustment: 24 Effective length of query: 232 Effective length of database: 235 Effective search space: 54520 Effective search space used: 54520 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