Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate AO353_28645 AO353_28645 hypothetical protein
Query= BRENDA::P37887 (308 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28645 Length = 318 Score = 65.1 bits (157), Expect = 2e-15 Identities = 55/167 (32%), Positives = 82/167 (49%), Gaps = 14/167 (8%) Query: 23 LADENSADVYLKLEYMNPGSSVKDRIGLAMIEAAEKEGKLKAGNTIIEPTSGNTGIGLAM 82 LA+ V++K E P + K R G+ + ++E G I+ T GN G LA+ Sbjct: 31 LAERLGCTVWVKHENHTPTGAFKVRGGITFMHWLKREHPGIKG--IVSATRGNHGQSLAL 88 Query: 83 VAAAKGLKAILVMPDTMSMERRNLLRAYGAELVLTPGAEGMKGAIKKAEELAEKHG-YFV 141 A A GLKA++V+P+ S+E+ N +RA+G E+V A ++A LA+ HG Y V Sbjct: 89 AAGALGLKALIVVPEGNSVEKNNAMRAFGGEVV--ECGRDFDEAREEAARLAQAHGLYLV 146 Query: 142 PQQFNNPSNPEIHR--QTTGKEIVEQFGDDQLDAFVAGIGTGGTITG 186 P P + E+ + T E+ + D LD IG G I G Sbjct: 147 P-----PFHAELVKGVATYALELFKAAPD--LDTVYVPIGCGSGICG 186 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: 179 Number of extensions: 5 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: 308 Length of database: 318 Length adjustment: 27 Effective length of query: 281 Effective length of database: 291 Effective search space: 81771 Effective search space used: 81771 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