Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate WP_059150049.1 V474_RS03025 NADH-quinone oxidoreductase subunit G
Query= uniprot:Q39TW6 (218 letters) >NCBI__GCF_001046635.1:WP_059150049.1 Length = 672 Score = 94.0 bits (232), Expect = 6e-24 Identities = 62/201 (30%), Positives = 94/201 (46%), Gaps = 27/201 (13%) Query: 6 LQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVEVRGWPKLVAG 65 +++DG E+ G T+L AA+ G IP C+HE+L G CR+C VEV+ G PK A Sbjct: 4 VKVDGIEIEVPAGATVLQAAELAGKEIPRFCYHERLSIAGNCRMCLVEVK-PGPPKPQAS 62 Query: 66 CIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAHAP---------DSEELKALAQEYGADRD 116 C P G +RT +E + K R+ ++E +L + P +L+ + YG Sbjct: 63 CALPAADGQEIRTDSEMVKKAREGVMEFLLINHPLDCPICDQGGECDLQDQSVAYGRGGS 122 Query: 117 RFEKHP----------------SFCIHCGLCVRYCAEIKKKNAVGFVDRGSNREISFIPE 160 R+ +H + CIHC CVR+ E+ + +G + RG + +I+ E Sbjct: 123 RYHEHKRAVTEKYMGPLIKTTMTRCIHCTRCVRFSEEVAGVDEIGALYRGESMQITTYLE 182 Query: 161 IAAKECWDCKECFPLCPTSAL 181 AA LCP AL Sbjct: 183 KAAHHEMSA-NVIDLCPVGAL 202 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: 301 Number of extensions: 16 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: 218 Length of database: 672 Length adjustment: 30 Effective length of query: 188 Effective length of database: 642 Effective search space: 120696 Effective search space used: 120696 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: 50 (23.9 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