Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate PP_2930 PP_2930 putative L-serine dehydratase
Query= BRENDA::P20132 (328 letters) >FitnessBrowser__Putida:PP_2930 Length = 305 Score = 289 bits (739), Expect = 7e-83 Identities = 155/313 (49%), Positives = 204/313 (65%), Gaps = 12/313 (3%) Query: 7 LHVKTPIRDSMALSKMAGTSVYLKMDSAQPSGSFKIRGIGHFCKRWAKQGCAHFVCSSAG 66 LH+ TP+ +S LS AG +++LK+D+ QP GSFK+RG+GH C+ +G HFV SS G Sbjct: 3 LHIHTPLIESRPLSLAAGRNIWLKLDALQPCGSFKLRGVGHACEVHHARGARHFVSSSGG 62 Query: 67 NAGMAAAYAARQLGVPATIVVPSTTPALTIERLKNEGATVKVVGELLDEAFELAKALAKN 126 NAG+A AYA R+LGVP T+V+P TT + L E A V V G EA LA+ L Sbjct: 63 NAGLAVAYAGRKLGVPVTVVIPETTTERAKQLLHLEDAKVVVQGSSWQEANALAQTLV-- 120 Query: 127 NPGWVYIPPFDDPLIWEGHASIVKELKETLWEKPGAIALSVGGGGLLCGVVQGLQEVGWG 186 P +I PFDDPL+W GHAS+V E+ E KP A+ LSVGGGGLL GVV+GL+ GWG Sbjct: 121 GPNDAFIHPFDDPLLWAGHASLVDEVAEA-GLKPDAVVLSVGGGGLLSGVVEGLKRNGWG 179 Query: 187 DVPVIAMETFGAHSFHAATTAGKLVSLPKITSVAKALGVKTVGAQALKLFQEHPIFSEVI 246 DVPV+A+ET GA S HAA AG V L +I SVA +LG K V QAL Q+HP+ S ++ Sbjct: 180 DVPVLAVETEGAASLHAAMQAGHSVELERIASVATSLGAKRVADQALMCVQQHPVHSHLV 239 Query: 247 SDQEAVAAIEKFVDDEKILVEPACGAALAAVYSHVIQKLQLEGNLRTPLPSLVVIVCGGS 306 SD+ A+ A E+F+ D ++LVEPACGAALA Y + L +++V+VCGG+ Sbjct: 240 SDRAALEACERFLLDHRVLVEPACGAALAVAY---------DAKALGALRNVLVVVCGGA 290 Query: 307 NISLAQLRALKEQ 319 +L Q++A +Q Sbjct: 291 TATLEQIQAWLQQ 303 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: 262 Number of extensions: 9 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: 305 Length adjustment: 27 Effective length of query: 301 Effective length of database: 278 Effective search space: 83678 Effective search space used: 83678 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 17 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