Align UPF0280 protein MA_1715 (characterized, see rationale)
to candidate BPHYT_RS21475 BPHYT_RS21475 hypothetical protein
Query= uniprot:Y1715_METAC (253 letters) >FitnessBrowser__BFirm:BPHYT_RS21475 Length = 312 Score = 63.5 bits (153), Expect = 5e-15 Identities = 41/129 (31%), Positives = 66/129 (51%), Gaps = 13/129 (10%) Query: 91 IGPMSAVAGTISALAVEAMVKAGAKYAIVDNGGDIA--LINDRSVVVGIYA--------- 139 I PM+AVAG+++ + A + G A V+NGGDIA L + VG++A Sbjct: 93 ITPMAAVAGSVADELITAFAREGVSRAFVNNGGDIALYLTEGQQYRVGVFADLASFSAVR 152 Query: 140 -GQSPIKNLGLIFEPRDSITGVCTSAGTVGPSISFGMADAAAIFSDDVSLADAAATALGN 198 + + L + ++ G+ TS G G S S G+AD+ + + + + ADAAAT + N Sbjct: 153 LSRDQALDANLTLDASLAVRGIATS-GWRGRSFSLGIADSVTVLARNAAAADAAATVIAN 211 Query: 199 EVGIGKEAV 207 V + E + Sbjct: 212 AVDLDHEGI 220 Lambda K H 0.317 0.133 0.379 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: 152 Number of extensions: 7 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: 253 Length of database: 312 Length adjustment: 26 Effective length of query: 227 Effective length of database: 286 Effective search space: 64922 Effective search space used: 64922 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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