Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate GFF4108 PS417_21045 cysteine synthase
Query= BRENDA::P37887 (308 letters) >FitnessBrowser__WCS417:GFF4108 Length = 304 Score = 228 bits (582), Expect = 1e-64 Identities = 127/298 (42%), Positives = 177/298 (59%), Gaps = 4/298 (1%) Query: 6 NSITELIGNTPIVKLNRLADENSADVYLKLEYMNPGSSVKDRIGLAMIEAAEKEGKL--K 63 NSI ++IG TPIV+L + +++ +VY KLE +NPG S K RI L MI AE+ G L Sbjct: 4 NSILDVIGQTPIVRLAQFSEDLGIEVYAKLESLNPGGSHKARIALGMILDAERRGVLIRD 63 Query: 64 AGNTIIEPTSGNTGIGLAMVAAAKGLKAILVMPDTMSMERRNLLRAYGAELVLTPGAEGM 123 +G TIIEP+ GNTGIGL M G K +LV+PD S E++ LLR YGA++VL+ G Sbjct: 64 SGQTIIEPSGGNTGIGLVMAGNVLGYKVVLVIPDNYSPEKQKLLRLYGAKVVLSDSRLGN 123 Query: 124 KGAIKKAEELA-EKHGYFVPQQFNNPSNPEIHRQTTGKEIVEQFGDDQLDAFVAGIGTGG 182 +K EL E Y + Q N +NP+ HR TT EI+ FG+ + D FV GIGTGG Sbjct: 124 NSHGEKCMELQLENPSYVMLNQQRNGANPQTHRDTTAPEILRAFGEKRADYFVCGIGTGG 183 Query: 183 TITGAGEVLKEAYPSIKIYAVEPSDSPVLSGGKPGPHKIQGIGAGFVPDILNTEVYDEIF 242 ITG GE LK A+P +++ VEP + +L + PH IQG+ G +P ILN +V D + Sbjct: 184 HITGIGETLKTAWPELRVMGVEPEECDLLK-NQHAPHHIQGLSIGLIPSILNLDVIDGML 242 Query: 243 PVKNEEAFEYARRAAREEGILGGISSGAAIYAALQVAKKLGKGKKVLAIIPSNGERYL 300 V ++ + +R R + I G+SS A + A ++A +L VL ++ N + YL Sbjct: 243 KVSRQDCIDMMKRIMRTDAISLGLSSAANMVAIARLAPELPPETVVLTMVYDNADSYL 300 Lambda K H 0.313 0.134 0.373 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: 234 Number of extensions: 10 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: 308 Length of database: 304 Length adjustment: 27 Effective length of query: 281 Effective length of database: 277 Effective search space: 77837 Effective search space used: 77837 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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