GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Burkholderia phytofirmans PsJN

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate BPHYT_RS12615 BPHYT_RS12615 dihydrodipicolinate synthase

Query= BRENDA::Q9I4W3
         (292 letters)



>FitnessBrowser__BFirm:BPHYT_RS12615
          Length = 308

 Score =  348 bits (892), Expect = e-100
 Identities = 174/290 (60%), Positives = 217/290 (74%)

Query: 2   IAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIR 61
           I GS+ A++TP    G LD  +  KL+D+H+ EGTNA+V VGT+GESATL VEEH+ +++
Sbjct: 18  IRGSIPAIITPMLEDGSLDLPAFRKLIDWHIAEGTNALVVVGTSGESATLSVEEHVLMVK 77

Query: 62  RVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRH 121
             V+   GRIPVIAG+G NST EA+ LT+ AK  GADA L V PYYNKPTQEG+Y+HF  
Sbjct: 78  TAVEHTAGRIPVIAGSGGNSTTEAIELTQQAKEVGADATLQVVPYYNKPTQEGIYRHFAK 137

Query: 122 IAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDF 181
           IAE V +P ILYNVPGRT  DM  +T+ R ++VP IIG+KEATG++ RA  +I+   K F
Sbjct: 138 IAETVDLPVILYNVPGRTVADMSNDTILRCAQVPGIIGVKEATGNIDRAAHLIKSAPKHF 197

Query: 182 LVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHK 241
            +YSGDD TA+ LMLLGG GNISVTANVAPRAMSDLC AA+  DA  AR I+ +L+ LHK
Sbjct: 198 GIYSGDDPTAIALMLLGGHGNISVTANVAPRAMSDLCKAALAADAKTAREIHLKLLSLHK 257

Query: 242 ALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291
            LFIESNPIP KWAL ++G +  GIRLPLT L  + HE +R A+R+ G+L
Sbjct: 258 NLFIESNPIPAKWALQQLGRVQGGIRLPLTPLDAQYHEVVRGALREAGLL 307


Lambda     K      H
   0.319    0.134    0.393 

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: 297
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: 308
Length adjustment: 27
Effective length of query: 265
Effective length of database: 281
Effective search space:    74465
Effective search space used:    74465
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: 48 (23.1 bits)

Align candidate BPHYT_RS12615 BPHYT_RS12615 (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.29366.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   4.7e-112  359.5   0.0   5.3e-112  359.3   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS12615  BPHYT_RS12615 dihydrodipicolinat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS12615  BPHYT_RS12615 dihydrodipicolinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.3   0.0  5.3e-112  5.3e-112       1     285 [.      20     303 ..      20     304 .. 0.99

  Alignments for each domain:
  == domain 1  score: 359.3 bits;  conditional E-value: 5.3e-112
                                TIGR00674   1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 
                                              g+++A+iTP+ edgs+d+ a+ kli+ +i++g++a+vvvGt GEsatLs+eE++ ++++ave +++r+pv
  lcl|FitnessBrowser__BFirm:BPHYT_RS12615  20 GSIPAIITPMLEDGSLDLPAFRKLIDWHIAEGTNALVVVGTSGESATLSVEEHVLMVKTAVEHTAGRIPV 89 
                                              589******************************************************************* PP

                                TIGR00674  71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvsl 140
                                              iaG g+n+t+eaielt++a+++g+d++l+v+PyYnkPtqeG+y+hf +iae+v+lP+ilYnvP+Rt++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS12615  90 IAGSGGNSTTEAIELTQQAKEVGADATLQVVPYYNKPTQEGIYRHFAKIAETVDLPVILYNVPGRTVADM 159
                                              ********************************************************************** PP

                                TIGR00674 141 epetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapke 210
                                              + +t++r a+ + i+++Kea+g+++r+ ++++ a+++f ++sGdD ++ ++++lG++G iSV++nvap+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS12615 160 SNDTILRCAQVPGIIGVKEATGNIDRAAHLIKSAPKHFGIYSGDDPTAIALMLLGGHGNISVTANVAPRA 229
                                              ********************************************************************** PP

                                TIGR00674 211 lkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklk 280
                                              +++++kaal+ d + areih kll+l+k lfie+NPip K+al+ lg +++  +RlPLt+l+ + +e ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS12615 230 MSDLCKAALAADAKTAREIHLKLLSLHKNLFIESNPIPAKWALQQLGRVQG-GIRLPLTPLDAQYHEVVR 298
                                              ***************************************************.**************9999 PP

                                TIGR00674 281 evlke 285
                                               +l+e
  lcl|FitnessBrowser__BFirm:BPHYT_RS12615 299 GALRE 303
                                              88875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (308 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: 7.03
//
[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