Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate CA265_RS15860 CA265_RS15860 threonine dehydratase
Query= BRENDA::Q04513 (436 letters) >FitnessBrowser__Pedo557:CA265_RS15860 Length = 416 Score = 376 bits (966), Expect = e-109 Identities = 196/412 (47%), Positives = 264/412 (64%), Gaps = 7/412 (1%) Query: 25 DIQTAQARISSVIAPTPLQYCPRLSEETGAEIYLKREDLQDVRSYKIRGALNSGAQLTQE 84 D Q+A R+ V+ TPL++ LS A IYLKREDLQ VRSYK+RGA N + L Q+ Sbjct: 10 DFQSASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAYNKISSLPQD 69 Query: 85 QRDAGIVAASAGNHAQGVAYVCKSLGVQGRIYVPVQTPKQKRDRIMVHGGEFVSLVVTGN 144 G+V ASAGNHAQGVAY CK LG++G I++P TPKQK + + GG+ V +V+ G+ Sbjct: 70 ALINGVVCASAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGDNVEVVLVGD 129 Query: 145 NFDEASAAAHEDAERTGATLIEPFDARNTVIGQGTVAAEILSQLTSMGKSADHVMVPVGG 204 FD+ A + AT I PFD + GQ TV EI L + D +++PVGG Sbjct: 130 TFDDCLKEALAYSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLPDL----DMIVMPVGG 185 Query: 205 GGLLAGVVSYMADMAPRTAIVGIEPAGAASMQAALHNGGPITLETVDPFVDGAAVKRVGD 264 GGL +GV +YM + P +VG+EP GA SM A+ GGP TLE +D FVDGAAVKR+G Sbjct: 186 GGLASGVSAYMKTVKPEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAVKRIGH 245 Query: 265 LNYTIVEKNQGRVHMMSATEGAVCTEMLDLYQNEGIIAEPAGALSIAGLKEM-SFAPGSV 323 + Y ++ ++H++ EG +CT +L LY + I+ EPAGALS+A L ++ G Sbjct: 246 ITYEYCKELLDQMHLI--PEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKDQITGKT 303 Query: 324 VVCIISGGNNDVLRYAEIAERSLVHRGLKHYFLVNFPQKPGQLRHFLEDILGPDDDITLF 383 VVCI+SGGNND+ R EI E+SL+ GLKHYF+V FPQ+PG L+ F+ ++LGP DDIT F Sbjct: 304 VVCIVSGGNNDIERMQEIKEKSLLFEGLKHYFIVRFPQRPGALKLFVNEVLGPQDDITRF 363 Query: 384 EYLKRNNRETGTALVGIHLSEASGLDSLLERMEESAIDSRRLEPGTPEYEYL 435 E++K+ N+E G ALVGI LS + SLL+RM++ + L +EYL Sbjct: 364 EFIKKTNKENGPALVGIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYL 415 Lambda K H 0.316 0.133 0.373 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: 454 Number of extensions: 19 Number of successful extensions: 6 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: 436 Length of database: 416 Length adjustment: 32 Effective length of query: 404 Effective length of database: 384 Effective search space: 155136 Effective search space used: 155136 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 (21.6 bits) S2: 51 (24.3 bits)
Align candidate CA265_RS15860 CA265_RS15860 (threonine dehydratase)
to HMM TIGR02079 (ilvA: threonine dehydratase (EC 4.3.1.19))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02079.hmm # target sequence database: /tmp/gapView.12567.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02079 [M=410] Accession: TIGR02079 Description: THD1: threonine dehydratase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-193 629.3 0.3 1.5e-193 629.1 0.3 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS15860 CA265_RS15860 threonine dehydrat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS15860 CA265_RS15860 threonine dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 629.1 0.3 1.5e-193 1.5e-193 3 410 .] 11 416 .] 9 416 .] 0.99 Alignments for each domain: == domain 1 score: 629.1 bits; conditional E-value: 1.5e-193 TIGR02079 3 iekakkrlkevvketPlqknerlsekykaeiylkredlqevrsyklrGaynklkqlsdeelekgvvca 70 + a +rlk vvk+tPl+ n+ ls++y+a+iylkredlq+vrsyklrGaynk+++l ++ l +gvvca lcl|FitnessBrowser__Pedo557:CA265_RS15860 11 FQSASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAYNKISSLPQDALINGVVCA 78 57899*************************************************************** PP TIGR02079 71 saGnhaqGvayacrklgvkgtvfmPvttPkqkvdkvklfGgefievilvGdtfdeaaaaakkavekeg 138 saGnhaqGvay+c+klg+kg++fmP tPkqkv+++ +fGg+++ev+lvGdtfd++ +a +++ lcl|FitnessBrowser__Pedo557:CA265_RS15860 79 SAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGDNVEVVLVGDTFDDCLKEALAYSAEKS 146 ******************************************************************** PP TIGR02079 139 ktlipPfddkdiieGqgtvaveileqleeekidlvlvpvGGGGlisGvtsylkekskktkiigvePeG 206 +t+ipPfdd+++ieGq+tv+vei e+l++ d++++pvGGGGl+sGv++y+k+ ++ k++gveP G lcl|FitnessBrowser__Pedo557:CA265_RS15860 147 ATFIPPFDDEKVIEGQATVGVEIYEDLPD--LDMIVMPVGGGGLASGVSAYMKTVKPEVKLVGVEPLG 212 *****************************..6************************************ PP TIGR02079 207 apslkaslkagevvtldkidkfvdGaavkrvGdlnfkalkkvvdevtlveegavcstildlynkegiv 274 aps+ ++++ g + tl++id+fvdGaavkr+G+++++ +k+++d++ l++eg++c+til+lyn+++iv lcl|FitnessBrowser__Pedo557:CA265_RS15860 213 APSMVTAMEYGGPFTLEEIDRFVDGAAVKRIGHITYEYCKELLDQMHLIPEGKICTTILKLYNEDAIV 280 ******************************************************************** PP TIGR02079 275 aePaGalsiaaleelseeikgktvvcvvsGgnndierleeikersllyeGlkhyflvkfpqraGalre 342 +ePaGals+aal++l+++i+gktvvc+vsGgnndier++eike+sll+eGlkhyf+v+fpqr+Gal+ lcl|FitnessBrowser__Pedo557:CA265_RS15860 281 VEPAGALSVAALDQLKDQITGKTVVCIVSGGNNDIERMQEIKEKSLLFEGLKHYFIVRFPQRPGALKL 348 ******************************************************************** PP TIGR02079 343 flndvlGPndditkfeyvkksnretGevliGielsdkedfeGllerlkaadieyeainenetlyellv 410 f+n+vlGP+ddit+fe++kk+n+e+G++l+Giels+k+d++ ll+r+k ++ e+ ++n+++tl+e+lv lcl|FitnessBrowser__Pedo557:CA265_RS15860 349 FVNEVLGPQDDITRFEFIKKTNKENGPALVGIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYLV 416 ******************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (410 nodes) Target sequences: 1 (416 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.56 // [ok]
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