Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate 208732 threonine synthase
Query= reanno::Miya:8501211 (492 letters) >MicrobesOnline__882:208732 Length = 482 Score = 798 bits (2062), Expect = 0.0 Identities = 387/482 (80%), Positives = 429/482 (89%), Gaps = 1/482 (0%) Query: 10 PGHDFPTARTRMEYVCLGCGERRGIDELLYTCPSCGGVYLLEDLDFDTLAEQRTGPEWRA 69 P DFP R+RMEYVCLGCG R IDELLYTCPSCGGV+LLEDLDFD LA+ R+G +WR Sbjct: 2 PSCDFPGWRSRMEYVCLGCGARHSIDELLYTCPSCGGVFLLEDLDFDHLADHRSGDDWRT 61 Query: 70 LFDARAATRTTALRGIFRFYELMAPVLEEEDIVYLGEGNTPIVEAAPVLRDAVGIPFAFK 129 LFD+RA+TR +LRGIFRFYELMAPVLEE+DI+YLGEGNTP+V+A+P L +VG FA+K Sbjct: 62 LFDSRASTRCRSLRGIFRFYELMAPVLEEDDIIYLGEGNTPVVDASPALERSVGQRFAYK 121 Query: 130 NDGQNPSASFKDRGMACAFSYLKALVRKHGWDEVLTVCASTGDTSAAAALYASYVGGPVK 189 NDGQNPSASFKDRGMACAFSYL+ALVRKHGWDEVLT+CASTGDTSAAAALYASYVG P+K Sbjct: 122 NDGQNPSASFKDRGMACAFSYLRALVRKHGWDEVLTICASTGDTSAAAALYASYVGSPIK 181 Query: 190 SVVLLPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALLNSKNSWRIL 249 S V+LPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALLNSKNSWRIL Sbjct: 182 SAVILPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALLNSKNSWRIL 241 Query: 250 GQESYAFEVAQWYGWDMKGQCVFVPIGNAGNVTAIMAGFLKLLRLGVIDALPRVIGVQSH 309 GQESYAFEVAQWYGWDM G+CVFVPIGNAGN+TA+M+GFLK+ RLG+IDALPRV GVQSH Sbjct: 242 GQESYAFEVAQWYGWDMAGKCVFVPIGNAGNITAVMSGFLKMHRLGIIDALPRVFGVQSH 301 Query: 310 HADPVWRYYSQPDPATRTYAPVTVQPSVAQAAMIGNPVSFPRVKALADRFIAEGGERAFS 369 HADPV+RYYS DP R Y PVTVQPSVAQAAMIGNPVSFPRV+ LA+RF A GG AF Sbjct: 302 HADPVYRYYSVEDPRQRHYEPVTVQPSVAQAAMIGNPVSFPRVRHLAERFEALGGPGAFQ 361 Query: 370 VVQVTEQEIMDAMIRGNRHGHIACTQGGECLAGLIKARELGLVSQGEHAVLDATAHSLKF 429 VVQVTEQ IMD+MIR NRHGHIACTQGGECLAGL++A+ELGLV + E AVLDATAHSLKF Sbjct: 362 VVQVTEQAIMDSMIRANRHGHIACTQGGECLAGLLRAKELGLVDKDETAVLDATAHSLKF 421 Query: 430 AGFQDMYFTNSFPPEYGVTPDASLANAPALVVSPEDKARLSPEAYTLAAAKAVVARLGLA 489 +GFQDMYFTN FPP YGVTPDA+L NAP+LV+ EDK L+ E YT+ AA+ + A+LGLA Sbjct: 422 SGFQDMYFTNGFPPAYGVTPDATLGNAPSLVLHDEDKVALA-EKYTVEAAQRIAAKLGLA 480 Query: 490 KK 491 K Sbjct: 481 GK 482 Lambda K H 0.320 0.136 0.416 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: 821 Number of extensions: 33 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: 492 Length of database: 482 Length adjustment: 34 Effective length of query: 458 Effective length of database: 448 Effective search space: 205184 Effective search space used: 205184 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: 52 (24.6 bits)
Align candidate 208732 (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.9937.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-57 181.3 0.0 1.9e-57 180.9 0.0 1.1 1 lcl|MicrobesOnline__882:208732 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:208732 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.9 0.0 1.9e-57 1.9e-57 4 336 .. 81 419 .. 77 423 .. 0.84 Alignments for each domain: == domain 1 score: 180.9 bits; conditional E-value: 1.9e-57 TIGR00260 4 yreilevt.ekdlvdlaegstelfr.spklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne...... 74 y+ + +v e d++ l eg+t++++ sp+l++ vg+ + k+++ +P+ +FKDrg +a ++++++ l ++ lcl|MicrobesOnline__882:208732 81 YELMAPVLeEDDIIYLGEGNTPVVDaSPALERSVGQ-RFAYKNDGQNPSASFKDRG---MACAFSYLRALVRKhgwdev 155 56667788899*************835889999999.*******************...********999988899999 PP TIGR00260 75 tvlcAtsGdtgaaaa.ealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedkeklkl 152 + +cA++Gdt+aaaa +a + + +k v++P+gk+ ++l + l ++a+vl+i G FDd+ ++v++++e+ + ++l lcl|MicrobesOnline__882:208732 156 LTICASTGDTSAAAAlYASYVGSPIKSAVILPHGKVT--PQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALL 232 999*******99876366666777999**********..9*******************************98888888 PP TIGR00260 153 nsvNsinparieaqktyafeiveqlgk.espdkvvvpvp.sgnfgailkGflekkelg....lpieklaiaaegaadiv 225 ns N ri++q +yafe+++ +g+ + + v vp++ +gn++a++ Gfl++++lg lp + ++++ a +++ lcl|MicrobesOnline__882:208732 233 NSKN---SWRILGQESYAFEVAQWYGWdMAGKCVFVPIGnAGNITAVMSGFLKMHRLGiidaLP-RVFGVQSHHADPVY 307 8888...66******************556677999****************************.*************9 PP TIGR00260 226 rrflksg....dlepkedkeTlstAmdignpsnveralelarrslgnledlke...svsdeeileaikklaeeegylle 297 r + + + ep + + +++A ignp++++r+ +la+r + + +v++++i++ + a+++g ++ lcl|MicrobesOnline__882:208732 308 RYYSVEDprqrHYEPVTVQPSVAQAAMIGNPVSFPRVRHLAERFEALGGPGAFqvvQVTEQAIMDSM-IRANRHGHIAC 385 988644311214555555588999999************9999876654322122266766666655.55666666677 PP TIGR00260 298 phtavavaalkklvekgvsatadpaKFeevvealtgnkl 336 + ++ +a+l++ e g +d++ e++v+ t ++l lcl|MicrobesOnline__882:208732 386 TQGGECLAGLLRAKELG---LVDKD--ETAVLDATAHSL 419 8999*********9999...77777..777775555555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (482 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: 13.18 // [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