Align dihydrodipicolinate synthase; EC 4.2.1.52 (characterized)
to candidate WP_010530679.1 ON01_RS08885 4-hydroxy-tetrahydrodipicolinate synthase
Query= CharProtDB::CH_021853 (292 letters) >NCBI__GCF_000224785.1:WP_010530679.1 Length = 288 Score = 360 bits (923), Expect = e-104 Identities = 167/285 (58%), Positives = 231/285 (81%) Query: 4 FGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYR 63 FG + TAMVTPFD N +DFAKTTKL+ +L++NG+ +VVGGTTGESPTLT++EK+AL+R Sbjct: 3 FGNLLTAMVTPFDANNQVDFAKTTKLIEHLLENGSEGLVVGGTTGESPTLTTDEKIALFR 62 Query: 64 HVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHFKA 123 H V VV++RVPVIAG+GSN+T ASI LTK A + GVD VMLVAPYYNKP+QEG+Y HF A Sbjct: 63 HTVKVVNRRVPVIAGSGSNSTQASITLTKAAEKSGVDGVMLVAPYYNKPNQEGLYHHFAA 122 Query: 124 IAESTPLPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADDF 183 IA T LPVMLYNVPGR++V+IS +T++RLS+I+NIV++KDA GD+ ++ +IE DDF Sbjct: 123 IAGETRLPVMLYNVPGRTVVKISAETIIRLSQIDNIVSVKDASGDLDLVSNVIEHADDDF 182 Query: 184 AVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVTD 243 +VYSG+D +TLP +A+G G+VSV +H+ GN+M+ M+ A+Q+G+ +A +H+ L+ V + Sbjct: 183 SVYSGEDSITLPLLALGGDGVVSVVAHIAGNDMKGMVNAYQSGDVVRAASIHRKLLPVMN 242 Query: 244 SLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQ 288 +F PSP PVKTAL + G++VG VRLPL+ +++ ER TL++++Q Sbjct: 243 GMFAQPSPVPVKTALNITGVNVGGVRLPLMAMSDAERETLRNLIQ 287 Lambda K H 0.316 0.132 0.362 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: 273 Number of extensions: 7 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: 288 Length adjustment: 26 Effective length of query: 266 Effective length of database: 262 Effective search space: 69692 Effective search space used: 69692 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 (21.6 bits) S2: 48 (23.1 bits)
Align candidate WP_010530679.1 ON01_RS08885 (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.3893720.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-113 362.0 0.3 9.1e-113 361.8 0.3 1.0 1 NCBI__GCF_000224785.1:WP_010530679.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010530679.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 361.8 0.3 9.1e-113 9.1e-113 2 284 .. 6 287 .. 5 288 .] 0.99 Alignments for each domain: == domain 1 score: 361.8 bits; conditional E-value: 9.1e-113 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGt 74 +ltA++TPf+++++vdfa+ klie+++e+g++++vv GtTGEs+tL+++Ek+++++ +v++v+ rvpviaG NCBI__GCF_000224785.1:WP_010530679.1 6 LLTAMVTPFDANNQVDFAKTTKLIEHLLENGSEGLVVGGTTGESPTLTTDEKIALFRHTVKVVNRRVPVIAGS 78 79*********************************************************************** PP TIGR00674 75 gsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkr 147 gsn+t+ +i+ltk aek+gvdgv++v+PyYnkP+qeGly+hf aia e++lP++lYnvP+Rt+v+++ et++r NCBI__GCF_000224785.1:WP_010530679.1 79 GSNSTQASITLTKAAEKSGVDGVMLVAPYYNKPNQEGLYHHFAAIAGETRLPVMLYNVPGRTVVKISAETIIR 151 ************************************************************************* PP TIGR00674 148 LaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaale 220 L++ +iv++K+asgdl+ vs+++++a++df+v+sG+D++tl++lalG+ Gv+SV++++a++++k mv+a++ NCBI__GCF_000224785.1:WP_010530679.1 152 LSQIDNIVSVKDASGDLDLVSNVIEHADDDFSVYSGEDSITLPLLALGGDGVVSVVAHIAGNDMKGMVNAYQS 224 ************************************************************************* PP TIGR00674 221 gdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlk 284 gd+ +a+ ih+kll++++ +f ++ P+pvKtal+++g+ ++ +RlPL+++s+ ++e+l++ ++ NCBI__GCF_000224785.1:WP_010530679.1 225 GDVVRAASIHRKLLPVMNGMFAQPSPVPVKTALNITGVNVG-GVRLPLMAMSDAERETLRNLIQ 287 *****************************************.*****************99886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (288 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: 00:00:00.00 # Mc/sec: 11.92 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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