Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate CA265_RS23465 CA265_RS23465 threonine synthase
Query= BRENDA::P00934 (428 letters) >FitnessBrowser__Pedo557:CA265_RS23465 Length = 435 Score = 344 bits (882), Expect = 3e-99 Identities = 188/433 (43%), Positives = 260/433 (60%), Gaps = 8/433 (1%) Query: 1 MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60 MKLY+ + + +VSF +AV + +++GL+ P ++P+ I + K + I S Sbjct: 1 MKLYSTNNKDLRVSFKEAVFNSMPQDKGLYMPIEIPQLDPEFIQNIEKYALPEIAYTIAS 60 Query: 61 AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120 + DEIP E L+ + A F AP ++ LELFHGP+LAFKDFG RFM++++ + Sbjct: 61 TLLKDEIPAEDLKALIDDAINFEAPAVKLDDKTYVLELFHGPSLAFKDFGARFMSRVMAY 120 Query: 121 IA--GDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIE 178 G++ + +L ATSGDTG AVA F G+PN +V ILYP GK+SP+QE T G NI Sbjct: 121 FLKDGEQLLDVLVATSGDTGGAVALGFLGVPNTRVTILYPEGKVSPIQELQLTTNGENIR 180 Query: 179 TVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETR 238 V + G FD CQALVKQAF D+EL L SANSINISRL+ Q YYF AQL ++ Sbjct: 181 AVEVKGTFDDCQALVKQAFADDELNAKFRLTSANSINISRLIPQTFYYFNTYAQLKKQGF 240 Query: 239 NQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLS 298 +V SVPSGNFG++ AGLLA LGLPVK+FIAATNVNDTVPRFL G + K + T S Sbjct: 241 KDVVFSVPSGNFGNIGAGLLAYKLGLPVKQFIAATNVNDTVPRFLESGVYETKPSTQTYS 300 Query: 299 NAMDVSQPNNWPRVEELFRRKIWQLKEL--GYAAVDDETTQQTMRELKELGYTSEPHAAV 356 NAMDV P+NW R+ +LF + + +K++ Y DDET +L Y + PH A+ Sbjct: 301 NAMDVGAPSNWVRIMDLFHKDVEAIKKVVTAYRFTDDETLAGIKEINSKLNYVACPHTAI 360 Query: 357 AYRAL----RDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHN 412 AY A+ R+ + +FL TAH KF + A + +++P+++ P + Sbjct: 361 AYLAVEKYRRENPSDESAAVFLSTAHACKFPDIFPADIAAKIEIPEQVKALESKPKHADQ 420 Query: 413 LPADFAALRKLMM 425 L DF +K ++ Sbjct: 421 LGVDFEGFKKYLL 433 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: 530 Number of extensions: 28 Number of successful extensions: 4 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: 435 Length adjustment: 32 Effective length of query: 396 Effective length of database: 403 Effective search space: 159588 Effective search space used: 159588 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 CA265_RS23465 CA265_RS23465 (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.10338.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-93 298.7 0.1 3.8e-93 298.3 0.1 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS23465 CA265_RS23465 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS23465 CA265_RS23465 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 298.3 0.1 3.8e-93 3.8e-93 12 327 .. 66 393 .. 56 399 .. 0.93 Alignments for each domain: == domain 1 score: 298.3 bits; conditional E-value: 3.8e-93 TIGR00260 12 ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvl 77 e++++dl++ +++++++a ++ + yv+elfhgP+laFKD+g +f++ +++++l++g++ vl lcl|FitnessBrowser__Pedo557:CA265_RS23465 66 EIPAEDLKALIDDAINFEAPAVKLDD-KTYVLELFHGPSLAFKDFGARFMSRVMAYFLKDGEQllDVL 132 789999999999************99.99**********************************878** PP TIGR00260 78 cAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeife 145 +AtsGdtg a+a ++ g +n +v +LyP+gk+sp++e +t+ en++ +++kG+FDd+q+lvk++f lcl|FitnessBrowser__Pedo557:CA265_RS23465 133 VATSGDTGGAVALGFLGVPNTRVTILYPEGKVSPIQELQLTTNGENIRAVEVKGTFDDCQALVKQAFA 200 ***********************************77777889************************* PP TIGR00260 146 dke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglp 210 d+e k l s+Nsin++r+ q y+f+ +ql+k+ + vv++vpsgnfg+i +G l++k + lp lcl|FitnessBrowser__Pedo557:CA265_RS23465 201 DDElnaKFRLTSANSINISRLIPQTFYYFNTYAQLKKQGFKDVVFSVPSGNFGNIGAGLLAYKLG-LP 267 8888889***************************************************8887776.** PP TIGR00260 211 ieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlke..sv 276 k +iaa++++d+v+rfl+sg e+k + +T+s+Amd+g psn+ r+++l+++ + ++++ + + lcl|FitnessBrowser__Pedo557:CA265_RS23465 268 -VKQFIAATNVNDTVPRFLESGVYETKPSTQTYSNAMDVGAPSNWVRIMDLFHKDVEAIKKVVTayRF 334 .8999*****************88888899******************************99655699 PP TIGR00260 277 sdeeileaikklaeeegyllephtavavaalkklvekg...vs.....atadpaKFeev 327 +d+e+l ik++ + +y++ phta+a+ a++k ++ s +ta+ KF+++ lcl|FitnessBrowser__Pedo557:CA265_RS23465 335 TDDETLAGIKEINSKLNYVACPHTAIAYLAVEKYRRENpsdESaavflSTAHACKFPDI 393 *********************************999887662256789********987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (435 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: 8.58 // [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