GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Lentibacillus jeotgali Grbi

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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