Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_020176197.1 A3OQ_RS0114835 cysteine synthase A
Query= BRENDA::A0A0F6AQU1 (342 letters) >NCBI__GCF_000385335.1:WP_020176197.1 Length = 343 Score = 471 bits (1212), Expect = e-137 Identities = 237/337 (70%), Positives = 270/337 (80%) Query: 4 SVLDTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLRPGG 63 +V++ IG+TPLI+L +ASE TGC I GKAEF+NPG SVKDRA L II DA KRG L+PGG Sbjct: 6 NVIEAIGHTPLIKLRRASEETGCTILGKAEFMNPGGSVKDRAGLAIIEDAIKRGTLKPGG 65 Query: 64 VIVEGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPAAPYRNPN 123 +IVEGTAGNTGIGL++VA ALGY T IVIPETQSQEKKD LRL GAELIEVPA Y NPN Sbjct: 66 LIVEGTAGNTGIGLSLVANALGYHTVIVIPETQSQEKKDLLRLQGAELIEVPAVAYSNPN 125 Query: 124 NYVRLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFVAAVG 183 NYV+LSGRLAE+LAK P GAIWANQFDN NRQ H++TT EIW +T ++DGF A G Sbjct: 126 NYVKLSGRLAERLAKEHPAGAIWANQFDNVANRQGHMDTTGPEIWVETEGKVDGFCCAAG 185 Query: 184 SGGTLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEGDSITEGIGQGRITANL 243 +GGT+AG + LK +N IKIALADP GAAL+A+YT GEL + G SITEGIGQGRITANL Sbjct: 186 TGGTIAGVGMALKAKNDKIKIALADPMGAALYAYYTKGELASSGSSITEGIGQGRITANL 245 Query: 244 EGFTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKDLGPGHTIVTVLC 303 E D +YQI D EAL IL+ L E EGL LGGSSGIN+AGAIRLAK+LGPGHTIVT+L Sbjct: 246 ENAPIDAAYQITDEEALPILYDLAEHEGLLLGGSSGINVAGAIRLAKELGPGHTIVTILA 305 Query: 304 DYGNRYQSKLFNPAFLRGKSLPVPRWLEKKTEIDIPF 340 D G RYQSKLFNPAFLR K+LPVP W++K I F Sbjct: 306 DSGARYQSKLFNPAFLREKNLPVPGWMDKAPSIKPDF 342 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: 407 Number of extensions: 13 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: 343 Length adjustment: 29 Effective length of query: 313 Effective length of database: 314 Effective search space: 98282 Effective search space used: 98282 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 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