Align Predicted asd-S-ferredoxin by GapMind curators (no experimental data)
to candidate WP_011989405.1 CKL_RS04110 2Fe-2S iron-sulfur cluster-binding protein
Query= predicted:A6UQ02 (132 letters) >NCBI__GCF_000016505.1:WP_011989405.1 Length = 253 Score = 43.5 bits (101), Expect = 2e-09 Identities = 26/59 (44%), Positives = 32/59 (54%), Gaps = 9/59 (15%) Query: 82 CIDCGSCVVHCP---VGALSVDSD--YKILLDEDE----CIGCKNCAKVCPVNAIKVFE 131 C CG CV C VG LS+ + YK L D+ CIGC +CA VCP NAI + + Sbjct: 129 CALCGLCVKACKAVGVGVLSLVNKGIYKKLDTSDKSTQKCIGCGSCANVCPTNAIDIID 187 Score = 29.3 bits (64), Expect = 4e-05 Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 3/47 (6%) Query: 77 KDDNLCIDCGSCVVHCPVGALSV---DSDYKILLDEDECIGCKNCAK 120 K CI CGSC CP A+ + D +I ++ + + C C + Sbjct: 163 KSTQKCIGCGSCANVCPTNAIDIIDKDGKREIWGNKFKMVKCDCCGE 209 Lambda K H 0.321 0.140 0.421 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: 101 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 132 Length of database: 253 Length adjustment: 19 Effective length of query: 113 Effective length of database: 234 Effective search space: 26442 Effective search space used: 26442 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: 44 (21.6 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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