Align N-succinylglutamate synthase (characterized)
to candidate CA265_RS18550 CA265_RS18550 N-acetyltransferase
Query= reanno::Cola:Echvi_3845 (224 letters) >FitnessBrowser__Pedo557:CA265_RS18550 Length = 232 Score = 276 bits (706), Expect = 2e-79 Identities = 138/218 (63%), Positives = 168/218 (77%), Gaps = 3/218 (1%) Query: 1 MTKSQFIIQTAGVQHCKYAETIVDEMALSAKARGTGIAKRSPDYIIQKMMEGKAVIALSK 60 M ++FI+Q A +H +AE IV EMA SAKARGTGIAKRSP+YI KM EGK+VIA K Sbjct: 1 MDINEFIVQVALPEHRVFAEEIVTEMAESAKARGTGIAKRSPEYISNKMQEGKSVIAFHK 60 Query: 61 EGEWAGFCYIEAWGHGKFVANSGLIVSPNFRKSGLAREIKKAVFKLSRSKFPHAKIFGLT 120 +G WAGFCYIE W HG+FVANSGL+VSP +RK+GLA+ IK +F LSR +P AKIFGLT Sbjct: 61 DGSWAGFCYIETWSHGQFVANSGLVVSPKYRKAGLAKAIKNEIFGLSRKLYPKAKIFGLT 120 Query: 121 TGAAVMKINSELGYVPVSYSDLTDDEEFWKGCQSCVNYEILKSKNRQNCLCTAMLYVPKD 180 TG AVMKINS+LGY PV+YS+LT DEEFWKGCQSCVN+EILK K R+NC+CTAMLY P Sbjct: 121 TGLAVMKINSDLGYEPVTYSELTQDEEFWKGCQSCVNFEILKMKERKNCMCTAMLYDPA- 179 Query: 181 QKKKEVAMK--KDFGKNLNLFERLVRMKRAVFTGIKKK 216 +KK EVA + ++ K L+ER +R+K+ + K K Sbjct: 180 EKKHEVAKQFAEELQKKPKLYERFMRIKQRLVVKPKPK 217 Lambda K H 0.320 0.134 0.395 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: 206 Number of extensions: 10 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: 224 Length of database: 232 Length adjustment: 23 Effective length of query: 201 Effective length of database: 209 Effective search space: 42009 Effective search space used: 42009 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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