GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Nitratiruptor tergarcus DSM 16512

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_084276196.1 B8779_RS08465 4-hydroxy-tetrahydrodipicolinate synthase

Query= BRENDA::O67216
         (294 letters)



>NCBI__GCF_900176045.1:WP_084276196.1
          Length = 295

 Score =  264 bits (674), Expect = 2e-75
 Identities = 136/290 (46%), Positives = 194/290 (66%), Gaps = 3/290 (1%)

Query: 3   QGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFA 62
           +G++ ALITPFK+G+VD E    LI+  +D+  D ++  GTTGES TLT +EH+K IE A
Sbjct: 5   KGAMTALITPFKDGKVDEEKYAKLIQRQIDHAIDVVVPVGTTGESATLTHDEHKKCIEIA 64

Query: 63  VKRAAGR-IKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTV 121
           V+   G   KV+AG G N+THEA+ L   A++ GAD  L V PYYNKPTQ GLY+H+K +
Sbjct: 65  VEVCKGTSTKVMAGAGSNSTHEAIDLAQFAQKAGADAILSVSPYYNKPTQEGLYQHYKAL 124

Query: 122 AQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESF 181
           A  VDIP+++YN+P RT V+I  +T+F+L  E ENI   KE+T +++R  E++ +  E +
Sbjct: 125 ANAVDIPVLLYNVPGRTGVDIKPETVFRLFDEVENIYGIKEATGSIERCVELLAKRPELY 184

Query: 182 SVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFK 241
            V+SGDD++  P++A G  GVISV  N++P ++  L+ A L G F  A+ I+  L D+ K
Sbjct: 185 -VISGDDTINYPIIANGGMGVISVTANLLPDKMSMLVHAGLAGQFDTAKMINDELFDINK 243

Query: 242 VLFIETNPIPVKTACWMLGMCEK-EFRLPLTEMSPENENKLREVLKKYNL 290
            LFIE+NPIP+K A +  G+ +  E+RLPL   S EN  K+   L KY +
Sbjct: 244 ALFIESNPIPIKAAMYHAGLLDTLEYRLPLVPPSKENMAKIENALTKYKV 293


Lambda     K      H
   0.318    0.136    0.390 

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: 244
Number of extensions: 13
Number of successful extensions: 4
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: 294
Length of database: 295
Length adjustment: 26
Effective length of query: 268
Effective length of database: 269
Effective search space:    72092
Effective search space used:    72092
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_084276196.1 B8779_RS08465 (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.238864.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-113  362.1   0.2   8.5e-113  361.9   0.2    1.0  1  NCBI__GCF_900176045.1:WP_084276196.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900176045.1:WP_084276196.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.9   0.2  8.5e-113  8.5e-113       2     285 ..       7     290 ..       6     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 361.9 bits;  conditional E-value: 8.5e-113
                             TIGR00674   2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvkn.rvpviaG 73 
                                            +tAliTPfk+ + vd ++++kli++qi++ +d +v+vGtTGEsatL+++E+kk+ie+ave++k+   +v+aG
  NCBI__GCF_900176045.1:WP_084276196.1   7 AMTALITPFKDGK-VDEEKYAKLIQRQIDHAIDVVVPVGTTGESATLTHDEHKKCIEIAVEVCKGtSTKVMAG 78 
                                           689******9988.**************************************************95689**** PP

                             TIGR00674  74 tgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvk 146
                                           +gsn+t+eai+l+++a+k+g+d++l+v+PyYnkPtqeGly+h+ka+a++v++P++lYnvP+Rtgv+++petv+
  NCBI__GCF_900176045.1:WP_084276196.1  79 AGSNSTHEAIDLAQFAQKAGADAILSVSPYYNKPTQEGLYQHYKALANAVDIPVLLYNVPGRTGVDIKPETVF 151
                                           ************************************************************************* PP

                             TIGR00674 147 rLaeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaa 218
                                           rL++eve i +iKea+g++er++e+ a+ + +++v sGdD+++ +i+a G+ GviSV++n++p++++ +v+a 
  NCBI__GCF_900176045.1:WP_084276196.1 152 RLFDEVEnIYGIKEATGSIERCVELLAKRP-ELYVISGDDTINYPIIANGGMGVISVTANLLPDKMSMLVHAG 223
                                           *****999*******************998.9***************************************** PP

                             TIGR00674 219 legdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285
                                           l+g+++ a+ i+ +l+++ kalfie+NPip+K+a++ +gl  + e+RlPL++ s+e+  k++++l++
  NCBI__GCF_900176045.1:WP_084276196.1 224 LAGQFDTAKMINDELFDINKALFIESNPIPIKAAMYHAGLLDTLEYRLPLVPPSKENMAKIENALTK 290
                                           ***************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (295 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.62
//
[ok]

This GapMind analysis is from Jul 25 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