Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011385748.1 AMB_RS17140 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_000009985.1:WP_011385748.1 Length = 467 Score = 493 bits (1268), Expect = e-144 Identities = 253/463 (54%), Positives = 324/463 (69%), Gaps = 1/463 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 MKYVSTRG AP L F D LLAGLARDGGLYLP+ +P F+A IRA+RG SY E+A+ V+ Sbjct: 1 MKYVSTRGAAPALDFDDVLLAGLARDGGLYLPESWPVFSAADIRAMRGLSYAELAVRVMR 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PF G + A+ R+ E+YG F H AV PL Q N++V+ELFHGPTLAFKD A+QL+ Sbjct: 61 PFVEGCLTEAELTRLCAESYGAFAHPAVAPLKQLGHNQWVMELFHGPTLAFKDYALQLVG 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R+ D+VL ++G++ TIVGATSGDTG AAIEA R DI IL P+GRVS VQ+RQMT+ Sbjct: 121 RLFDHVLKKKGQKVTIVGATSGDTGSAAIEACRDRAAVDIVILHPHGRVSEVQRRQMTTV 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 SNV ++++G FDDCQ+LVK +FND F D ++LS VNSINWAR+M Q+VYYF A ++ Sbjct: 181 LSSNVRNVAVDGTFDDCQDLVKALFNDAAFRDEMNLSAVNSINWARVMAQIVYYFAAGVA 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LGAPD +SF+VPTGNFG++FAGY AK MGLP+E+LII +N NDIL+R E G + GV Sbjct: 241 LGAPDVPMSFSVPTGNFGNVFAGYAAKLMGLPVEKLIIGSNTNDILTRFFEGGVMKADGV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 T SPSMDIQ+SSNFERL+F A G D AAV LM +++G + + +A+R F Sbjct: 301 VPTLSPSMDIQVSSNFERLMFLALGGDGAAVAKLMDDFRKNGAMVMPQGAWTAMREVFEG 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVA-REKASGTAPMVVLATAHPAKFPDAV 419 R + T A + S+ G LDPHS IGV A + A+ MV LATAHPAKFPDAV Sbjct: 361 YRFDDEATLAAMRSLKRSTGETLDPHSVIGVAAALKGHAARDCSMVALATAHPAKFPDAV 420 Query: 420 KAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462 + A G+ P LP + DL +R E + N+ ++++YVR +R Sbjct: 421 EKATGIRPGLPPHMADLFERTERLDRMGNDADLLKQYVRAFAR 463 Lambda K H 0.320 0.135 0.389 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: 551 Number of extensions: 18 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: 463 Length of database: 467 Length adjustment: 33 Effective length of query: 430 Effective length of database: 434 Effective search space: 186620 Effective search space used: 186620 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 WP_011385748.1 AMB_RS17140 (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.31869.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-86 276.2 0.0 2.8e-86 275.7 0.0 1.1 1 lcl|NCBI__GCF_000009985.1:WP_011385748.1 AMB_RS17140 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011385748.1 AMB_RS17140 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 275.7 0.0 2.8e-86 2.8e-86 12 334 .. 69 426 .. 57 430 .. 0.91 Alignments for each domain: == domain 1 score: 275.7 bits; conditional E-value: 2.8e-86 TIGR00260 12 ekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tv 76 e++l l++ s+ +f+ p++a +++g n +v elfhgPtlaFKD +lq v+ l+ ++l+++ + t+ lcl|NCBI__GCF_000009985.1:WP_011385748.1 69 EAELTRLCAESYGAFAHPAVAplKQLGH-NQWVMELFHGPTLAFKDYALQLVGRLFDHVLKKKGQkvTI 136 789999*************998899999.******************************98887668** PP TIGR00260 77 lcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeif 144 ++AtsGdtg+aa+ea + +a v++v+L P+g++s v +++t+l +n++ +a++G+FDd+qdlvk++f lcl|NCBI__GCF_000009985.1:WP_011385748.1 137 VGATSGDTGSAAIEACRDRAAVDIVILHPHGRVSEVqRRQMTTVLSSNVRNVAVDGTFDDCQDLVKALF 205 ************************************99******************************* PP TIGR00260 145 edke...klklnsvNsinparieaqktyafeiveqlgkespd.kvvvpvpsgnfgailkGflekkelgl 209 +d +++l++vNsin+ar+ aq++y+f + +lg +pd + ++vp gnfg++++G+ +k ++ l lcl|NCBI__GCF_000009985.1:WP_011385748.1 206 NDAAfrdEMNLSAVNSINWARVMAQIVYYFAAGVALG--APDvPMSFSVPTGNFGNVFAGYAAKLMG-L 271 9776788******************************..6662589**************8888777.* PP TIGR00260 210 pieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke... 274 p+ekl i ++ + di++rf ++g ++ + Tls++mdi +sn+er+++ + ++ + +l lcl|NCBI__GCF_000009985.1:WP_011385748.1 272 PVEKLIIGSNTN-DILTRFFEGGVMKADGVVPTLSPSMDIQVSSNFERLMFlALGGDGAAVAKLMDdfr 339 ***********9.**********66666666********************444444555555544899 PP TIGR00260 275 ......................svsdeeileaikklaeeegyllephtavavaalkklvekg.vs.... 316 + de++l a++ l ++ g +l+ph+ ++vaa +k +++ s lcl|NCBI__GCF_000009985.1:WP_011385748.1 340 kngamvmpqgawtamrevfegyRFDDEATLAAMRSLKRSTGETLDPHSVIGVAAALKGHAARdCSmval 408 9********************************************************999987334568 PP TIGR00260 317 atadpaKFeevvealtgn 334 ata+paKF+++ve tg lcl|NCBI__GCF_000009985.1:WP_011385748.1 409 ATAHPAKFPDAVEKATGI 426 *************88885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (467 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 9.11 // [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