Align serine racemase (EC 5.1.1.18) (characterized)
to candidate PP_3191 PP_3191 putative threonine ammonia-lyase / dehydratase
Query= BRENDA::Q9GZT4 (340 letters) >FitnessBrowser__Putida:PP_3191 Length = 350 Score = 187 bits (474), Expect = 4e-52 Identities = 115/312 (36%), Positives = 175/312 (56%), Gaps = 15/312 (4%) Query: 11 DVEKAHINIRDSIHLTPVLTSSILNQLTGRNLFFKCELFQKTGSFKIRGALNAVRSLVPD 70 +++ AH +R ++ +TP+L S L+ LTG + KCE Q TGSFK RGA N +R L + Sbjct: 39 NIQDAHAALRPAVSITPLLHSPRLSALTGCEVLLKCEHLQHTGSFKFRGASNKMRLLPAE 98 Query: 71 ALERKPKAVVTHSSGNHGQALTYAAKLEGIPAYIVVPQTAPDCKKLAIQAYGASIVYCEP 130 A + + V+ SSGNHGQAL A K+ G+P + A K A++A GA +V C P Sbjct: 99 A---RKQGVIAASSGNHGQALALAGKMAGVPVKVYTTTGASAYKTEAMRALGAEVV-CLP 154 Query: 131 SDESRENVAKRVTEETEGI-MVHPNQEPAVIAGQGTIALEVLNQVPLVDALVVPVGGGGM 189 +D + + +G+ V P + VIAGQGTI +E+L Q P +DA+ V VGGGGM Sbjct: 155 TDPLSAELEAARQAKAQGVPFVSPYNDLQVIAGQGTIGMELLEQAPDLDAVFVAVGGGGM 214 Query: 190 LAGIAITVKALKPSVKVYAAEPSNADDCYQSKLKGKLMPNLYPPETIADGVKSSI--GLN 247 ++GI ++ LKP ++ P+N D Q LK + L ET++DG + G Sbjct: 215 ISGIGAALRVLKPGTEIIGCWPAN-DPTLQQSLKAGEIIELDACETLSDGTAGGVEPGSI 273 Query: 248 TWPIIRDLVDDIFTVTEDEIKCATQLVWERMKLLIEPTAGVGVAAV--LSQHFQTVSPEV 305 T+P+ + L+ D V+EDEI+CA + + + +IE A V VA + L++ +Q Sbjct: 274 TFPLCQALLTDTVLVSEDEIRCAMRDIASSERWIIEGAAAVAVAGMQRLAERYQG----- 328 Query: 306 KNICIVLSGGNV 317 K + ++L G N+ Sbjct: 329 KRVAVILCGRNI 340 Lambda K H 0.317 0.133 0.385 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: 271 Number of extensions: 11 Number of successful extensions: 3 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: 340 Length of database: 350 Length adjustment: 29 Effective length of query: 311 Effective length of database: 321 Effective search space: 99831 Effective search space used: 99831 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: 49 (23.5 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