Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate SMc01174 SMc01174 cysteine synthase A
Query= BRENDA::A0A0F6AQU1 (342 letters) >FitnessBrowser__Smeli:SMc01174 Length = 361 Score = 536 bits (1381), Expect = e-157 Identities = 260/338 (76%), Positives = 292/338 (86%) Query: 4 SVLDTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLRPGG 63 SVL+ IGNTPLIRL SE TGC+I GKAEFLNPGQSVKDRAAL+IIR AEK G LRPGG Sbjct: 21 SVLEAIGNTPLIRLKAVSEATGCNILGKAEFLNPGQSVKDRAALWIIRQAEKSGQLRPGG 80 Query: 64 VIVEGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPAAPYRNPN 123 VIVEGTAGNTGIGL +V ALGYRT IVIPETQSQEKKDALRLLGAEL+EVPA PYRNPN Sbjct: 81 VIVEGTAGNTGIGLAVVGSALGYRTVIVIPETQSQEKKDALRLLGAELVEVPAVPYRNPN 140 Query: 124 NYVRLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFVAAVG 183 NYV++SGRLA QLA+TEPNGAIWANQFDN NRQAH++TTA EIWRDT ++DGF+ AVG Sbjct: 141 NYVKISGRLAAQLAETEPNGAIWANQFDNVANRQAHVDTTAPEIWRDTDGKVDGFICAVG 200 Query: 184 SGGTLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEGDSITEGIGQGRITANL 243 SGGTLAG A GL+ RN IKI +ADP GAAL+ FY GELK+ G SITEGIGQGRITANL Sbjct: 201 SGGTLAGVAEGLRARNAAIKIGIADPEGAALYNFYAHGELKSSGSSITEGIGQGRITANL 260 Query: 244 EGFTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKDLGPGHTIVTVLC 303 E FTPDF+YQIPDAEA+ +F L+E+EG+C+GGS+GINIAGA+RLA+DLGPGHTIVT+LC Sbjct: 261 EDFTPDFAYQIPDAEAVPYVFDLIEKEGICVGGSTGINIAGAVRLARDLGPGHTIVTILC 320 Query: 304 DYGNRYQSKLFNPAFLRGKSLPVPRWLEKKTEIDIPFE 341 DYGNRYQSKLFNP FL K LPVP WL+ + I +P+E Sbjct: 321 DYGNRYQSKLFNPDFLTSKGLPVPDWLKTASNIAVPYE 358 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: 468 Number of extensions: 8 Number of successful extensions: 1 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: 361 Length adjustment: 29 Effective length of query: 313 Effective length of database: 332 Effective search space: 103916 Effective search space used: 103916 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