GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Burkholderia phytofirmans PsJN

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate BPHYT_RS29250 BPHYT_RS29250 dihydrodipicolinate synthase

Query= SwissProt::Q9X1K9
         (294 letters)



>FitnessBrowser__BFirm:BPHYT_RS29250
          Length = 307

 Score =  164 bits (414), Expect = 3e-45
 Identities = 96/296 (32%), Positives = 156/296 (52%), Gaps = 15/296 (5%)

Query: 1   MFRGVGTAIVTPFKNGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVS 60
           +F G+   ++TPF +G +D  +   LVR     G+  L+ LGTTGE   ++  E++ +++
Sbjct: 3   IFSGIWVPLITPFADGAVDHAALRALVRRYTGAGIAGLVALGTTGEPAALDAAEQDAVLA 62

Query: 61  RTLEIV--------DGK-IPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYNKPTQ 111
             L+          DG+ +PV+ G   N T      + Q   L   GVL+  PYY +P+Q
Sbjct: 63  TILDEAQSAAHLARDGQALPVVAGVSGNHTASMRVRIGQLNALPLAGVLMAAPYYIRPSQ 122

Query: 112 EGLYQHYKYISERTDLGIVVYNVPGRTGVNVLPETAARIAADLKNVVGIKEANPDIDQID 171
            G+  H+  +++ ++  +V+Y++P RTGV +  +T   +A   +    I+        +D
Sbjct: 123 AGIVAHFMALADASEKPVVLYDIPYRTGVRLELDTLLALATHPR----IQAVKDCAGSLD 178

Query: 172 RTVSLTKQARSDFMVWSGNDDRTFYLLCAGGDGVISVVSNVAPKQMVELCAEYFSGNLEK 231
            T++L + AR    V +G D   F  LC GG G I+  ++V P++ VE+     +G L  
Sbjct: 179 TTLALIRDAR--LQVLAGEDINIFNTLCLGGSGAIAASAHVRPERFVEMYRALAAGRLAD 236

Query: 232 SREVHRKLRPLMKALFVETNPIPVKAALNLMGFIENELRLPLVPASEKTVELLRNV 287
            R +   L PL++ALFVE NP PVKA L   G I +ELR+P+  AS   +E L  +
Sbjct: 237 GRRIFHALAPLIEALFVEPNPAPVKALLAAQGLIRDELRMPMTRASGALIERLEGL 292


Lambda     K      H
   0.316    0.135    0.378 

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: 183
Number of extensions: 5
Number of successful extensions: 3
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: 307
Length adjustment: 27
Effective length of query: 267
Effective length of database: 280
Effective search space:    74760
Effective search space used:    74760
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 (21.5 bits)
S2: 48 (23.1 bits)

Align candidate BPHYT_RS29250 BPHYT_RS29250 (dihydrodipicolinate 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.29910.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    1.1e-73  233.5   0.0    1.3e-73  233.3   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS29250  BPHYT_RS29250 dihydrodipicolinat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS29250  BPHYT_RS29250 dihydrodipicolinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.3   0.0   1.3e-73   1.3e-73       4     279 ..       9     289 ..       6     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 233.3 bits;  conditional E-value: 1.3e-73
                                TIGR00674   4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvkn....... 66 
                                              + liTPf +   vd aal  l+++   +g+ ++v++GtTGE a+L   E+ +v+ + ++ ++        
  lcl|FitnessBrowser__BFirm:BPHYT_RS29250   9 VPLITPFADGA-VDHAALRALVRRYTGAGIAGLVALGTTGEPAALDAAEQDAVLATILDEAQSaahlard 77 
                                              679****8877.***********************************************99999999999 PP

                                TIGR00674  67 ..rvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPs 134
                                                 +pv+aG+++n t+     + +++ l+ +gvl+ +PyY +P+q G+++hf a+a+++e+P++lY++P 
  lcl|FitnessBrowser__BFirm:BPHYT_RS29250  78 gqALPVVAGVSGNHTASMRVRIGQLNALPLAGVLMAAPYYIRPSQAGIVAHFMALADASEKPVVLYDIPY 147
                                              999*************999999************************************************ PP

                                TIGR00674 135 RtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVas 204
                                              Rtgv le +t+++La++++i a+K+++g+l+    +++ a   ++vl+G+D    + l+lG++G i   +
  lcl|FitnessBrowser__BFirm:BPHYT_RS29250 148 RTGVRLELDTLLALATHPRIQAVKDCAGSLDTTLALIRDA--RLQVLAGEDINIFNTLCLGGSGAIAASA 215
                                              *********************************9999966..5*************************** PP

                                TIGR00674 205 nvapkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelsee 274
                                              +v p+++ em++a ++g+ ++ r i + l +l++alf+e+NP pvK++la++gli   elR+P+t +s  
  lcl|FitnessBrowser__BFirm:BPHYT_RS29250 216 HVRPERFVEMYRALAAGRLADGRRIFHALAPLIEALFVEPNPAPVKALLAAQGLIRD-ELRMPMTRASGA 284
                                              ********************************************************9.*******99977 PP

                                TIGR00674 275 kkekl 279
                                                e+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS29250 285 LIERL 289
                                              66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (307 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.94
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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