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.13821.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.73
//
[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