Align cysteine synthase; EC 2.5.1.47 (characterized)
to candidate SMc01174 SMc01174 cysteine synthase A
Query= CharProtDB::CH_013302 (370 letters) >FitnessBrowser__Smeli:SMc01174 Length = 361 Score = 322 bits (826), Expect = 8e-93 Identities = 176/351 (50%), Positives = 232/351 (66%), Gaps = 16/351 (4%) Query: 10 ATAALRSAAESPYNVRVSQAQGFVNGLTEAIGNTPLIRLKRLSEETGSNILAKAEFQNPG 69 A A +RS +N+ V + + EAIGNTPLIRLK +SE TG NIL KAEF NPG Sbjct: 2 ANAGIRSVQREVFNMPV------LPSVLEAIGNTPLIRLKAVSEATGCNILGKAEFLNPG 55 Query: 70 GSVKDRAALYVVKDAEERGLLKPGGTVVEGTAGNTGIGLAHVCRSKGYKLVIYMPNTQSQ 129 SVKDRAAL++++ AE+ G L+PGG +VEGTAGNTGIGLA V + GY+ VI +P TQSQ Sbjct: 56 QSVKDRAALWIIRQAEKSGQLRPGGVIVEGTAGNTGIGLAVVGSALGYRTVIVIPETQSQ 115 Query: 130 GKIDLLRLLGAEVYPVPAVAFDNPENYNHKARRHAESL-----DNAVWTNQFDNTANRRA 184 K D LRLLGAE+ VPAV + NP NY + R A L + A+W NQFDN ANR+A Sbjct: 116 EKKDALRLLGAELVEVPAVPYRNPNNYVKISGRLAAQLAETEPNGAIWANQFDNVANRQA 175 Query: 185 HIETTGPEIWAQTGGKLDAFTCSTGTGGTLAGITYYLKQASGGRVKSFLADPPGSVLHSY 244 H++TT PEIW T GK+D F C+ G+GGTLAG+ L+ A +K +ADP G+ L+++ Sbjct: 176 HVDTTAPEIWRDTDGKVDGFICAVGSGGTLAGVAEGLR-ARNAAIKIGIADPEGAALYNF 234 Query: 245 IQSGGKLVERSGSSITEGIGQGRITDNLQPDVGTLDGSLNISDEKTIEMIYRCLDEEGLY 304 G ++ SGSSITEGIGQGRIT NL+ T D + I D + + ++ +++EG+ Sbjct: 235 YAHGE--LKSSGSSITEGIGQGRITANLED--FTPDFAYQIPDAEAVPYVFDLIEKEGIC 290 Query: 305 LGASSALNVVAAKEVAEKLGKGSTVVTILADGAYRYADRLFSKSWLESKGL 355 +G S+ +N+ A +A LG G T+VTIL D RY +LF+ +L SKGL Sbjct: 291 VGGSTGINIAGAVRLARDLGPGHTIVTILCDYGNRYQSKLFNPDFLTSKGL 341 Lambda K H 0.314 0.133 0.381 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: 456 Number of extensions: 30 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: 370 Length of database: 361 Length adjustment: 30 Effective length of query: 340 Effective length of database: 331 Effective search space: 112540 Effective search space used: 112540 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: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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