Align threonine deaminase (EC 4.3.1.19) (characterized)
to candidate WP_069663723.1 BCR25_RS11385 threonine ammonia-lyase IlvA
Query= reanno::Pedo557:CA265_RS15860 (416 letters) >NCBI__GCF_001730305.1:WP_069663723.1 Length = 418 Score = 448 bits (1152), Expect = e-130 Identities = 216/411 (52%), Positives = 294/411 (71%), Gaps = 4/411 (0%) Query: 10 DFQSASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAYNKISSLPQD 69 D + A LK VV +TPL+++ LS Y N+YLKREDLQ VRS+KLRGAY I P + Sbjct: 8 DVEQAYATLKKVVTKTPLQYDMYLSQKYQCNVYLKREDLQKVRSFKLRGAYYAIKQTPHE 67 Query: 70 ALINGVVCASAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGDNVEVVLVGD 129 L NGVVCASAGNHAQGVA++C ++ + IFMP TP+QK+ Q FGGD V V L+GD Sbjct: 68 VLKNGVVCASAGNHAQGVAFTCHEMNVAATIFMPTTTPQQKISQVKFFGGDEVTVQLIGD 127 Query: 130 TFDDCLKEALAYSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLPD----LDMIVMPVGG 185 TFD K A Y+ FI PF+D ++ GQ TV VE++++ + +D ++ +GG Sbjct: 128 TFDASAKAAKEYAEIHHQAFIDPFNDLNIMAGQGTVAVEVFQEAQESEFQVDYLLAAIGG 187 Query: 186 GGLASGVSAYMKTVKPEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAVKRIGH 245 GGL SGVS Y K++ P ++GVEPLGA SM A + G P L+ +++FVDGAAVK++G+ Sbjct: 188 GGLVSGVSTYTKSISPTTAVIGVEPLGAQSMRAAFDEGRPVMLDSVEKFVDGAAVKQVGN 247 Query: 246 ITYEYCKELLDQMHLIPEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKDQITGKTVV 305 +TYE +D++ + EG++C+TIL+LY + AIVVEPAGALSV+AL+ +KD+I GK VV Sbjct: 248 LTYEQTLAYVDELLAVDEGQVCSTILELYTKQAIVVEPAGALSVSALELMKDEIRGKNVV 307 Query: 306 CIVSGGNNDIERMQEIKEKSLLFEGLKHYFIVRFPQRPGALKLFVNEVLGPQDDITRFEF 365 CI+SGGNNDI RM+EI+E+SL+FEGLKHYF++ FPQRPGAL+ FV ++LGP DDITRFE+ Sbjct: 308 CIISGGNNDINRMEEIEERSLIFEGLKHYFVINFPQRPGALREFVTDILGPDDDITRFEY 367 Query: 366 IKKTNKENGPALVGIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYLV 416 KK N+ GP ++GI L NK + +LL +M F + I+L+ + +L+ LV Sbjct: 368 TKKVNRGTGPVVLGILLKNKEELPNLLDKMAQFDPKYIDLSDNPSLYALLV 418 Lambda K H 0.318 0.138 0.392 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: 472 Number of extensions: 17 Number of successful extensions: 2 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: 416 Length of database: 418 Length adjustment: 31 Effective length of query: 385 Effective length of database: 387 Effective search space: 148995 Effective search space used: 148995 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)
Align candidate WP_069663723.1 BCR25_RS11385 (threonine ammonia-lyase IlvA)
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.aa/TIGR02079.hmm # target sequence database: /tmp/gapView.160115.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-191 622.8 1.2 1.4e-191 622.6 1.2 1.0 1 NCBI__GCF_001730305.1:WP_069663723.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069663723.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 622.6 1.2 1.4e-191 1.4e-191 2 410 .] 8 418 .] 7 418 .] 0.99 Alignments for each domain: == domain 1 score: 622.6 bits; conditional E-value: 1.4e-191 TIGR02079 2 diekakkrlkevvketPlqknerlsekykaeiylkredlqevrsyklrGaynklkqlsdeelekgvvcasaGn 74 d+e+a+ +lk+vv++tPlq++ +ls+ky++++ylkredlq+vrs+klrGay+++kq +e l++gvvcasaGn NCBI__GCF_001730305.1:WP_069663723.1 8 DVEQAYATLKKVVTKTPLQYDMYLSQKYQCNVYLKREDLQKVRSFKLRGAYYAIKQTPHEVLKNGVVCASAGN 80 89*********************************************************************** PP TIGR02079 75 haqGvayacrklgvkgtvfmPvttPkqkvdkvklfGgefievilvGdtfdeaaaaakkavekegktlipPfdd 147 haqGva++c++++v +t+fmP+ttP+qk+++vk+fGg+ + v l+Gdtfd++a aak+ +e +++ +i Pf+d NCBI__GCF_001730305.1:WP_069663723.1 81 HAQGVAFTCHEMNVAATIFMPTTTPQQKISQVKFFGGDEVTVQLIGDTFDASAKAAKEYAEIHHQAFIDPFND 153 ************************************************************************* PP TIGR02079 148 kdiieGqgtvaveileqleee..kidlvlvpvGGGGlisGvtsylkekskktkiigvePeGapslkaslkage 218 +i++Gqgtvave++++ +e+ ++d++l+++GGGGl+sGv++y k++s++t++igveP Ga s++a++ +g+ NCBI__GCF_001730305.1:WP_069663723.1 154 LNIMAGQGTVAVEVFQEAQESefQVDYLLAAIGGGGLVSGVSTYTKSISPTTAVIGVEPLGAQSMRAAFDEGR 226 ****************9999889************************************************** PP TIGR02079 219 vvtldkidkfvdGaavkrvGdlnfkalkkvvdevtlveegavcstildlynkegivaePaGalsiaaleelse 291 +v ld ++kfvdGaavk+vG+l+++++ + vde+ +v+eg+vcstil+ly+k++iv+ePaGals++ale +++ NCBI__GCF_001730305.1:WP_069663723.1 227 PVMLDSVEKFVDGAAVKQVGNLTYEQTLAYVDELLAVDEGQVCSTILELYTKQAIVVEPAGALSVSALELMKD 299 ************************************************************************* PP TIGR02079 292 eikgktvvcvvsGgnndierleeikersllyeGlkhyflvkfpqraGalreflndvlGPndditkfeyvkksn 364 ei+gk+vvc++sGgnndi+r+eei+ersl++eGlkhyf+++fpqr+Galref+ d+lGP+ddit+fey+kk+n NCBI__GCF_001730305.1:WP_069663723.1 300 EIRGKNVVCIISGGNNDINRMEEIEERSLIFEGLKHYFVINFPQRPGALREFVTDILGPDDDITRFEYTKKVN 372 ************************************************************************* PP TIGR02079 365 retGevliGielsdkedfeGllerlkaadieyeainenetlyellv 410 r+tG+v++Gi l++ke++ ll++++++d +y ++ +n ly llv NCBI__GCF_001730305.1:WP_069663723.1 373 RGTGPVVLGILLKNKEELPNLLDKMAQFDPKYIDLSDNPSLYALLV 418 *******************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (410 nodes) Target sequences: 1 (418 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: 00:00:00.01 # Mc/sec: 15.36 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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