Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_043743637.1 AMB_RS06615 cysteine synthase A
Query= BRENDA::A0A0F6AQU1 (342 letters) >NCBI__GCF_000009985.1:WP_043743637.1 Length = 334 Score = 469 bits (1207), Expect = e-137 Identities = 232/326 (71%), Positives = 264/326 (80%) Query: 6 LDTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLRPGGVI 65 LD+IGNTPLIRL +ASE TGC+I GKAEFLNPG SVKDRAAL II+DAE++GLL+PGGVI Sbjct: 9 LDSIGNTPLIRLKRASEETGCNILGKAEFLNPGGSVKDRAALAIIQDAERKGLLKPGGVI 68 Query: 66 VEGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPAAPYRNPNNY 125 VEGTAGNTGIGL +VA ALGYRT IV+PETQSQEKKD LRL+GA+L VPA PY NP NY Sbjct: 69 VEGTAGNTGIGLALVANALGYRTVIVMPETQSQEKKDMLRLVGADLRLVPAVPYANPGNY 128 Query: 126 VRLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFVAAVGSG 185 VR S LA +LAKTEPNG +WANQFDNT NR H TT QEIWR T +D F AVG+G Sbjct: 129 VRYSETLANELAKTEPNGVLWANQFDNTANRMGHFNTTGQEIWRQTDGTVDAFTCAVGTG 188 Query: 186 GTLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEGDSITEGIGQGRITANLEG 245 GTLAGT + LKE N +IK+ LADP G+AL+ Y GELKAEG SITEGIGQGRIT NL+G Sbjct: 189 GTLAGTGMALKEHNKDIKVVLADPMGSALYHHYAHGELKAEGTSITEGIGQGRITRNLDG 248 Query: 246 FTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKDLGPGHTIVTVLCDY 305 D Q+ D EAL ++F LV +EGL LGGSSGIN+ AI++A+ LGPGHT+VTVLCDY Sbjct: 249 APIDDQVQVTDHEALPLIFDLVRQEGLVLGGSSGINVMAAIKVARILGPGHTVVTVLCDY 308 Query: 306 GNRYQSKLFNPAFLRGKSLPVPRWLE 331 G RYQSKLFNPAFLR ++LPVP WLE Sbjct: 309 GTRYQSKLFNPAFLRERNLPVPHWLE 334 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: 427 Number of extensions: 16 Number of successful extensions: 1 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: 334 Length adjustment: 28 Effective length of query: 314 Effective length of database: 306 Effective search space: 96084 Effective search space used: 96084 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 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