Alignments for a candidate for dapE in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Burkholderia phytofirmans PsJN

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate BPHYT_RS12200 BPHYT_RS12200 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__BFirm:BPHYT_RS12200
          Length = 379

 Score =  470 bits (1209), Expect = e-137
 Identities = 231/376 (61%), Positives = 281/376 (74%), Gaps = 4/376 (1%)

Query: 6   SLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRR----GTKAP 61
           +L L ++LI+R SVTPDD+ CQ+LL ERL  +GF  E +      N+W  +    GT   
Sbjct: 4   TLALTEQLIARASVTPDDQHCQRLLIERLAALGFEHETIESNGVTNLWAVKRGVDGTAGK 63

Query: 62  VVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHP 121
           ++ FAGHTDVVPTGP+E+W S PFEP  RDG+LYGRGAADMK SIA FV A E FVA HP
Sbjct: 64  LLAFAGHTDVVPTGPLEQWRSAPFEPTHRDGKLYGRGAADMKASIAGFVVASEEFVAAHP 123

Query: 122 NHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRG 181
            H+G+IA LITSDEEG A DGT KVV+ L+ R E +DYCIVGEPT+  + GDM+KNGRRG
Sbjct: 124 AHRGTIAFLITSDEEGPATDGTVKVVEALQERGERMDYCIVGEPTSSAQFGDMVKNGRRG 183

Query: 182 SLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGG 241
           S+SG L VKG QGHIAYPHLA NPVH  APAL EL  E WD+GNEYFPPT++Q+SNI+ G
Sbjct: 184 SMSGKLIVKGVQGHIAYPHLAKNPVHLLAPALAELVAERWDDGNEYFPPTTWQVSNIHSG 243

Query: 242 TGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGK 301
           TGATNVIPG  +V FNFRFST ST  GL+ RVHAILDKHG++YDLQW+ SG PFLT  G 
Sbjct: 244 TGATNVIPGHADVMFNFRFSTASTVEGLQARVHAILDKHGLEYDLQWTVSGLPFLTPRGD 303

Query: 302 LTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDI 361
           L++    AI +  G+  ELSTTGGTSDGRFI  I +++IE GP NA+IH+I+E++ +  I
Sbjct: 304 LSNALAKAIKDETGLNTELSTTGGTSDGRFIARICKQVIEFGPLNASIHKIDEHIEVAHI 363

Query: 362 PKLSAVYEGILARLLA 377
             L  VY  +L +L+A
Sbjct: 364 EPLKNVYRRVLEQLIA 379


Lambda     K      H
   0.317    0.135    0.400 

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: 496
Number of extensions: 17
Number of successful extensions: 2
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: 381
Length of database: 379
Length adjustment: 30
Effective length of query: 351
Effective length of database: 349
Effective search space:   122499
Effective search space used:   122499
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: 50 (23.9 bits)

Align candidate BPHYT_RS12200 BPHYT_RS12200 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

# 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/TIGR01246.hmm
# target sequence database:        /tmp/gapView.24845.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01246  [M=370]
Accession:   TIGR01246
Description: dapE_proteo: succinyl-diaminopimelate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   4.8e-164  531.6   0.0   5.5e-164  531.5   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS12200  BPHYT_RS12200 succinyl-diaminopi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS12200  BPHYT_RS12200 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.5   0.0  5.5e-164  5.5e-164       3     370 .]       6     377 ..       4     377 .. 0.98

  Alignments for each domain:
  == domain 1  score: 531.5 bits;  conditional E-value: 5.5e-164
                                TIGR01246   3 elakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt....eepvlvfaGhtDvvP 68 
                                              +l+++Li r svtP+d+ +q l++erL +lgfe e++e ++++nlwa ++       + l+faGhtDvvP
  lcl|FitnessBrowser__BFirm:BPHYT_RS12200   6 ALTEQLIARASVTPDDQHCQRLLIERLAALGFEHETIESNGVTNLWAVKRGvdgtAGKLLAFAGHTDVVP 75 
                                              6899******************************************9765445558899*********** PP

                                TIGR01246  69 aGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGt 138
                                              +G+le+W+s pfep++rdGklygrGaaDmk+s+a fvva+e+fv++++ h+G++++litsDeeg a dGt
  lcl|FitnessBrowser__BFirm:BPHYT_RS12200  76 TGPLEQWRSAPFEPTHRDGKLYGRGAADMKASIAGFVVASEEFVAAHPAHRGTIAFLITSDEEGPATDGT 145
                                              ********************************************************************** PP

                                TIGR01246 139 kkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvl 208
                                              +kvve l+er e +dy++vgeP+s+ + GD++k+GrrGs++gkl +kG+qGh+aYPh+a+nPvh ++p+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS12200 146 VKVVEALQERGERMDYCIVGEPTSSAQFGDMVKNGRRGSMSGKLIVKGVQGHIAYPHLAKNPVHLLAPAL 215
                                              ********************************************************************** PP

                                TIGR01246 209 keliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkld 278
                                              +el+a+++D+Gne+fpp+  q++ni++gtga+nviPg+++v+fn+rfs+ +++e l+ +v++ildkh+l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS12200 216 AELVAERWDDGNEYFPPTTWQVSNIHSGTGATNVIPGHADVMFNFRFSTASTVEGLQARVHAILDKHGLE 285
                                              ********************************************************************** PP

                                TIGR01246 279 YelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvn 348
                                              Y+l+w++sg pflt +g+l +++a+ai+  ++ ++elst+GGtsD+rfia++  +v+e+G++n++ihk++
  lcl|FitnessBrowser__BFirm:BPHYT_RS12200 286 YDLQWTVSGLPFLTPRGDLSNALAKAIKDETGLNTELSTTGGTSDGRFIARICKQVIEFGPLNASIHKID 355
                                              ********************************************************************** PP

                                TIGR01246 349 eavkiedleklsevyeklleel 370
                                              e+++++ +e l++vy+++le+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS12200 356 EHIEVAHIEPLKNVYRRVLEQL 377
                                              *******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (379 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.67
//
[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