Alignments for a candidate for dapA in Burkholderia phytofirmans PsJN

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.31869.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: 7.38
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis