Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate GFF1378 PGA1_c13950 cysteine synthase CysK
Query= BRENDA::A0A0F6AQU1 (342 letters) >FitnessBrowser__Phaeo:GFF1378 Length = 344 Score = 474 bits (1220), Expect = e-138 Identities = 232/328 (70%), Positives = 272/328 (82%), Gaps = 2/328 (0%) Query: 3 NSVLDTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLRPG 62 + + D IG+TPLIRL++ S+ TGC+I GKAEF+NPGQSVKDRAALYII+DA RG L+PG Sbjct: 5 HDLADAIGHTPLIRLNRVSDETGCEILGKAEFMNPGQSVKDRAALYIIKDAIARGDLKPG 64 Query: 63 GVIVEGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPAAPYRNP 122 G IVEGTAGNTGIGL +V ++G++T IVIPETQS+EKKD LRL GA+L++VPAAPYRNP Sbjct: 65 GTIVEGTAGNTGIGLALVGASMGFKTVIVIPETQSEEKKDMLRLAGAQLVQVPAAPYRNP 124 Query: 123 NNYVRLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFVAAV 182 NN+VR S RLA++LAKTEPNGAIWANQFDN NRQAH+ETTA EIW T ++DGFV AV Sbjct: 125 NNFVRYSERLAKELAKTEPNGAIWANQFDNVANRQAHVETTAPEIWEQTGGKVDGFVCAV 184 Query: 183 GSGGTLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEGDSITEGIGQGRITAN 242 GSGGTLAG A L+ + +KI LADP GAAL+++YTTGE+ EG SI EGIGQ RIT N Sbjct: 185 GSGGTLAGVADALQPK--GVKIGLADPMGAALYSYYTTGEIATEGGSIAEGIGQVRITKN 242 Query: 243 LEGFTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKDLGPGHTIVTVL 302 LEGF PDF YQI D +AL +F L+ EEGL LGGSS INIAGA+R+AKD+GPG TIVTVL Sbjct: 243 LEGFKPDFCYQIEDRDALPYVFDLLHEEGLVLGGSSAINIAGAVRMAKDMGPGKTIVTVL 302 Query: 303 CDYGNRYQSKLFNPAFLRGKSLPVPRWL 330 CDYG RYQSKLFNP FLR K+LPVP W+ Sbjct: 303 CDYGTRYQSKLFNPDFLREKNLPVPDWM 330 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: 442 Number of extensions: 21 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 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