Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate Echvi_3959 Echvi_3959 dihydrodipicolinate synthase
Query= SwissProt::Q9JZR4 (291 letters) >FitnessBrowser__Cola:Echvi_3959 Length = 286 Score = 221 bits (562), Expect = 2e-62 Identities = 116/279 (41%), Positives = 175/279 (62%), Gaps = 4/279 (1%) Query: 4 GSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIEAV 63 G+ VAL+TP +++G+I Y L +I+ I+ G D +V +GTTGE++T+S +E ++ A Sbjct: 6 GTGVALVTPFDEEGNIDYNGLDKVIEHVIQGGADYLVVMGTTGEASTMSRKEKHDILAAA 65 Query: 64 VKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKTIA 123 VK R+P++ G GANNT AI + +G LSV PYYNKP+QEGIYQH+ +A Sbjct: 66 VKTNNGRLPIVYGIGANNTQAAIDEIDETDLSGVAALLSVSPYYNKPTQEGIYQHYIKVA 125 Query: 124 EATSIPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEGFVV 183 +A+ +P+I+YNVPGRT+ ++T T LRL+E P I+GVKEASG++ +++I + P F++ Sbjct: 126 DASPVPIILYNVPGRTMSNITAATTLRLSEHPKIIGVKEASGDMVQCMDIIRKKPSDFLL 185 Query: 184 LSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIYDTM 243 +SGDD GGHG I+V ANA P +F +C + + +A RL+ I M Sbjct: 186 ISGDDMLTTSLKAIGGHGAISVLANAYPDIFKTICHGSAEESLA----ATFRLLDINAWM 241 Query: 244 FCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVR 282 + E +P K + +G C VRLPL+ TE+ K++ Sbjct: 242 YVESNPVGVKNLLKHMGVCGDQVRLPLLRATESLDKKIK 280 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: 226 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: 286 Length adjustment: 26 Effective length of query: 265 Effective length of database: 260 Effective search space: 68900 Effective search space used: 68900 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 Echvi_3959 Echvi_3959 (dihydrodipicolinate synthase)
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.3198.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-93 299.2 0.1 1.2e-93 299.0 0.1 1.0 1 lcl|FitnessBrowser__Cola:Echvi_3959 Echvi_3959 dihydrodipicolinate s Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_3959 Echvi_3959 dihydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 299.0 0.1 1.2e-93 1.2e-93 4 283 .. 9 283 .. 6 286 .] 0.97 Alignments for each domain: == domain 1 score: 299.0 bits; conditional E-value: 1.2e-93 TIGR00674 4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsn 77 +Al+TPf+e+g++d++ l+k+ie+ i+ g d +vv+GtTGE+ t+s +Ek++++ av+++++r+p++ G+g+n lcl|FitnessBrowser__Cola:Echvi_3959 9 VALVTPFDEEGNIDYNGLDKVIEHVIQGGADYLVVMGTTGEASTMSRKEKHDILAAAVKTNNGRLPIVYGIGAN 82 7************************************************************************* PP TIGR00674 78 ateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaee 151 +t+ ai+ ++e++ +gv+++l+v+PyYnkPtqeG+y+h+ ++a+++ +PiilYnvP+Rt +++ t++rL+e+ lcl|FitnessBrowser__Cola:Echvi_3959 83 NTQAAIDEIDETDLSGVAALLSVSPYYNKPTQEGIYQHYIKVADASPVPIILYNVPGRTMSNITAATTLRLSEH 156 ************************************************************************** PP TIGR00674 152 veivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdtee 225 ++i+++Keasgd+ +++ i+++++ df + sGdD lt+++ a+G++G iSV++n p+ +k +++ +e++ + lcl|FitnessBrowser__Cola:Echvi_3959 157 PKIIGVKEASGDMVQCMDIIRKKPSDFLLISGDDMLTTSLKAIGGHGAISVLANAYPDIFKTICHGSAEESLAA 230 **********************************************************9999999877777766 PP TIGR00674 226 areihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevl 283 +ll++ ++++e+NP++vK +l+ +g++ ++RlPL ++e+ +k+ke lcl|FitnessBrowser__Cola:Echvi_3959 231 T----FRLLDINAWMYVESNPVGVKNLLKHMGVCGD-QVRLPLLRATESLDKKIKELA 283 6....9****************************98.***************999865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (286 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: 00:00:00.00 # Mc/sec: 9.55 // [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