Align O-ureido-L-serine synthase; Cysteine synthase homolog DscD; O-acetylserine sulfhydrylase; EC 2.6.99.3; EC 2.5.1.47 (characterized)
to candidate WP_011338724.1 RSPH17029_RS13980 pyridoxal-phosphate dependent enzyme
Query= SwissProt::D2Z027 (324 letters) >NCBI__GCF_000015985.1:WP_011338724.1 Length = 358 Score = 307 bits (787), Expect = 2e-88 Identities = 164/332 (49%), Positives = 216/332 (65%), Gaps = 24/332 (7%) Query: 3 LFNSILDTIGRTPIVRLQRMAPEHTSVYVKVESFNPGGSVKDRLALSVVLDAEAKGLLKP 62 L++S+LDT+G TP++R+ ++PE ++YVK E FNP SVKDRLAL+++ AE G LKP Sbjct: 15 LYDSVLDTVGNTPVIRINNLSPEGVTIYVKAEFFNPAASVKDRLALNIIEAAERSGKLKP 74 Query: 63 GDTIVECTSGNVGIALAMVAAARGYRFVAVMGDTYSVERRKLIRAYGGKLVLFPGHLGSK 122 G T+VE TSGN GI LAMV A +GY V M + +SVERR+L+R G K+VL P G K Sbjct: 75 GMTVVEATSGNTGIGLAMVCAQKGYPLVITMSEAFSVERRRLMRLLGAKVVLTP--RGGK 132 Query: 123 GGNLI--ADELAEKYGWFRARQFDNPANPSYHRETTASEILADFAGKRLDHFVTGFGTTG 180 G + A ELAE GWF A QF+ AN H TTA EI+ADFAG+RLD FVTG+GT G Sbjct: 133 GFGMYRKAQELAEANGWFLASQFETDANADIHEATTAREIVADFAGERLDWFVTGYGTGG 192 Query: 181 TLTGVGQMLRVARPEVRVVALEPSNAAMLARG----------------EWSPHQIQGLAP 224 T+TGV ++LR RPEV++V EP+NA ++A G + H IQG P Sbjct: 193 TVTGVARVLRRERPEVKIVLSEPANAQLVASGVPQDRNADGTAASGHPAFEAHPIQGWTP 252 Query: 225 NFVPGV----LDRSVIDDLVTMDEVTARDTSRRLAAEEGIFAGISAGATVATALSIAEHA 280 +F+P V LD D+L+ + +R LAA+EGI G+S G+T A A +AE A Sbjct: 253 DFIPKVLQEGLDAGAYDELIPVAGEDGMKWARELAAKEGILTGVSGGSTFAVARQVAERA 312 Query: 281 PEGTVLLAMLPDTGERYLSTFLFDGVDEGSDD 312 P+G+V+LAMLPDTGERY+ST LF + E ++ Sbjct: 313 PKGSVILAMLPDTGERYMSTPLFQAIGEDMNE 344 Lambda K H 0.319 0.136 0.395 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: 329 Number of extensions: 19 Number of successful extensions: 4 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: 324 Length of database: 358 Length adjustment: 28 Effective length of query: 296 Effective length of database: 330 Effective search space: 97680 Effective search space used: 97680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 16 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