Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate 7023929 Shewana3_1141 threonine synthase (RefSeq)
Query= BRENDA::P00934 (428 letters) >FitnessBrowser__ANA3:7023929 Length = 427 Score = 479 bits (1233), Expect = e-140 Identities = 249/421 (59%), Positives = 303/421 (71%), Gaps = 2/421 (0%) Query: 1 MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60 M+LYNLK +++VSF +AV GLGK++GLFFP +P L +I+ +L + FV RS K+L Sbjct: 1 MELYNLKHPSQKVSFKEAVQLGLGKDRGLFFPTQIPV--LHDIEALLAMPFVERSKKVLG 58 Query: 61 AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120 A++ E+ Q+ +++ V AF F P+ V+ CLELFHGPTLAFKDFG RFMAQ + Sbjct: 59 AWLASELGQDAVDKLVERAFNFDLPLVAVDEQRSCLELFHGPTLAFKDFGARFMAQCINA 118 Query: 121 IAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETV 180 A D +TILTATSGDTGAAVA AFYGL V VV+LYP+GKIS LQEK+F TLG NI TV Sbjct: 119 FAQDSRLTILTATSGDTGAAVADAFYGLDKVNVVVLYPKGKISELQEKMFTTLGKNIHTV 178 Query: 181 AIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ 240 A+ DFDACQ LVKQAF+D +++ L LNSANSINISRLLAQICYYFEAVAQ Q Sbjct: 179 AVASDFDACQHLVKQAFEDSDVRDGLHLNSANSINISRLLAQICYYFEAVAQSKQRHEAD 238 Query: 241 LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNA 300 V++VPSGNFG+LTAGL AK++GLPVKRFIAATN NDTVPR+L G W P TQAT+SNA Sbjct: 239 PVIAVPSGNFGNLTAGLFAKAMGLPVKRFIAATNANDTVPRYLESGDWQPNPTQATMSNA 298 Query: 301 MDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRA 360 MDVS+P+NWPRVE + + W L +L + + T + + EL GY SEPHAA+A RA Sbjct: 299 MDVSEPSNWPRVEAICEKLGWPLADLVGIRLSEAQTSEALAELHAKGYVSEPHAAIAARA 358 Query: 361 LRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL 420 L L P E G+FLGTAHPAKFK+ V+ L L LP EL P+LS L ADFA L Sbjct: 359 LTLNLVPDEVGIFLGTAHPAKFKDVVDRELNLDLPLPAELKAVEHKPILSAELAADFAQL 418 Query: 421 R 421 + Sbjct: 419 K 419 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: 509 Number of extensions: 19 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: 428 Length of database: 427 Length adjustment: 32 Effective length of query: 396 Effective length of database: 395 Effective search space: 156420 Effective search space used: 156420 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 7023929 Shewana3_1141 (threonine synthase (RefSeq))
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.26294.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-102 328.8 0.0 2.4e-102 328.5 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7023929 Shewana3_1141 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023929 Shewana3_1141 threonine synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 328.5 0.0 2.4e-102 2.4e-102 2 329 .. 51 385 .. 50 392 .. 0.92 Alignments for each domain: == domain 1 score: 328.5 bits; conditional E-value: 2.4e-102 TIGR00260 2 vryreilevt...ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgnet 75 +r++++l + e + ++++ + ++f+++ + v + + ++elfhgPtlaFKD+g +f+a+ +++++++ + t lcl|FitnessBrowser__ANA3:7023929 51 ERSKKVLGAWlasELGQDAVDKLVERAFNFDLPLVAVDE-QRSCLELFHGPTLAFKDFGARFMAQCINAFAQDSRLT 126 566666666655566777888889999999999999998.778********************************** PP TIGR00260 76 vlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke...k 149 +l+AtsGdtgaa+a a++g v+vvvLyPkgkis ++ek++t+l +n++++a+ dFD++q+lvk++fed+ lcl|FitnessBrowser__ANA3:7023929 127 ILTATSGDTGAAVADAFYGLDKVNVVVLYPKGKISELQEKMFTTLGKNIHTVAVASDFDACQHLVKQAFEDSDvrdG 203 **********************************************************************7777789 PP TIGR00260 150 lklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivr 226 l lns+Nsin++r++aq++y+fe+v+q +++++ v++vpsgnfg++++G ++k ++ lp k++iaa++a+d+v+ lcl|FitnessBrowser__ANA3:7023929 204 LHLNSANSINISRLLAQICYYFEAVAQSKQRHEADPVIAVPSGNFGNLTAGLFAKAMG-LP-VKRFIAATNANDTVP 278 ***************************************************9999998.**.99************* PP TIGR00260 227 rflksgdlepkedkeTlstAmdignpsnveralelarrslgnledl.kesvsdeeileaikklaeeegyllephtav 302 r+l+sgd++p +++T+s+Amd+++psn++r++++ ++ ++ l dl + ++s+++++ea +l + +gy+ eph+a+ lcl|FitnessBrowser__ANA3:7023929 279 RYLESGDWQPNPTQATMSNAMDVSEPSNWPRVEAICEKLGWPLADLvGIRLSEAQTSEALAEL-HAKGYVSEPHAAI 354 *****************************************9888625688888888888776.568********** PP TIGR00260 303 avaalkklvekg.vs...atadpaKFeevve 329 a +al + + v+ +ta+paKF++vv lcl|FitnessBrowser__ANA3:7023929 355 AARALTLNLVPDeVGiflGTAHPAKFKDVVD 385 ****97666666555778***********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (427 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: 12.37 // [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