Alignments for a candidate for dapE in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Acidovorax sp. GW101-3H11

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate Ac3H11_2298 N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18)

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2298
          Length = 397

 Score =  442 bits (1137), Expect = e-129
 Identities = 226/394 (57%), Positives = 279/394 (70%), Gaps = 16/394 (4%)

Query: 4   TQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDT----KNIWLRRG-- 57
           +++L LA++LI+ PS+TPDD  C  LLA RL  +GF  E L  G       N+W +R   
Sbjct: 2   SRTLHLAEQLIALPSITPDDAGCLNLLAARLAPLGFECERLDSGPADFRVSNLWAKRPLP 61

Query: 58  ------TKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVT 111
                      V FAGHTDVVPTGP+ +W S PF P  +DG+LYGRGA+DMKTSIA FV 
Sbjct: 62  RDQLAQAAIKTVVFAGHTDVVPTGPLAQWSSDPFVPTHKDGKLYGRGASDMKTSIAAFVV 121

Query: 112 ACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKL 171
           A E F+A  P     +A L+TSDEEG ++DGT  VV+ LKAR E +DYCIVGEPT+V+K 
Sbjct: 122 AVEEFLAATPEPLVQLAFLLTSDEEGPSVDGTKVVVEQLKARGEPLDYCIVGEPTSVEKT 181

Query: 172 GDMIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPT 231
           GDMIKNGRRG+LSG L+V+G QGHIAYP LA NP+H   PAL EL   VWD GN +FPPT
Sbjct: 182 GDMIKNGRRGTLSGKLSVRGIQGHIAYPQLARNPIHQALPALAELAATVWDHGNAFFPPT 241

Query: 232 SFQISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCS 291
           S+QISN++GGTGATNVIPGE+ + FNFRFSTEST  GL+QRVHA+LD+HG++YDL+W+  
Sbjct: 242 SWQISNMHGGTGATNVIPGEVVIDFNFRFSTESTAEGLQQRVHAMLDRHGLEYDLRWTLG 301

Query: 292 GQPFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQ 351
           GQPFLT  G+L    + AI     I  ELSTTGGTSDGRFI  I  ++IELGP NA+IH+
Sbjct: 302 GQPFLTTPGELVTAVQQAITAETSITTELSTTGGTSDGRFIAQICPQVIELGPPNASIHK 361

Query: 352 INENVRLNDIPKLSAVY----EGILARLLAGNAV 381
           I+E+V + DI  L  +Y    E + A+ LA  AV
Sbjct: 362 IDEHVVVADIEPLKNIYRRTLENLHAQALAATAV 395


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: 467
Number of extensions: 14
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: 397
Length adjustment: 30
Effective length of query: 351
Effective length of database: 367
Effective search space:   128817
Effective search space used:   128817
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 Ac3H11_2298 (N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18))
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.20759.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   6.4e-155  501.6   0.0   7.3e-155  501.4   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2298  N-succinyl-L,L-diaminopimelate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2298  N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.4   0.0  7.3e-155  7.3e-155       2     370 .]       5     385 ..       4     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 501.4 bits;  conditional E-value: 7.3e-155
                                        TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefe....dtknlwatrgt...... 53 
                                                      l+la++Li ++s+tP+dag+++l+a+rL  lgfe+e+l  +     + nlwa+r        
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2298   5 LHLAEQLIALPSITPDDAGCLNLLAARLAPLGFECERLDSGpadfRVSNLWAKRPLprdqla 66 
                                                      689***********************************9984433478*****988888888 PP

                                        TIGR01246  54 ..eepvlvfaGhtDvvPaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvk 113
                                                          +++vfaGhtDvvP+G+l +Wssdpf p+++dGklygrGa Dmk+s+aafvva+e+f++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2298  67 qaAIKTVVFAGHTDVVPTGPLAQWSSDPFVPTHKDGKLYGRGASDMKTSIAAFVVAVEEFLA 128
                                                      7666799******************************************************* PP

                                        TIGR01246 114 knadhkGslsllitsDeegeaidGtkkvvetlkerdelidyavvgePssvkklGDvikiGrr 175
                                                      + ++   +l++l+tsDeeg ++dGtk vve lk+r e +dy++vgeP+sv+k GD+ik+Grr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2298 129 ATPEPLVQLAFLLTSDEEGPSVDGTKVVVEQLKARGEPLDYCIVGEPTSVEKTGDMIKNGRR 190
                                                      ************************************************************** PP

                                        TIGR01246 176 GsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffppsslqianieagt 237
                                                      G ++gkl+++GiqGh+aYP++a+nP+h+a+p+l+el+a+ +D+Gn+ffpp+s qi+n+++gt
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2298 191 GTLSGKLSVRGIQGHIAYPQLARNPIHQALPALAELAATVWDHGNAFFPPTSWQISNMHGGT 252
                                                      ************************************************************** PP

                                        TIGR01246 238 gasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklik 299
                                                      ga+nviPge+ + fn+rfs+e+++e l+++v+++ld+h+l+Y+l+w+l g+pflt  g+l++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2298 253 GATNVIPGEVVIDFNFRFSTESTAEGLQQRVHAMLDRHGLEYDLRWTLGGQPFLTTPGELVT 314
                                                      ************************************************************** PP

                                        TIGR01246 300 kvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklse 361
                                                      +v++ai+  + +++elst+GGtsD+rfia++  +v+elG+ n++ihk++e+v ++d+e l++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2298 315 AVQQAITAETSITTELSTTGGTSDGRFIAQICPQVIELGPPNASIHKIDEHVVVADIEPLKN 376
                                                      ************************************************************** PP

                                        TIGR01246 362 vyeklleel 370
                                                      +y+++le+l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2298 377 IYRRTLENL 385
                                                      ******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (397 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.61
//
[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