Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_086510078.1 BZY95_RS11575 hydroxyectoine utilization dehydratase EutB
Query= BRENDA::Q74FW6 (402 letters) >NCBI__GCF_002151265.1:WP_086510078.1 Length = 334 Score = 220 bits (561), Expect = 4e-62 Identities = 130/324 (40%), Positives = 183/324 (56%), Gaps = 9/324 (2%) Query: 7 IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPR-- 64 I +A R+ + RT L+ SH SE+ I K E LQ +GAFK+RGA N + + Sbjct: 13 IYQARRRIAGQALRTPLVRSHALSERFDADILLKLETLQPSGAFKLRGAANMIAALIERH 72 Query: 65 --EALAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGR 122 +AL GV+TAS GNH + VA++A LGVP+T+ + P KV A GAEV G Sbjct: 73 GCDALEAGVVTASTGNHGRAVAYAAARLGVPATICLSRLVPANKVAAIEALGAEVRRVGE 132 Query: 123 NFDEAYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLI 182 + DEA+ + ERG + PFDDPL+ AGQGTIGLE++++ PD+ ++V + GGGL+ Sbjct: 133 SQDEAFGEVERLIRERGMTLIPPFDDPLIAAGQGTIGLELMEDAPDLDRVIVGLSGGGLL 192 Query: 183 AGIATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLAD--GIAVKKPGVNT 240 GI A++ P RI GV + + SLQ G+ V V +LAD G + T Sbjct: 193 GGIGAAVKAIRPEARITGVSLSRGAAMWQSLQAGRPVAVEEVESLADSLGGGIGLDNRCT 252 Query: 241 FPIIRDLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCV 300 F ++R+++DE V E IA A+V +LE KLLVEGA AV LAAL + + + Sbjct: 253 FSLVREVMDEHYQVSEAAIAQAMVDILEHEKLLVEGAAAVGLAALAEHGIEVRGQRVALI 312 Query: 301 LSGGNIDVKTISVVVERGLVAAGR 324 LSG + ++T+ +AAGR Sbjct: 313 LSGNGVALETLD---RARRIAAGR 333 Lambda K H 0.319 0.137 0.383 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: 257 Number of extensions: 13 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: 402 Length of database: 334 Length adjustment: 30 Effective length of query: 372 Effective length of database: 304 Effective search space: 113088 Effective search space used: 113088 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: 49 (23.5 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