Align L-aspartate semialdehyde sulfurtransferase iron-sulfur subunit (characterized)
to candidate BPHYT_RS32435 BPHYT_RS32435 formate dehydrogenase-N subunit beta
Query= SwissProt::Q8TPT3 (130 letters) >FitnessBrowser__BFirm:BPHYT_RS32435 Length = 310 Score = 50.4 bits (119), Expect = 2e-11 Identities = 28/78 (35%), Positives = 37/78 (47%), Gaps = 6/78 (7%) Query: 58 KALESRGAIVAILDRPIHRDEEECVECGACISVCPMNVYSFDE------TWSLCVDEKKC 111 KA S GAIV + + EE C+ CG CI+ CP N+ + +LC D Sbjct: 110 KACPSPGAIVQYTNGIVDFHEENCIGCGYCITGCPFNIPRISKQDNRAYKCTLCSDRVAV 169 Query: 112 IQCGMCIKMCPHGALKLG 129 Q C+K CP GA+ G Sbjct: 170 GQEPACVKTCPTGAIMFG 187 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: 151 Number of extensions: 14 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 130 Length of database: 310 Length adjustment: 20 Effective length of query: 110 Effective length of database: 290 Effective search space: 31900 Effective search space used: 31900 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: 45 (21.9 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