Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_011384252.1 AMB_RS09340 CBS domain-containing protein
Query= BRENDA::A0A0F6AQU1 (342 letters) >NCBI__GCF_000009985.1:WP_011384252.1 Length = 455 Score = 206 bits (523), Expect = 1e-57 Identities = 119/321 (37%), Positives = 179/321 (55%), Gaps = 8/321 (2%) Query: 5 VLDTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLRPGGV 64 +L IGNTPLI L+ + C ++ K E NP S+KDRAAL ++R AE+ GLLRPGG Sbjct: 7 LLCQIGNTPLIELTNL-DTAPCRLFVKLESRNPSGSIKDRAALSMVRAAERDGLLRPGGH 65 Query: 65 IVEGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPA-APYRNPN 123 +VE TAGNTG+ L ++A GYR +VIP+ +K LR +GAE++ + P R+P Sbjct: 66 LVEATAGNTGLALALLAAHRGYRLTLVIPDKAGLDKVSHLRAMGAEVVLARSDVPRRHPE 125 Query: 124 NYVRLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFVAAVG 183 +Y ++ RLA + GA + +QF+N N AH + T E+W ++D VA G Sbjct: 126 HYQNVASRLAGE------TGAHFIDQFNNPANPAAHEDGTGPELWEQMGGRVDAVVAGAG 179 Query: 184 SGGTLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEGDSITEGIGQGRITANL 243 SGGTL G + R+ ++ LADP G+ L + TG + G + EGIG I Sbjct: 180 SGGTLTGLSRFFARRSPATEMVLADPRGSVLADYVRTGRVGEAGSWLVEGIGGDSIPMVS 239 Query: 244 EGFTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKDLGPGHTIVTVLC 303 + +Y + D E+ ++ EGL +G SSG +A A+R ++ + T++C Sbjct: 240 DFSRVTRAYSVSDRESFATARLVLRIEGLLVGSSSGTLLAAALRYCREQTAPKRVATLVC 299 Query: 304 DYGNRYQSKLFNPAFLRGKSL 324 D GNR+ S+L + ++L + L Sbjct: 300 DAGNRHLSRLHDESWLADQGL 320 Lambda K H 0.316 0.137 0.398 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: 388 Number of extensions: 23 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: 342 Length of database: 455 Length adjustment: 31 Effective length of query: 311 Effective length of database: 424 Effective search space: 131864 Effective search space used: 131864 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: 41 (21.6 bits) S2: 50 (23.9 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