Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate H281DRAFT_04028 H281DRAFT_04028 threonine dehydratase
Query= CharProtDB::CH_024588 (329 letters) >FitnessBrowser__Burk376:H281DRAFT_04028 Length = 324 Score = 219 bits (559), Expect = 6e-62 Identities = 126/325 (38%), Positives = 197/325 (60%), Gaps = 7/325 (2%) Query: 1 MHITYDLPV-AIDDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKI 59 M + LP DD+++A RL G ++T + S+ F+ER +F K EN QR G+FK Sbjct: 1 MQPMHPLPAPTFDDVLDAAARLEGVAHRTPVLTSSTFNERTGASVFFKCENFQRMGAFKF 60 Query: 60 RGAFNKLSSLTDAEKRK-GVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATC 118 RGA+N +S DAE+RK GV+ S+GNHAQ ++LS + GI ++MP AP +KVAAT Sbjct: 61 RGAYNAISHF-DAEQRKAGVLTYSSGNHAQAIALSARLAGIRATIIMPHDAPAAKVAATK 119 Query: 119 DYSAEVVLHGDNFNDTIAKVSE-IVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVD 177 Y EV+ + D + + ++ + E G IPPYD P VIAGQGT E++++ +D Sbjct: 120 GYGGEVISY-DRYKENREEIGRRLAEERGMTLIPPYDHPHVIAGQGTAVKELIDETGPLD 178 Query: 178 NVIVPIGGGGLIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADG 237 + V +GGGGLI G A++ +++P VIGV+ + + S GEI T T+ADG Sbjct: 179 MLFVCLGGGGLIGGSALSAAALSPDCTVIGVEPQAGNDGQQSLARGEIVHIDTPRTIADG 238 Query: 238 CDVSRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKL 297 + G+ T+ I+R+LV I V+++++ ++M QR K+V E G LA AA+L+G + Sbjct: 239 AASTHLGDYTFAIIRKLVARIETVTDEQLIDTMRFFAQRMKIVVEPTGCLAAAAVLNGVV 298 Query: 298 DQYIQNRKTVSIISGGNIDLSRVSQ 322 ++ ++ ++SGGN+DL +++Q Sbjct: 299 P--VKGKRVGVVVSGGNVDLEKLAQ 321 Lambda K H 0.318 0.136 0.386 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: 226 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: 329 Length of database: 324 Length adjustment: 28 Effective length of query: 301 Effective length of database: 296 Effective search space: 89096 Effective search space used: 89096 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