Align Uncharacterized protein (characterized, see rationale)
to candidate GFF4148 HP15_4088 protein of unknown function, cysteine-rich region domain protein
Query= uniprot:B2TBW0 (256 letters) >FitnessBrowser__Marino:GFF4148 Length = 279 Score = 147 bits (370), Expect = 3e-40 Identities = 95/247 (38%), Positives = 130/247 (52%), Gaps = 19/247 (7%) Query: 12 VALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTER-- 69 V LF C +D F+PE G+ T+ LLER G++V +PQEQ+CCGQP SG EA R Sbjct: 32 VTLFGTCVVDLFFPEAGLDTIRLLEREGVRVHFPQEQSCCGQPAWTSGYRDEAKAVARAQ 91 Query: 70 VFARNFAGYDYIVGPSASCIHHVREHLTAL--EQTDEVKKVRANA---YELVEFLHDVVG 124 + + +G +V PS SC R H AL ++ D +K+V A A +EL EFL V Sbjct: 92 LDILDRSGLPVVV-PSGSCAGMFRHHYPALFADEPDTLKRVEALAERTFELTEFLLKVCR 150 Query: 125 AREFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPD 184 + P ++ LH SCSA R + R LL+ ++G+E + Sbjct: 151 V-QLADRGAPSKIALHTSCSARREMNT----------HLHARELLQQLEGVERIDHDHES 199 Query: 185 ECCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARF 244 ECCGFGGTFSV VS M +DK R +++GA +V+ D CLM+ G E+ K R Sbjct: 200 ECCGFGGTFSVRMPEVSGAMVKDKTRSLIDSGAVEMVTADGGCLMNINGSLEKQKESFRG 259 Query: 245 IHIAQVL 251 H+A L Sbjct: 260 RHLASFL 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: 251 Number of extensions: 14 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: 256 Length of database: 279 Length adjustment: 25 Effective length of query: 231 Effective length of database: 254 Effective search space: 58674 Effective search space used: 58674 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