Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate BWI76_RS04255 BWI76_RS04255 threonine synthase
Query= BRENDA::P00934 (428 letters) >FitnessBrowser__Koxy:BWI76_RS04255 Length = 426 Score = 786 bits (2029), Expect = 0.0 Identities = 390/425 (91%), Positives = 406/425 (95%) Query: 1 MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60 MKLYNLKDHNEQVSFAQAVTQGLGK+QGLFFPHDLPEFSLTEIDEML+ D V+RSAKILS Sbjct: 1 MKLYNLKDHNEQVSFAQAVTQGLGKHQGLFFPHDLPEFSLTEIDEMLQQDLVSRSAKILS 60 Query: 61 AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120 AFIGDEIPQ++L+ R+ AF FPAPV+ V+ DVGCLELFHGPTLAFKDFGGRFMAQMLTH Sbjct: 61 AFIGDEIPQDVLQARIGNAFTFPAPVSKVQDDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120 Query: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV Sbjct: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180 Query: 181 AIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ 240 AIDGDFDACQALVKQAFDDEELK ALGLNSANSINISRLLAQICYYFEAVAQLPQE RNQ Sbjct: 181 AIDGDFDACQALVKQAFDDEELKAALGLNSANSINISRLLAQICYYFEAVAQLPQEARNQ 240 Query: 241 LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNA 300 LV+SVPSGNFGDLTAGLLAKSLGLP+KRFIAATN NDTVPRFL DG WSPKATQATLSNA Sbjct: 241 LVISVPSGNFGDLTAGLLAKSLGLPIKRFIAATNANDTVPRFLQDGNWSPKATQATLSNA 300 Query: 301 MDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRA 360 MDVSQPNNWPRVEELFRRKIW+L ELGYAAVDDETT++TMRELK +GYTSEPHAA+AYRA Sbjct: 301 MDVSQPNNWPRVEELFRRKIWRLNELGYAAVDDETTKETMRELKAIGYTSEPHAAIAYRA 360 Query: 361 LRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL 420 LRDQL PGEYGLFLGTAHPAKFKESVE IL ETL LPKELAERADLPLLSHNLPADFAAL Sbjct: 361 LRDQLQPGEYGLFLGTAHPAKFKESVEEILQETLPLPKELAERADLPLLSHNLPADFAAL 420 Query: 421 RKLMM 425 RKLMM Sbjct: 421 RKLMM 425 Lambda K H 0.319 0.135 0.395 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: 730 Number of extensions: 24 Number of successful extensions: 1 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: 428 Length of database: 426 Length adjustment: 32 Effective length of query: 396 Effective length of database: 394 Effective search space: 156024 Effective search space used: 156024 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: 51 (24.3 bits)
Align candidate BWI76_RS04255 BWI76_RS04255 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))
# 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/TIGR00260.hmm # target sequence database: /tmp/gapView.23673.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00260 [M=340] Accession: TIGR00260 Description: thrC: threonine synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-128 414.7 0.0 1.8e-128 414.5 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS04255 BWI76_RS04255 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS04255 BWI76_RS04255 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 414.5 0.0 1.8e-128 1.8e-128 1 338 [. 52 396 .. 52 398 .. 0.96 Alignments for each domain: == domain 1 score: 414.5 bits; conditional E-value: 1.8e-128 TIGR00260 1 vvryreilevt...ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltka 68 v r+++il+++ e+++ l+++ ++f++p++ ++v+ ++ ++elfhgPtlaFKD+g++f+a++lt++ lcl|FitnessBrowser__Koxy:BWI76_RS04255 52 VSRSAKILSAFigdEIPQDVLQARIGNAFTFPAPVSKVQD-DVGCLELFHGPTLAFKDFGGRFMAQMLTHI 121 5688999999999999************************.****************************** PP TIGR00260 69 lelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdl 139 ++++ t+l+AtsGdtgaa+a+a++g +nvkvv+LyP+gkisp++ekl+++l +n++++ai+GdFD++q+l lcl|FitnessBrowser__Koxy:BWI76_RS04255 122 AGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETVAIDGDFDACQAL 192 *********************************************************************** PP TIGR00260 140 vkeifedke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkel 207 vk++f+d+e +l+lns+Nsin++r++aq++y+fe+v+ql++e+++++v++vpsgnfg++++G l +k+l lcl|FitnessBrowser__Koxy:BWI76_RS04255 193 VKQAFDDEElkaALGLNSANSINISRLLAQICYYFEAVAQLPQEARNQLVISVPSGNFGDLTAG-LLAKSL 262 ******877788****************************************************.778888 PP TIGR00260 208 glpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsd 278 glp k++iaa++a+d+v+rfl++g+++pk++++Tls+Amd+++p+n++r++el+rr+ + l++l+++++d lcl|FitnessBrowser__Koxy:BWI76_RS04255 263 GLP-IKRFIAATNANDTVPRFLQDGNWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWRLNELGYAAVD 332 8**.899**************************************************************** PP TIGR00260 279 eeileaikklaeeegyllephtavavaalkklvekgvs....atadpaKFeevvealtgnklkd 338 +e+++++++ ++ gy+ eph+a+a++al+++++ g + +ta+paKF+e+ve ++ ++l lcl|FitnessBrowser__Koxy:BWI76_RS04255 333 DETTKETMRELKAIGYTSEPHAAIAYRALRDQLQPGEYglflGTAHPAKFKESVEEILQETLPL 396 ************************************555889*************888777765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (426 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: 11.92 // [ok]
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