Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_092345908.1 BLU87_RS06435 cysteine synthase A
Query= metacyc::MONOMER-20568 (299 letters) >NCBI__GCF_900107645.1:WP_092345908.1 Length = 318 Score = 198 bits (503), Expect = 2e-55 Identities = 124/315 (39%), Positives = 171/315 (54%), Gaps = 22/315 (6%) Query: 2 IYDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLH 61 IY + +IGNTPLVR+N + P V +YAK+EG NP SVK RI MI A G L Sbjct: 4 IYTDNSLSIGNTPLVRLNRVIPTSGVNVYAKIEGRNPGYSVKCRIGASMIWDAIKTGTLK 63 Query: 62 PGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGT 121 PG +IE TSGNTGI LA + KG + + M + +S ERR+++KA GA +ILT G Sbjct: 64 PGMELIEPTSGNTGIALAFVAAAKGIPLTLTMPDTMSKERRRVLKALGANLILTPGAKGM 123 Query: 122 DGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSG 181 GAI + ++ P Y NQF N N H +TT EIW T G ++ VGT G Sbjct: 124 AGAILEAEQIANSKPELYVLLNQFKNPANPAIHEQTTGPEIWNDTDGNFDVLISGVGTGG 183 Query: 182 TLMGVGKNLRE-KNPEIKIIEAQPTKG----------------HYIQGLKSMEEAIVPAI 224 T+ GV + +++ K +I + +PT H IQG+ + +PA Sbjct: 184 TISGVTRYIKKTKGKQIISVAVEPTDSPVISQHLAGEPLQPGPHKIQGIGA---GFIPAN 240 Query: 225 YQADKIDEHILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKID-SGV-IVVL 282 D ID + +EE+ AR + +EG+ G+S GAA+ A +LA + + SG IVV+ Sbjct: 241 LDLDVIDRVEKVTNEESLDFARRLAKEEGLLSGISCGAAVAVAARLAAEAEFSGKNIVVI 300 Query: 283 FADRGEKYLSTKLFD 297 D GE+YLS+ LFD Sbjct: 301 LPDSGERYLSSVLFD 315 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: 306 Number of extensions: 11 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: 318 Length adjustment: 27 Effective length of query: 272 Effective length of database: 291 Effective search space: 79152 Effective search space used: 79152 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 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