Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_043743637.1 AMB_RS06615 cysteine synthase A
Query= metacyc::MONOMER-20568 (299 letters) >NCBI__GCF_000009985.1:WP_043743637.1 Length = 334 Score = 199 bits (505), Expect = 9e-56 Identities = 123/316 (38%), Positives = 170/316 (53%), Gaps = 21/316 (6%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61 I D L++IGNTPL+R+ + + K E NP GSVKDR AL +I+ AE +G L Sbjct: 4 IRDGFLDSIGNTPLIRLKRASEETGCNILGKAEFLNPGGSVKDRAALAIIQDAERKGLLK 63 Query: 62 PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDK-KLG 120 PG I+E T+GNTGIGLA++ GY +IVM E S E++ M++ GA++ L Sbjct: 64 PGGVIVEGTAGNTGIGLALVANALGYRTVIVMPETQSQEKKDMLRLVGADLRLVPAVPYA 123 Query: 121 TDGAIRKVA-----ELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVA 175 G + + EL K P NQF N N++ H+ TT +EIW QT GTV F Sbjct: 124 NPGNYVRYSETLANELAKTEPNGVLWANQFDNTANRMGHFNTTGQEIWRQTDGTVDAFTC 183 Query: 176 AVGTSGTLMGVGKNLREKNPEIKIIEAQPTKG----HYIQG-LKSMEEAIVPAIYQ---- 226 AVGT GTL G G L+E N +IK++ A P HY G LK+ +I I Q Sbjct: 184 AVGTGGTLAGTGMALKEHNKDIKVVLADPMGSALYHHYAHGELKAEGTSITEGIGQGRIT 243 Query: 227 ----ADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG-VIVV 281 ID+ + + EA ++V QEG+ +G SSG ++AA K+A + G +V Sbjct: 244 RNLDGAPIDDQVQVTDHEALPLIFDLVRQEGLVLGGSSGINVMAAIKVARILGPGHTVVT 303 Query: 282 LFADRGEKYLSTKLFD 297 + D G +Y S KLF+ Sbjct: 304 VLCDYGTRYQS-KLFN 318 Lambda K H 0.315 0.133 0.367 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: 326 Number of extensions: 17 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: 299 Length of database: 334 Length adjustment: 27 Effective length of query: 272 Effective length of database: 307 Effective search space: 83504 Effective search space used: 83504 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: 42 (22.0 bits) S2: 48 (23.1 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