Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate Ac3H11_277 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
Query= SwissProt::Q9JZR4 (291 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_277 Length = 299 Score = 323 bits (827), Expect = 4e-93 Identities = 160/291 (54%), Positives = 208/291 (71%), Gaps = 1/291 (0%) Query: 2 LQGSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIE 61 L GS+VAL+TPM+ DGS+ Y LR LIDWHI GTD I VGTTGES T++VEEH +I Sbjct: 8 LTGSIVALVTPMHADGSVDYPALRKLIDWHIAEGTDCIGVVGTTGESPTVNVEEHCEIIR 67 Query: 62 AVVKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKT 121 V+ AKRVP++AG GAN+T EAI L++ A GAD L VVPYYNKP+QEG +QHFK Sbjct: 68 VAVEQSAKRVPIMAGCGANSTAEAIELAKFARGVGADSQLQVVPYYNKPTQEGQFQHFKA 127 Query: 122 IAEATS-IPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEG 180 IAEAT +P+++YNVPGR+V M +DT+LRLA++P I+G+KEA+GNI LI P+G Sbjct: 128 IAEATGDLPIVLYNVPGRSVADMQHDTVLRLAQVPGIIGIKEATGNIERAQWLIRDVPQG 187 Query: 181 FVVLSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIY 240 F V SGDD TA+ MLCGGHG I+V AN AP+L ++C AAL GD A E+ +L+P++ Sbjct: 188 FGVYSGDDPTAVALMLCGGHGNISVTANVAPRLMHELCVAALAGDARRAMEIQFKLMPVH 247 Query: 241 DTMFCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVRAALKASGQL 291 +F E +P KWA++ +G C +RLP+ PL +A V AAL++SG L Sbjct: 248 KNLFVEANPIPVKWAMARMGLCGGTMRLPMTPLASGNEAVVEAALRSSGLL 298 Lambda K H 0.317 0.133 0.386 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: 315 Number of extensions: 8 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: 291 Length of database: 299 Length adjustment: 26 Effective length of query: 265 Effective length of database: 273 Effective search space: 72345 Effective search space used: 72345 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate Ac3H11_277 (4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
# 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/TIGR00674.hmm # target sequence database: /tmp/gapView.21303.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00674 [M=286] Accession: TIGR00674 Description: dapA: 4-hydroxy-tetrahydrodipicolinate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-112 361.0 0.0 1.8e-112 360.8 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277 4-hydroxy-tetrahydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 360.8 0.0 1.8e-112 1.8e-112 1 284 [. 10 293 .. 10 295 .. 0.99 Alignments for each domain: == domain 1 score: 360.8 bits; conditional E-value: 1.8e-112 TIGR00674 1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavel 63 g+++Al+TP+++dgsvd+ al kli+ +i++g+d i vvGtTGEs+t ++eE+ ++i+vave lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277 10 GSIVALVTPMHADGSVDYPALRKLIDWHIAEGTDCIGVVGTTGESPTVNVEEHCEIIRVAVEQ 72 589************************************************************ PP TIGR00674 64 vknrvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeev.el 125 +++rvp++aG+g+n+t+eaiel+k+a+ +g+d+ l+v+PyYnkPtqeG+++hfkaiae++ +l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277 73 SAKRVPIMAGCGANSTAEAIELAKFARGVGADSQLQVVPYYNKPTQEGQFQHFKAIAEATgDL 135 ***********************************************************99** PP TIGR00674 126 PiilYnvPsRtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDalt 188 Pi+lYnvP+R++++++ +tv+rLa+ + i++iKea+g++er++ +++ +++ f v+sGdD ++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277 136 PIVLYNVPGRSVADMQHDTVLRLAQVPGIIGIKEATGNIERAQWLIRDVPQGFGVYSGDDPTA 198 *************************************************************** PP TIGR00674 189 leilalGakGviSVasnvapkelkemvkaalegdteeareihqkllklfkalfietNPipvKt 251 +++++G++G iSV++nvap++++e++ aal+gd ++a ei+ kl++++k lf+e+NPipvK+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277 199 VALMLCGGHGNISVTANVAPRLMHELCVAALAGDARRAMEIQFKLMPVHKNLFVEANPIPVKW 261 *************************************************************** PP TIGR00674 252 alallgliekdelRlPLtelseekkeklkevlk 284 a+a +gl+ + ++RlP+t+l + ++ ++++l+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_277 262 AMARMGLCGG-TMRLPMTPLASGNEAVVEAALR 293 **********.****************999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (299 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8.10 // [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