Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate HSERO_RS00265 HSERO_RS00265 threonine dehydratase
Query= BRENDA::B1N2N4 (423 letters) >FitnessBrowser__HerbieS:HSERO_RS00265 Length = 401 Score = 286 bits (731), Expect = 1e-81 Identities = 165/400 (41%), Positives = 245/400 (61%), Gaps = 12/400 (3%) Query: 26 TISDVYAASKRIKGYAYYTALEYSNTISKKVGCKTYLKLENLQKTGSFKVRGAVNKIATL 85 T++D+ AA++R++G T S T+S+ VG + +LK ENLQ T SFK RGA NK+ + Sbjct: 3 TLNDIEAAARRLQGQILETPCVESRTLSQIVGAQVFLKFENLQFTASFKERGACNKLVDV 62 Query: 86 TEEEK-KRGVVAASAGNHAQGVAFASTSAGCKATIVMPEFASTAKVTATRGYGAEVVLHG 144 RGVVA SAGNHAQGVA+ + G ATIVMP F K+ TRG+GA VVLHG Sbjct: 63 AASGGGARGVVAMSAGNHAQGVAYHAQRLGLPATIVMPRFTPGVKIERTRGFGANVVLHG 122 Query: 145 KVFDESLAYAMQLCKEEGKTFVHPFNDPWVMAGQGTIALEILEQLEKCDVIIGAIGGGGL 204 + + +A +L ++EG TFVHP++D ++AGQGT+ALE+++ + D ++ +IGGGGL Sbjct: 123 DTLEAARTHAYELAEKEGLTFVHPYDDEAIIAGQGTVALEMMKAVPDLDCLVVSIGGGGL 182 Query: 205 MSGVAFAAKQIKPEIRIIGVQAAECPSM--AVSKAEHKICCVKTAKTMADGIAVKAPGDK 262 ++G+A AA+ IKPEI I+GVQ P+M AV EH + A T+A+GIAV PG Sbjct: 183 LAGMAVAARAIKPEIEIVGVQTRRFPTMVNAVKGTEHPV----GASTIAEGIAVGTPGTL 238 Query: 263 TAPVLLKYVDEIVTVDEESIAQAMLLMLERCKIVSEGSGATPVAALLSGKIKGLTEDTNV 322 T ++ + DE++ VDE I QA+L++LE K + EG+GA +AAL+ + V Sbjct: 239 TRAIIAREADELLLVDEGDIEQAVLMLLEIEKTLVEGAGAAGLAALV--RYPDRFRGKRV 296 Query: 323 VCIVSGGNLDVNVINKVIERGLVKAGRKVEFTVEIADVPGAIKDLLAHITEEKATVVGVA 382 ++SGGN+D ++ +IERG+V+AGR V DVPG + + + E A V V Sbjct: 297 GLVLSGGNIDPLLLTAIIERGMVRAGRLARVKVSSRDVPGTLARITGIVAEAGANVDEVH 356 Query: 383 TRRPAT--SAIGICLCDVQMECYGVEHRDKIFDVLKEAGY 420 +R T +A + + ++ ++ G H ++ L+ AG+ Sbjct: 357 HQRAFTLLAAQNVDI-ELVLQTRGRPHLAQVLQALRAAGF 395 Lambda K H 0.317 0.133 0.378 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: 359 Number of extensions: 15 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: 423 Length of database: 401 Length adjustment: 31 Effective length of query: 392 Effective length of database: 370 Effective search space: 145040 Effective search space used: 145040 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: 50 (23.9 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