Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate WP_011382646.1 AMB_RS01005 cysteine synthase A
Query= metacyc::MONOMER-20568 (299 letters) >NCBI__GCF_000009985.1:WP_011382646.1 Length = 319 Score = 243 bits (620), Expect = 4e-69 Identities = 136/307 (44%), Positives = 181/307 (58%), Gaps = 12/307 (3%) Query: 2 IYDNILETIGNTPLVRINHL--NPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGK 59 IYD+I++TIG TPLVR + K + KLE FNP SVKDRI MIE AE G+ Sbjct: 12 IYDSIIDTIGATPLVRFKRMAAEAGSKADIVGKLEFFNPLASVKDRIGFAMIEAAEVSGQ 71 Query: 60 LHPGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKL 119 L PG TIIE TSGNTGI LA + KGY +I+ M E +S+ERRKM++ GAEI+LT Sbjct: 72 LKPGGTIIEPTSGNTGIALAFVAAAKGYKLILCMPESMSLERRKMLQLLGAEIVLTPASK 131 Query: 120 GTDGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGT 179 G GA+R+ EL+ PG P QF NE N H +TTAEEIW T G V V+ VGT Sbjct: 132 GMTGAVRQAEELLASTPGAIM-PQQFKNEANPAIHERTTAEEIWNDTNGKVDIIVSGVGT 190 Query: 180 SGTLMGVGKNLREKNPEIKIIEAQPTKGHYIQG-------LKSMEEAIVPAIYQADKIDE 232 GT+ G+G L+ + P +K++ +P + G ++ + VP I IDE Sbjct: 191 GGTISGIGHVLKARKPGLKMVAVEPEDSPVLSGGAPGPHKIQGIGAGFVPDILDKGVIDE 250 Query: 233 HILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSG--VIVVLFADRGEKY 290 + I +E A A AR+ EG+ +G+SSGAA+ AA +L + ++ +IV + E+Y Sbjct: 251 ILQIGNETALATARKAAKLEGVPVGISSGAAIAAALELGSRPENAGKLIVAIIPSFAERY 310 Query: 291 LSTKLFD 297 LST LFD Sbjct: 311 LSTALFD 317 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: 298 Number of extensions: 16 Number of successful extensions: 5 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: 319 Length adjustment: 27 Effective length of query: 272 Effective length of database: 292 Effective search space: 79424 Effective search space used: 79424 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