Align Uncharacterized protein (characterized, see rationale)
to candidate WP_035700904.1 BA79_RS03520 (Fe-S)-binding protein
Query= uniprot:B2TBW0 (256 letters) >NCBI__GCF_000691145.1:WP_035700904.1 Length = 238 Score = 159 bits (402), Expect = 5e-44 Identities = 90/247 (36%), Positives = 130/247 (52%), Gaps = 15/247 (6%) Query: 10 MKVALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTER 69 M+V+LF+ C ID P VG AT+E+LER G++V++P+EQ CCGQP NSG E + Sbjct: 1 MRVSLFVTCIIDTMQPHVGKATVEVLERLGVEVEFPEEQVCCGQPAFNSGYTKETIKAAK 60 Query: 70 VFARNFAGYDYIVGPSASCIHHVREHLTALEQT----DEVKKVRANAYELVEFLHDVVGA 125 + F +Y+V PS SC E+ ++ + + A YEL EF+ D++ Sbjct: 61 NMMKAFESAEYVVTPSGSCKAMFLEYPHLFKEDRAWFARAQALAAKTYELTEFIVDILHV 120 Query: 126 REFPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDE 185 + A + H SC R L+ + APF TLL VK + R + Sbjct: 121 TDV-GASLKGKATYHTSCHMTRLLR------IKEAPF----TLLSNVKDLVMEPLPRAEN 169 Query: 186 CCGFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFI 245 CCGFGGTFS+ P+S +M +KV+ GAEYI+ D CL++ G R+ + + Sbjct: 170 CCGFGGTFSIKMTPISEQMVDEKVQSIEETGAEYIIGADCGCLLNIGGRLNRLHKPVKVM 229 Query: 246 HIAQVLN 252 HIA+VLN Sbjct: 230 HIAEVLN 236 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: 210 Number of extensions: 17 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: 238 Length adjustment: 24 Effective length of query: 232 Effective length of database: 214 Effective search space: 49648 Effective search space used: 49648 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 24 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