Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_073040125.1 BUB04_RS12785 threonine synthase
Query= reanno::Miya:8501211 (492 letters) >NCBI__GCF_900129305.1:WP_073040125.1 Length = 499 Score = 569 bits (1467), Expect = e-167 Identities = 290/485 (59%), Positives = 354/485 (72%), Gaps = 10/485 (2%) Query: 15 PTARTRMEYVCLGCGERRGIDELLYTCPSCGGVYLLEDLDFDTLAEQRTGPEWRALFDAR 74 P R Y CLGC G+++LLYTCP C V +++D D+D L + +GP WR +FD R Sbjct: 16 PETAGRYVYRCLGCRATFGVEKLLYTCPECASVLMIQDEDWDRL-KAVSGPTWRRIFDYR 74 Query: 75 AATRTTALRGIFRFYELMAPVLEEEDIVYLGEGNTPIVEAAPVLRDAVGIPFAFKNDGQN 134 A T AL+GI+RF+EL+ +L + ++YLGEG+TP+V+A +RD G PF FKNDGQN Sbjct: 75 AMTTEPALKGIYRFHELLGSILPLDAVIYLGEGHTPVVQANGRMRDWTGRPFFFKNDGQN 134 Query: 135 PSASFKDRGMACAFSYLKALVRKHGWDEVLTVCASTGDTSAAAALYASYVGGPVKSVVLL 194 PSASFKDRGMA AFSYL L++ +VL VCASTGDTSAAAALYASY+ V S VLL Sbjct: 135 PSASFKDRGMASAFSYLNYLIKTQKLSQVLAVCASTGDTSAAAALYASYLVDGVTSAVLL 194 Query: 195 PHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALLNSKNSWRILGQESY 254 PHGKVTPQQLSQPLGSGA V+EIPGVFDDCMK+VE+LAE Y VAL+NSKN+WRILGQESY Sbjct: 195 PHGKVTPQQLSQPLGSGARVIEIPGVFDDCMKIVEYLAERYPVALMNSKNAWRILGQESY 254 Query: 255 AFEVAQWYGWDMKGQCVFVPIGNAGNVTAIMAGFLKLLRLGVIDALPRVIGVQSHHADPV 314 ++E+AQ + +D+ V VPIGNAGN+TA+MAGFLKL LG+I LP ++GVQSHHADPV Sbjct: 255 SYEIAQAFDYDVSDLVVTVPIGNAGNITAVMAGFLKLHDLGIITQLPWILGVQSHHADPV 314 Query: 315 WRYYSQPDPATRTYAPVTVQPSVAQAAMIGNPVSFPRVKALADRFIAEGGERAFSVVQVT 374 +RYY + DP R + PVTVQPSVAQAAMIGNPVS PRV L ++F + GGE+A VVQVT Sbjct: 315 YRYYLESDPQKRVFQPVTVQPSVAQAAMIGNPVSMPRVMQLVEQFRSIGGEKAVQVVQVT 374 Query: 375 EQEIMDAMIRGNRHGHIACTQGGECLAGLIKARELGLVSQGEHAVLDATAHSLKFAGFQD 434 EQEIMDAM+ NR+GHIACTQGGECLAG +A G + G+ VLDATAH+LKFA FQ+ Sbjct: 375 EQEIMDAMLLANRNGHIACTQGGECLAGFRRAVSDGNIPDGKVGVLDATAHALKFAVFQE 434 Query: 435 MYFTNSFPPEYGVTPDASLANAPALVVSPE------DKARLSPE---AYTLAAAKAVVAR 485 YF + F PE+GV P L N P LV P+ + P+ ++ A AV Sbjct: 435 KYFEDRFEPEFGVVPKEELRNRPVLVRPPQGVPCPVPGTAMDPQSFRSFVTATGDAVAEL 494 Query: 486 LGLAK 490 LGL + Sbjct: 495 LGLRR 499 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: 703 Number of extensions: 22 Number of successful extensions: 3 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: 499 Length adjustment: 34 Effective length of query: 458 Effective length of database: 465 Effective search space: 212970 Effective search space used: 212970 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 WP_073040125.1 BUB04_RS12785 (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.23542.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-57 179.1 0.0 8.2e-57 178.8 0.0 1.0 1 lcl|NCBI__GCF_900129305.1:WP_073040125.1 BUB04_RS12785 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900129305.1:WP_073040125.1 BUB04_RS12785 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.8 0.0 8.2e-57 8.2e-57 14 325 .. 100 430 .. 85 436 .. 0.84 Alignments for each domain: == domain 1 score: 178.8 bits; conditional E-value: 8.2e-57 TIGR00260 14 dlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne......tv 76 ++ l eg t++++++ + +++ + k+++ +P+ +FKDrg +a+++++++ l ++ + lcl|NCBI__GCF_900129305.1:WP_073040125.1 100 AVIYLGEGHTPVVQANGRMRDWTGRPFFFKNDGQNPSASFKDRG---MASAFSYLNYLIKTqklsqvLA 165 567899**************************************...*******998877777999899 PP TIGR00260 77 lcAtsGdtgaaaa.ealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeif 144 +cA++Gdt+aaaa +a + +v vL+P+gk+ ++l + l ++a+v++i G FDd+ ++v+ ++ lcl|NCBI__GCF_900129305.1:WP_073040125.1 166 VCASTGDTSAAAAlYASYLVDGVTSAVLLPHGKVT--PQQLSQPLGSGARVIEIPGVFDDCMKIVEYLA 232 9*******987663788889***************..9******************************* PP TIGR00260 145 edkeklklnsvNsinparieaqktyafeiveqlgkespdk.vvvpvp.sgnfgailkGflekkelg... 208 e+ + +++ns N ri++q +y +ei+++ + + +d v+vp++ +gn++a+++Gfl+++ lg lcl|NCBI__GCF_900129305.1:WP_073040125.1 233 ERYPVALMNSKN---AWRILGQESYSYEIAQAFDYDVSDLvVTVPIGnAGNITAVMAGFLKLHDLGiit 298 888888777777...99******************999961579************************* PP TIGR00260 209 .lpieklaiaaegaadivrrflksg.d...lepkedkeTlstAmdignpsnveralelar..rslgnle 270 lp l++++ a +++r +l+s + ++p + + +++A ignp++++r+++l++ rs g + lcl|NCBI__GCF_900129305.1:WP_073040125.1 299 qLP-WILGVQSHHADPVYRYYLESDpQkrvFQPVTVQPSVAQAAMIGNPVSMPRVMQLVEqfRSIGGEK 366 ***.******************99743222445555578899999************766334555555 PP TIGR00260 271 dlke.svsdeeileaikklaeeegyllephtavavaalkklvekg......vs...atadpaKFe 325 +++ +v+++ei++a+ +la+++g ++ + ++ +a+ ++ v +g v+ ata+ KF+ lcl|NCBI__GCF_900129305.1:WP_073040125.1 367 AVQVvQVTEQEIMDAM-LLANRNGHIACTQGGECLAGFRRAVSDGnipdgkVGvldATAHALKFA 430 5544277777777765.566666666668999***********9976654422677888888886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (499 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.95 // [ok]
This GapMind analysis is from Apr 10 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