Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate WP_011868494.1 MMARC5_RS03685 4-hydroxy-tetrahydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >NCBI__GCF_000016125.1:WP_011868494.1 Length = 270 Score = 200 bits (508), Expect = 3e-56 Identities = 113/272 (41%), Positives = 167/272 (61%), Gaps = 9/272 (3%) Query: 6 IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65 ++VA+ GA GRMG +I+ +G+ + AA++ G D GEL G GK GV + +S Sbjct: 2 VKVAVTGALGRMGSGIIKTITETDGLDVVAAIDIPNHPKKGLDIGELTGVGKIGVALSTS 61 Query: 66 --LDAV--KDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAAD- 120 L+ V + +V +DFT P +N + G +VIGTTGF + + +A ++ Sbjct: 62 DELEVVLKESGAEVLVDFTAPAPCVNTAKTAAKLGVNLVIGTTGFTSEQRAEMENAISEN 121 Query: 121 -IAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIA 179 +A + N++VGVN+ K LE A+ +GDY DIE+IE HH+ K DAPSGTAL E I Sbjct: 122 KVAATISQNYAVGVNIFFKTLELLAQKLGDY-DIELIEMHHKFKKDAPSGTALRAAEIIQ 180 Query: 180 HALDKDLKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASS 239 + L++D ++ R+G TGER I +R GD+VG+HTAMFA GERLE+THKASS Sbjct: 181 NNLNRDSN--LIFGRKGITGERTKEEICIHALRGGDVVGDHTAMFAADGERLELTHKASS 238 Query: 240 RMTFANGAVRSALWLSGKESGLFDMRDVLDLN 271 R +F +G + + +++ K+ G+++ DVLDLN Sbjct: 239 RQSFISGVILAVKFVAEKKEGIYNTFDVLDLN 270 Lambda K H 0.319 0.135 0.383 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: 207 Number of extensions: 10 Number of successful extensions: 5 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: 273 Length of database: 270 Length adjustment: 25 Effective length of query: 248 Effective length of database: 245 Effective search space: 60760 Effective search space used: 60760 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: 47 (22.7 bits)
Align candidate WP_011868494.1 MMARC5_RS03685 (4-hydroxy-tetrahydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))
# 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/TIGR00036.hmm # target sequence database: /tmp/gapView.27821.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00036 [M=270] Accession: TIGR00036 Description: dapB: 4-hydroxy-tetrahydrodipicolinate reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-108 346.9 5.7 4.8e-108 346.8 5.7 1.0 1 lcl|NCBI__GCF_000016125.1:WP_011868494.1 MMARC5_RS03685 4-hydroxy-tetrahy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016125.1:WP_011868494.1 MMARC5_RS03685 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 346.8 5.7 4.8e-108 4.8e-108 1 270 [] 1 268 [. 1 268 [. 0.99 Alignments for each domain: == domain 1 score: 346.8 bits; conditional E-value: 4.8e-108 TIGR00036 1 likvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvla 69 ++kvav+Ga GrmG+ +ik+++e+++l++vaa++ ++++k+g DiGel+g+gk+gv+++++ e++ vl+ lcl|NCBI__GCF_000016125.1:WP_011868494.1 1 MVKVAVTGALGRMGSGIIKTITETDGLDVVAAIDIPNHPKKGLDIGELTGVGKIGVALSTSDELEVVLK 69 58******************************************************************* PP TIGR00036 70 ekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnll 138 e+ a+vl+Dft p +++++k+a++ gv+lV+GTTGf+ e+++e+++++++++va+ i++N+a+Gvn++ lcl|NCBI__GCF_000016125.1:WP_011868494.1 70 ESGAEVLVDFTAPAPCVNTAKTAAKLGVNLVIGTTGFTSEQRAEMENAISENKVAATISQNYAVGVNIF 138 ********************************************************************* PP TIGR00036 139 lkllekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeei 207 +k+le +a++l+d+DiE+iE+HH+ KkDaPSGTAl++aeii+++ ++ +++++ +r+g+tGer+keei lcl|NCBI__GCF_000016125.1:WP_011868494.1 139 FKTLELLAQKLGDYDIELIEMHHKFKKDAPSGTALRAAEIIQNNLNR--DSNLIFGRKGITGERTKEEI 205 **********************************************6..7889**************** PP TIGR00036 208 GiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 i+a+Rggdvvg+ht +Fa dGerle+tHkassR++f++Gv++a++++++k+e++y++ dvld lcl|NCBI__GCF_000016125.1:WP_011868494.1 206 CIHALRGGDVVGDHTAMFAADGERLELTHKASSRQSFISGVILAVKFVAEKKEGIYNTFDVLD 268 *************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (270 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.28 // [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