Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate WP_036257391.1 DL86_RS01350 formate dehydrogenase subunit alpha
Query= uniprot:Q39TW6 (218 letters) >NCBI__GCF_000746085.1:WP_036257391.1 Length = 948 Score = 101 bits (251), Expect = 5e-26 Identities = 75/236 (31%), Positives = 107/236 (45%), Gaps = 34/236 (14%) Query: 4 INLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVEVR-GWPKL 62 + L IDG EV A EG +I+ AA +G IP LC + LE +G CR+C VE++ R G P Sbjct: 20 VTLTIDGVEVHAPEGTSIMRAAMEIGTQIPKLCASDMLEAFGSCRLCLVEIQGRNGTP-- 77 Query: 63 VAGCIYPVEKGLVVRTRNEKIDKIRKVLLE--------EMLAHAPDSE-ELKALAQEYGA 113 A C PV G+VV+T+ E++ +RK ++E + L A +S+ EL+ A G Sbjct: 78 -ASCTTPVAPGMVVKTQTERLKALRKGVMELYISDHPLDCLTCAANSDCELQTQAGAVGL 136 Query: 114 DRDRF-------------EKHPSF------CIHCGLCVRYCAEIKKKNAVGFVDRGSNRE 154 R+ E +P F CI C CVR C E++ A+ RG Sbjct: 137 REVRYGYDGANHFAEKKDESNPYFTYDPAKCIVCNRCVRACEEVQGTFALTIDGRGFESR 196 Query: 155 ISFIPE--IAAKECWDCKECFPLCPTSALQAAYVLAGALMTPPEEAHSGGCGCSCS 208 ++ + EC C C CPT+ L V+A CG C+ Sbjct: 197 VAPGQDEPFFESECVSCGACVQACPTATLTEKSVIAIGQPEHSAVTTCAYCGVGCT 252 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: 480 Number of extensions: 25 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: 948 Length adjustment: 32 Effective length of query: 186 Effective length of database: 916 Effective search space: 170376 Effective search space used: 170376 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 Apr 09 2024. 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