Align L-aspartate semialdehyde sulfurtransferase (EC 2.8.1.16) (characterized)
to candidate WP_011032195.1 MM_RS01325 CBS domain-containing protein
Query= BRENDA::Q8TPT4 (500 letters) >NCBI__GCF_000007065.1:WP_011032195.1 Length = 500 Score = 924 bits (2388), Expect = 0.0 Identities = 462/500 (92%), Positives = 485/500 (97%) Query: 1 MVEKSVHEINKKIEDGSVNVVTAEEMVGIVENLGVEGAAREVDVVTTGTFGAMCSSGLML 60 MV+KS+HEINKKIEDGSVNVVTAEEMVGIVE+LGVE AA+EVDVVTTGTFGAMCSSGLML Sbjct: 1 MVKKSIHEINKKIEDGSVNVVTAEEMVGIVEDLGVESAAKEVDVVTTGTFGAMCSSGLML 60 Query: 61 NLGHSEPPIKIQKLWFNNVEAYSGLAAVDAYLGAAQISDTRGIQYGGAHVIEDLLRGKEL 120 NLGHSEPPIKIQKLWFNNVEAYSG+AAVDAYLGAAQISDTRGIQYGGAHVIEDLLRGKE+ Sbjct: 61 NLGHSEPPIKIQKLWFNNVEAYSGIAAVDAYLGAAQISDTRGIQYGGAHVIEDLLRGKEI 120 Query: 121 DVHATSYGTDCYPRKVLDTRITLDDLNEAVLLNPRNAYQKYAAATNSSKRILNTYMGELL 180 +VHATSYGTDCYPRKVLDT ITL+DLNEAVLLNPRNAYQKY AATNSSKRILNTYMGELL Sbjct: 121 NVHATSYGTDCYPRKVLDTAITLEDLNEAVLLNPRNAYQKYNAATNSSKRILNTYMGELL 180 Query: 181 PNFGNVTYSGAGVLSPLSNDPDYETIGMGTRIFMGGAQGYIIGNGTQHSPSSSFGTLMLK 240 PNFGNVTYSGAGVLSPLSNDP YETIG GTRIF+GGAQGY+IGNGTQHSPS SFGTLMLK Sbjct: 181 PNFGNVTYSGAGVLSPLSNDPGYETIGTGTRIFLGGAQGYVIGNGTQHSPSGSFGTLMLK 240 Query: 241 GNLKEMSSDYLRAASFAGYGTTLYMGIGIPIPILNEKIAASTAVRDEDIFTDILDYAVGS 300 GNLKEMS DYLRAASFAGYGTTLYMGIGIPIPILNEK+AA+TAVRDEDI T +LDYA+GS Sbjct: 241 GNLKEMSPDYLRAASFAGYGTTLYMGIGIPIPILNEKLAAATAVRDEDITTSVLDYAIGS 300 Query: 301 RDKPVIKQVNYAELRSGSIELEGKNTPTSSLSSFKNARKIANELKEWVKHGKFFVSMPVE 360 RDKPV++QVNYAELRSGS+++EGK+ PTSSLSSFKNARKIANELKEWVKHGKFFVSMPVE Sbjct: 301 RDKPVVRQVNYAELRSGSVQIEGKDVPTSSLSSFKNARKIANELKEWVKHGKFFVSMPVE 360 Query: 361 KLSREGSAKSMKQTQAVPLVKDVMADFIVTIKKNQTVQDAAKKIWENSFNHLAVVSDTGE 420 KL EGSAK MKQTQAVPLVKDVM+DFIVTIKK+QTVQDAAKKIWENSFNHLAVVSDTGE Sbjct: 361 KLCSEGSAKPMKQTQAVPLVKDVMSDFIVTIKKDQTVQDAAKKIWENSFNHLAVVSDTGE 420 Query: 421 LVGILTAWDISKAVAENIFDSVESVMTKKVLTCAPNEPVDLAARRLDRYGVSAMPVIDTQ 480 LVGILTAWDISKAVAENIFDSVESVMTKKVLTCAPNEPVDLAARRLDRYGVSAMPVID Q Sbjct: 421 LVGILTAWDISKAVAENIFDSVESVMTKKVLTCAPNEPVDLAARRLDRYGVSAMPVIDAQ 480 Query: 481 RKVLGIITSDNISKLLARRY 500 +KVLGIITSDNISKL ARRY Sbjct: 481 KKVLGIITSDNISKLFARRY 500 Lambda K H 0.315 0.132 0.372 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: 969 Number of extensions: 23 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: 500 Length of database: 500 Length adjustment: 34 Effective length of query: 466 Effective length of database: 466 Effective search space: 217156 Effective search space used: 217156 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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