Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate CCNA_03740 CCNA_03740 cysteine synthase
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Caulo:CCNA_03740 Length = 328 Score = 250 bits (639), Expect = 3e-71 Identities = 137/307 (44%), Positives = 189/307 (61%), Gaps = 12/307 (3%) Query: 2 IYDNILETIGNTPLVRINHLNP--NPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGK 59 IYD+I++TIG+TPLVR+ L+ NPK ++ AKLE FNP SVKDRI + MIE EA+G Sbjct: 21 IYDSIIDTIGDTPLVRLPRLSAELNPKAEVLAKLEFFNPIASVKDRIGVSMIESLEAQGV 80 Query: 60 LHPGSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKL 119 L PG+TIIE TSGNTGI LA + KGY + +VM E +SIERRKM+ GA++ LT + Sbjct: 81 LKPGATIIEPTSGNTGIALAFVAAAKGYKLTLVMPESMSIERRKMLLLLGAKLELTPAEK 140 Query: 120 GTDGAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGT 179 G GA+ + EL++ PG P QF N N + H +TAEEIW T G V V+ VGT Sbjct: 141 GMRGAVTRAQELIEATPGAVM-PQQFENSANPLIHRVSTAEEIWNDTAGAVDAVVSGVGT 199 Query: 180 SGTLMGVGKNLREKNPEIKIIEAQPTKGHYIQG-------LKSMEEAIVPAIYQADKIDE 232 GT+ GVG+ L+ + P +K++ +P + G ++ + VP + ID+ Sbjct: 200 GGTITGVGQALKARKPSLKMVAVEPEASPVLSGGAPGPHKIQGIGAGFVPGVLDRGVIDD 259 Query: 233 HILIESEEAFAKAREIVAQEGIFIGMSSGAAMLAAQKLA--EKIDSGVIVVLFADRGEKY 290 + + +++AFA AR A EG+ +G+SSGAA+ AA LA + IVV+ E+Y Sbjct: 260 IVQVSNDDAFAMARRAAATEGLPVGISSGAALTAAFDLALRDAYKGKTIVVIIPSFAERY 319 Query: 291 LSTKLFD 297 LST LFD Sbjct: 320 LSTALFD 326 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: 292 Number of extensions: 11 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: 328 Length adjustment: 27 Effective length of query: 272 Effective length of database: 301 Effective search space: 81872 Effective search space used: 81872 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