Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate BPHYT_RS14995 BPHYT_RS14995 formate dehydrogenase subunit alpha
Query= uniprot:Q39TW6 (218 letters) >FitnessBrowser__BFirm:BPHYT_RS14995 Length = 982 Score = 107 bits (268), Expect = 6e-28 Identities = 71/237 (29%), Positives = 107/237 (45%), Gaps = 34/237 (14%) Query: 3 EINLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVE-VRGWPK 61 +I L+IDG+ V G +++ AA G+++P LC + LEP+G CR+C VE+E RG+P Sbjct: 48 DITLEIDGQSVTVPAGTSVMRAAVEAGVNVPKLCATDSLEPFGSCRLCLVEIEGKRGYP- 106 Query: 62 LVAGCIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAHAP---------DSEELKALAQEYG 112 A C PVE G+ VRT+ +++ +R+ ++E ++ P EL+ +A G Sbjct: 107 --ASCTTPVEAGMKVRTQTDRLQSLRRNVMELYISDHPLDCLTCPANGDCELQDMAGVTG 164 Query: 113 ADRDRF-------------EKHPSF------CIHCGLCVRYCAEIKKKNAVGFVDRGSNR 153 R+ E +P F CI C CVR C E + A+ RG Sbjct: 165 LREVRYGFDGANHLKDKKDESNPYFTYDASKCIVCNRCVRACEETQGTFALTIAGRGFES 224 Query: 154 EISFIPEI--AAKECWDCKECFPLCPTSALQAAYVLAGALMTPPEEAHSGGCGCSCS 208 ++ + EC C C CPT+ LQ V+ CG CS Sbjct: 225 RVAASENVPFMESECVSCGACVAACPTATLQEKTVIMLGQAEHSVVTTCAYCGVGCS 281 Lambda K H 0.320 0.137 0.432 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: 491 Number of extensions: 31 Number of successful extensions: 5 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: 218 Length of database: 982 Length adjustment: 33 Effective length of query: 185 Effective length of database: 949 Effective search space: 175565 Effective search space used: 175565 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: 51 (24.3 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