Align L-aspartate semialdehyde sulfurtransferase iron-sulfur subunit (characterized)
to candidate Dsui_3281 Dsui_3281 formate dehydrogenase, beta subunit, Fe-S containing
Query= SwissProt::Q8TPT3 (130 letters) >FitnessBrowser__PS:Dsui_3281 Length = 296 Score = 50.1 bits (118), Expect = 3e-11 Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 6/78 (7%) Query: 58 KALESRGAIVAILDRPIHRDEEECVECGACISVCPMNVYSFDE------TWSLCVDEKKC 111 KA S GAI+ + + +E C+ CG C+S CP NV + +LC D Sbjct: 111 KACPSPGAIIQYKNGIVDFHQENCIGCGYCVSGCPFNVPRINPKDNKAYKCNLCSDRVAV 170 Query: 112 IQCGMCIKMCPHGALKLG 129 Q C+K CP GA++ G Sbjct: 171 GQEPACVKTCPTGAIQFG 188 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: 156 Number of extensions: 15 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: 296 Length adjustment: 20 Effective length of query: 110 Effective length of database: 276 Effective search space: 30360 Effective search space used: 30360 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: 44 (21.6 bits)
This GapMind analysis is from Apr 09 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