Align L-aspartate semialdehyde sulfurtransferase iron-sulfur subunit (characterized)
to candidate WP_048065229.1 MA_RS09485 4Fe-4S binding protein
Query= SwissProt::Q8TPT3 (130 letters) >NCBI__GCF_000007345.1:WP_048065229.1 Length = 128 Score = 265 bits (677), Expect = 2e-76 Identities = 128/128 (100%), Positives = 128/128 (100%) Query: 3 MKIKICIPTERIQNPIISETIVETGILLNIMVANIDSTYGELIADVKDSRFARIKKALES 62 MKIKICIPTERIQNPIISETIVETGILLNIMVANIDSTYGELIADVKDSRFARIKKALES Sbjct: 1 MKIKICIPTERIQNPIISETIVETGILLNIMVANIDSTYGELIADVKDSRFARIKKALES 60 Query: 63 RGAIVAILDRPIHRDEEECVECGACISVCPMNVYSFDETWSLCVDEKKCIQCGMCIKMCP 122 RGAIVAILDRPIHRDEEECVECGACISVCPMNVYSFDETWSLCVDEKKCIQCGMCIKMCP Sbjct: 61 RGAIVAILDRPIHRDEEECVECGACISVCPMNVYSFDETWSLCVDEKKCIQCGMCIKMCP 120 Query: 123 HGALKLGE 130 HGALKLGE Sbjct: 121 HGALKLGE 128 Lambda K H 0.324 0.139 0.429 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: 232 Number of extensions: 9 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: 130 Length of database: 128 Length adjustment: 14 Effective length of query: 116 Effective length of database: 114 Effective search space: 13224 Effective search space used: 13224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 41 (20.4 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