Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_028585350.1 G494_RS0116150 serine dehydratase
Query= BRENDA::P20132 (328 letters) >NCBI__GCF_000429965.1:WP_028585350.1 Length = 311 Score = 290 bits (743), Expect = 2e-83 Identities = 152/313 (48%), Positives = 206/313 (65%), Gaps = 11/313 (3%) Query: 7 LHVKTPIRDSMALSKMAGTSVYLKMDSAQPSGSFKIRGIGHFCKRWAKQGCAHFVCSSAG 66 LH++TP+ S ALS + SV+LK+++ QPSGSFK+RG+GH C +A+QG F+ SS G Sbjct: 3 LHIETPLLPSRALSLESRRSVWLKLEALQPSGSFKLRGVGHACTHYARQGARRFISSSGG 62 Query: 67 NAGMAAAYAARQLGVPATIVVPSTTPALTIERLKNEGATVKVVGELLDEAFELAKALAKN 126 NAG+A AYA R+L +P T+VVP TTP E L E A V+V G EA ELA +L Sbjct: 63 NAGLATAYAGRRLEIPVTVVVPETTPERATELLAREQAEVRVHGASWQEANELALSLLGK 122 Query: 127 NPGWVYIPPFDDPLIWEGHASIVKELKETLWEKPGAIALSVGGGGLLCGVVQGLQEVGWG 186 N +++ PFDDPL+W+GHA ++ E+ KP AI L+VGGGGLLCGV QGL GW Sbjct: 123 NDAFLH--PFDDPLLWQGHAGLIDEVAAA-GLKPDAIILAVGGGGLLCGVAQGLHRHGWD 179 Query: 187 DVPVIAMETFGAHSFHAATTAGKLVSLPKITSVAKALGVKTVGAQALKLFQEHPIFSEVI 246 ++P+IA+ET G SFH A AG+LV L KI+ VA +LG V AQAL+ HP+ + ++ Sbjct: 180 ELPIIAVETEGTASFHGAVEAGRLVKLAKISGVATSLGANQVCAQALQWVGRHPVTTTLV 239 Query: 247 SDQEAVAAIEKFVDDEKILVEPACGAALAAVYSHVIQKLQLEGNLRTPLPSLVVIVCGGS 306 SD+ A++A E+F+DD ++LVEPACGAALA Y E L +++V+VCGG+ Sbjct: 240 SDRSALSACERFLDDHRLLVEPACGAALAVAYE--------ETALLERYRTVLVVVCGGA 291 Query: 307 NISLAQLRALKEQ 319 + QLR + Q Sbjct: 292 TATSEQLRQWRRQ 304 Lambda K H 0.318 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: 252 Number of extensions: 8 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: 328 Length of database: 311 Length adjustment: 28 Effective length of query: 300 Effective length of database: 283 Effective search space: 84900 Effective search space used: 84900 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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