Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate 3607874 Dshi_1282 formate dehydrogenase, alpha subunit (RefSeq)
Query= uniprot:Q39TW6 (218 letters) >FitnessBrowser__Dino:3607874 Length = 933 Score = 97.8 bits (242), Expect = 6e-25 Identities = 66/213 (30%), Positives = 92/213 (43%), Gaps = 31/213 (14%) Query: 4 INLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEK--LEPYGGCRICTVEVEVRGWPK 61 + +DG+ V A G TI + A G+ IP LCH P G CR C VE+E G Sbjct: 10 VTFTLDGQTVTAEAGQTIWEVANGRGLKIPHLCHKPAPGYRPDGNCRACMVEIE--GERV 67 Query: 62 LVAGCIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAHAPDSEELKA-------LAQEYGAD 114 L A CI +G+VV T + + + RK+++E ++ P E +A G Sbjct: 68 LAASCIREPSEGMVVTTSSARAETARKMVVEMLVTDQPARAEAHDRSAHFWDMADAAGVT 127 Query: 115 RDRFEK------------------HPSFCIHCGLCVRYCAEIKKKNAVGFVDRGSNREIS 156 RF K + CI CGLCVR C E++ + +G RG + Sbjct: 128 ESRFPKLEGPRIPLLDDSHVAMRVNLDACIQCGLCVRACREVQVNDVIGMAGRGHDAYPV 187 Query: 157 FIPE--IAAKECWDCKECFPLCPTSALQAAYVL 187 F + + C C EC CPT AL A +L Sbjct: 188 FDLDDPMGDSTCVACGECVQACPTGALMEAKLL 220 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: 484 Number of extensions: 23 Number of successful extensions: 6 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: 933 Length adjustment: 32 Effective length of query: 186 Effective length of database: 901 Effective search space: 167586 Effective search space used: 167586 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