Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate BPHYT_RS15425 BPHYT_RS15425 serine/threonine dehydratase
Query= CharProtDB::CH_024588 (329 letters) >FitnessBrowser__BFirm:BPHYT_RS15425 Length = 321 Score = 223 bits (569), Expect = 4e-63 Identities = 127/313 (40%), Positives = 192/313 (61%), Gaps = 6/313 (1%) Query: 12 DDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTD 71 DD+++A RL G ++T + S+ F+ER +F K EN QR G+FK RGA+N +S D Sbjct: 10 DDVLDAAARLNGVAHRTPVLTSSTFNERTGASVFFKCENFQRMGAFKFRGAYNAISHF-D 68 Query: 72 AEKRK-GVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDN 130 AE+RK GV+ S+GNHAQ ++LS + GI +VMP+ AP +KVAAT Y EV+ + D Sbjct: 69 AEQRKAGVLTYSSGNHAQAIALSARLAGIHATIVMPQDAPAAKVAATKGYGGEVITY-DR 127 Query: 131 FNDTIAKVSE-IVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGLI 189 + + ++ + E G IPPYD P VIAGQGT E++E+ +D + V +GGGGLI Sbjct: 128 YTENREEIGRRLAEERGMTLIPPYDHPHVIAGQGTAVKELIEETGPLDMLFVCLGGGGLI 187 Query: 190 AGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDVSRPGNLTYE 249 +G A+A +++P VIG++ E + S GEI T T+ADG + G+ T+ Sbjct: 188 SGSALAAAALSPACTVIGIEPEAGNDGQQSLARGEIVHIDTPRTIADGAASTHLGDYTFA 247 Query: 250 IVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQYIQNRKTVSI 309 I+R+LV I VS+ ++ +M QR K+V E G LA AA+L+G + + ++ + Sbjct: 248 IIRKLVAQIETVSDAQLIETMRFFAQRMKIVVEPTGCLAAAAVLNGIVP--VTGKRVGVV 305 Query: 310 ISGGNIDLSRVSQ 322 +SGGN+DL +++Q Sbjct: 306 VSGGNVDLEKLAQ 318 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: 237 Number of extensions: 10 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: 321 Length adjustment: 28 Effective length of query: 301 Effective length of database: 293 Effective search space: 88193 Effective search space used: 88193 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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