Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_002719301.1 RSPH17029_RS04175 cysteine synthase A
Query= BRENDA::A0A0F6AQU1 (342 letters) >NCBI__GCF_000015985.1:WP_002719301.1 Length = 344 Score = 512 bits (1318), Expect = e-150 Identities = 248/326 (76%), Positives = 281/326 (86%), Gaps = 2/326 (0%) Query: 7 DTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLRPGGVIV 66 + IGNTPLIRL KASELTGC+I GK EFLNPGQSVKDRAALYIIRDA +GLL+PGG IV Sbjct: 9 EAIGNTPLIRLRKASELTGCEILGKCEFLNPGQSVKDRAALYIIRDAVAKGLLQPGGTIV 68 Query: 67 EGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPAAPYRNPNNYV 126 EGTAGNTGIGL++V ++G+RT IVIPETQSQEKKD LRL GA L++VPAAPYRNPNNYV Sbjct: 69 EGTAGNTGIGLSLVGASMGFRTVIVIPETQSQEKKDMLRLAGAHLVQVPAAPYRNPNNYV 128 Query: 127 RLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFVAAVGSGG 186 R SGRLAE LA+TE GAIWANQFDNT NRQAH+ETT EIW T ++DGF+ AVGSGG Sbjct: 129 RYSGRLAEALARTEERGAIWANQFDNTANRQAHVETTGPEIWEQTDGKVDGFICAVGSGG 188 Query: 187 TLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEGDSITEGIGQGRITANLEGF 246 TLAG A+ L+ R +KI LADP GAALH+FYT G +A G SITEGIGQGRITANLEG Sbjct: 189 TLAGVAMALQPR--GVKIGLADPEGAALHSFYTEGTFEAPGSSITEGIGQGRITANLEGL 246 Query: 247 TPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKDLGPGHTIVTVLCDYG 306 TPDFSY+IPDAEAL I+F L++EEGLCLGGSSG+NIAGAIR+A+++GPGH IVTVLCDYG Sbjct: 247 TPDFSYRIPDAEALPIIFDLMQEEGLCLGGSSGVNIAGAIRMAREMGPGHRIVTVLCDYG 306 Query: 307 NRYQSKLFNPAFLRGKSLPVPRWLEK 332 NRYQSKLFNP FLR K LPVP+WL++ Sbjct: 307 NRYQSKLFNPQFLRDKGLPVPQWLDE 332 Lambda K H 0.316 0.137 0.398 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: 449 Number of extensions: 13 Number of successful extensions: 2 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: 342 Length of database: 344 Length adjustment: 29 Effective length of query: 313 Effective length of database: 315 Effective search space: 98595 Effective search space used: 98595 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: 49 (23.5 bits)
This GapMind analysis is from Apr 16 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