Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_006746078.1 THITH_RS02525 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q9I4W3 (292 letters) >NCBI__GCF_000227685.2:WP_006746078.1 Length = 294 Score = 392 bits (1006), Expect = e-114 Identities = 192/290 (66%), Positives = 234/290 (80%) Query: 1 MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60 M GSMVALVTP G +D +SL +LVD+H+ GT+AIVAVGTTGESATLD +EH VI Sbjct: 1 MFQGSMVALVTPMQPDGSIDHESLQRLVDWHIDAGTDAIVAVGTTGESATLDFDEHCMVI 60 Query: 61 RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFR 120 RVV+ VKGR+PVIAGTGAN+TREA+ LT A+ GADACLLVTPYYNKPTQEG+Y+H+R Sbjct: 61 ARVVEHVKGRLPVIAGTGANATREAIELTRCARDAGADACLLVTPYYNKPTQEGLYRHYR 120 Query: 121 HIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKD 180 +AEAV IPQILYNVPGRT+ D+LPETVERL+ VPNI+G+KEA G +R +E++ERVG Sbjct: 121 AVAEAVEIPQILYNVPGRTAVDLLPETVERLAGVPNIVGLKEALGSPERTRELVERVGGR 180 Query: 181 FLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLH 240 +YSGDDATA++ +L GG+G ISVTANVAP M ++CA A+ GDA+ AR +NDRL LH Sbjct: 181 LELYSGDDATALDFLLAGGQGVISVTANVAPALMHEMCALALAGDASRAREVNDRLDGLH 240 Query: 241 KALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGV 290 ALF+E+NPIPVKWA +GLIPEGIRLPLT LS H P+ +AMR+ G+ Sbjct: 241 HALFLEANPIPVKWATARLGLIPEGIRLPLTPLSEPFHAPVLEAMRRAGI 290 Lambda K H 0.319 0.134 0.393 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: 359 Number of extensions: 8 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: 292 Length of database: 294 Length adjustment: 26 Effective length of query: 266 Effective length of database: 268 Effective search space: 71288 Effective search space used: 71288 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: 48 (23.1 bits)
Align candidate WP_006746078.1 THITH_RS02525 (4-hydroxy-tetrahydrodipicolinate 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.13171.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-113 364.6 0.0 1.5e-113 364.3 0.0 1.0 1 lcl|NCBI__GCF_000227685.2:WP_006746078.1 THITH_RS02525 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000227685.2:WP_006746078.1 THITH_RS02525 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 364.3 0.0 1.5e-113 1.5e-113 2 274 .. 5 276 .. 4 287 .. 0.98 Alignments for each domain: == domain 1 score: 364.3 bits; conditional E-value: 1.5e-113 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 +++Al+TP++ dgs+d ++l++l++ +i++g+daiv+vGtTGEsatL ++E+ vi +ve vk+r+pv lcl|NCBI__GCF_000227685.2:WP_006746078.1 5 SMVALVTPMQPDGSIDHESLQRLVDWHIDAGTDAIVAVGTTGESATLDFDEHCMVIARVVEHVKGRLPV 73 799****************************************************************** PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 iaGtg+nat+eaielt+ a+++g+d++l+vtPyYnkPtqeGly+h+ a+ae+ve+P+ilYnvP+Rt+v+ lcl|NCBI__GCF_000227685.2:WP_006746078.1 74 IAGTGANATREAIELTRCARDAGADACLLVTPYYNKPTQEGLYRHYRAVAEAVEIPQILYNVPGRTAVD 142 ********************************************************************* PP TIGR00674 140 lepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvap 208 l petv rLa ++iv++Kea g+ er e++++++ ++++sGdDa++l++l+ G++GviSV++nvap lcl|NCBI__GCF_000227685.2:WP_006746078.1 143 LLPETVERLAGVPNIVGLKEALGSPERTRELVERVGGRLELYSGDDATALDFLLAGGQGVISVTANVAP 211 ********************************************************************* PP TIGR00674 209 kelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelsee 274 +++em++ al+gd ++are++ +l l++alf+e+NPipvK+a a lgli + +RlPLt+lse lcl|NCBI__GCF_000227685.2:WP_006746078.1 212 ALMHEMCALALAGDASRAREVNDRLDGLHHALFLEANPIPVKWATARLGLIPE-GIRLPLTPLSEP 276 ***************************************************99.9*******9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (294 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: 6.57 // [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