Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate RR42_RS11250 RR42_RS11250 cysteine synthase
Query= BRENDA::A0A0F6AQU1 (342 letters) >FitnessBrowser__Cup4G11:RR42_RS11250 Length = 336 Score = 381 bits (978), Expect = e-110 Identities = 195/319 (61%), Positives = 238/319 (74%), Gaps = 7/319 (2%) Query: 8 TIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLRPGGVIVE 67 TIG+TPLIRL+ SE TGC+I GKAEFLNPG SVKDRAALYIIRDAE+RG L+PGG +VE Sbjct: 10 TIGHTPLIRLAGLSEETGCEILGKAEFLNPGGSVKDRAALYIIRDAERRGALKPGGTVVE 69 Query: 68 GTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPAAPYRNPNNYVR 127 GTAGNTGIGL + A GYR +VIP+TQS EK D LRLLGAE+ VPAAPY +PNNY + Sbjct: 70 GTAGNTGIGLAHLCAARGYRCIVVIPDTQSPEKMDRLRLLGAEVRPVPAAPYADPNNYQK 129 Query: 128 LSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFVAAVGSGGT 187 ++GRLA+ E AIWANQFDN NRQAH ETT EIW DT+ +ID FV A G+GGT Sbjct: 130 VAGRLAQ-----ETENAIWANQFDNLANRQAHYETTGPEIWHDTAGKIDAFVCATGTGGT 184 Query: 188 LAGTAIGLKERNHN--IKIALADPHGAALHAFYTTGELKAEGDSITEGIGQGRITANLEG 245 LAG A LKE+ N ++I LADPHG+ L+ F E+KA+G+SITEGIG R+TANL Sbjct: 185 LAGVARFLKEKERNPPVRIVLADPHGSGLYHFVKHHEVKAKGNSITEGIGSSRVTANLAD 244 Query: 246 FTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKDLGPGHTIVTVLCDY 305 D + +I D +D+++ L+ EEGL +GGSSGIN+A A LA+++GPGHTIVT+LCD Sbjct: 245 TPIDDAVRIDDQACVDMVYRLLREEGLWVGGSSGINVAAAAWLAREMGPGHTIVTLLCDR 304 Query: 306 GNRYQSKLFNPAFLRGKSL 324 G+ Y +LFN +L K L Sbjct: 305 GDLYAGRLFNADWLAAKGL 323 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: 385 Number of extensions: 13 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: 342 Length of database: 336 Length adjustment: 28 Effective length of query: 314 Effective length of database: 308 Effective search space: 96712 Effective search space used: 96712 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: 49 (23.5 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