Align Homocysteine formation from aspartate semialdehyde (NIL/ferredoxin component) (characterized)
to candidate WP_027722440.1 H589_RS0113110 4Fe-4S dicluster domain-containing protein
Query= reanno::Miya:8499492 (147 letters) >NCBI__GCF_000425265.1:WP_027722440.1 Length = 147 Score = 48.1 bits (113), Expect = 6e-11 Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 6/77 (7%) Query: 68 IAYLREQDVTVTDVSQRISRDED----SCMHCGM--CTAICPTSALAMDIEARVVVFDKD 121 IAY E+ ++ D++ SC HC C A+C + AL D + + V+D D Sbjct: 33 IAYNEERAKGLSSCIMVFENDDNCVAVSCRHCQEPDCVAVCISGALTKDEISGITVYDSD 92 Query: 122 RCTACGLCTRVCPVGAM 138 +C C C CP GA+ Sbjct: 93 KCLGCWSCLMACPYGAI 109 Score = 25.4 bits (54), Expect = 4e-04 Identities = 8/15 (53%), Positives = 9/15 (60%) Query: 119 DKDRCTACGLCTRVC 133 D+D C CGLC C Sbjct: 7 DRDYCMGCGLCQLAC 21 Lambda K H 0.321 0.137 0.414 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: 108 Number of extensions: 7 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 147 Length of database: 147 Length adjustment: 16 Effective length of query: 131 Effective length of database: 131 Effective search space: 17161 Effective search space used: 17161 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 (21.9 bits) S2: 42 (20.8 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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