Alignments for a candidate for dapD in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Marinobacter adhaerens HP15

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Tetrahydrodipicolinate N-succinyltransferase; THDP succinyltransferase; THP succinyltransferase; Tetrahydropicolinate succinylase; EC 2.3.1.117 (characterized)
to candidate GFF1183 HP15_1160 tetrahydrodipicolinate succinylase

Query= SwissProt::G3XD76
         (344 letters)



>FitnessBrowser__Marino:GFF1183
          Length = 342

 Score =  473 bits (1218), Expect = e-138
 Identities = 235/340 (69%), Positives = 279/340 (82%), Gaps = 1/340 (0%)

Query: 6   FSLAFGVGTQNRQEAWLEVFYALPLLKPSSEIVAAVAPILGYAAGNQALTFTSQQAYQLA 65
           F+   G+GTQN Q  WLEVFY  P++ P + ++  ++  L Y  GNQA++ T++Q  QLA
Sbjct: 3   FAFGIGIGTQNNQGEWLEVFYQQPVMTPDNTLMDVISNALDYKGGNQAISATAEQLSQLA 62

Query: 66  DALKGI-DAAQSALLSRLAESQKPLVATLLAEDAAPSSTAEAYLKLHLLSHRLVKPHAVN 124
           +AL+ I    Q++L  + A S++P+V T+L  D   SST E YLKLHL+SHR+ KPH + 
Sbjct: 63  NALRQIGQTGQASLADKAAASKRPVVVTVLETDDTASSTPEVYLKLHLISHRMAKPHGLK 122

Query: 125 LSGIFPLLPNVAWTNIGAVDLAELAELQLEARLKGKLLEVFSVDKFPKMTDYVVPAGVRI 184
           L GIF LLPN+AWT+ GA+DL EL++ QL+ARL+G+ LEV SVDKFP+MTDYVVP GVRI
Sbjct: 123 LDGIFGLLPNLAWTSEGAIDLNELSDRQLQARLEGRTLEVKSVDKFPQMTDYVVPKGVRI 182

Query: 185 ADTARVRLGAYIGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGCSTMG 244
           ADTARVRLGAY+GEGTTVMHEGF+NFNAGTEG  MIEGR+SAGV VGKGSDLGGGCSTMG
Sbjct: 183 ADTARVRLGAYVGEGTTVMHEGFINFNAGTEGTSMIEGRISAGVMVGKGSDLGGGCSTMG 242

Query: 245 TLSGGGNIVISVGEGCLIGANAGIGIPLGDRNIVEAGLYITAGTKVALLDEQNALVKVVK 304
           TLSGGGNI+I+VGE CLIGANAGIGIPLGDR  VEAGLYITAGTKVALLD+ N LV+V+K
Sbjct: 243 TLSGGGNIIIAVGENCLIGANAGIGIPLGDRCKVEAGLYITAGTKVALLDDNNELVEVIK 302

Query: 305 ARDLAGQPDLLFRRNSQNGAVECKTNKTAIELNEALHAHN 344
           ARDLA Q DLLFRRNSQ GAVECKTNK+AIELNE LHA+N
Sbjct: 303 ARDLANQTDLLFRRNSQTGAVECKTNKSAIELNEELHANN 342


Lambda     K      H
   0.317    0.134    0.380 

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: 391
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: 344
Length of database: 342
Length adjustment: 29
Effective length of query: 315
Effective length of database: 313
Effective search space:    98595
Effective search space used:    98595
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: 49 (23.5 bits)

Align candidate GFF1183 HP15_1160 (tetrahydrodipicolinate succinylase)
to HMM TIGR03536 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))

# 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/TIGR03536.hmm
# target sequence database:        /tmp/gapView.1230.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03536  [M=341]
Accession:   TIGR03536
Description: DapD_gpp: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.9e-193  627.8   3.9   2.2e-193  627.6   3.9    1.0  1  lcl|FitnessBrowser__Marino:GFF1183  HP15_1160 tetrahydrodipicolinate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1183  HP15_1160 tetrahydrodipicolinate succinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  627.6   3.9  2.2e-193  2.2e-193       2     341 .]       3     342 .]       2     342 .] 1.00

  Alignments for each domain:
  == domain 1  score: 627.6 bits;  conditional E-value: 2.2e-193
                           TIGR03536   2 lslalGvgtknrkgewlevffptpllnpdeelveavaealgyegGnqaieltaeklealaaalkeagleeqaela 76 
                                         +++++G+gt+n++gewlevf+ +p++ pd++l++++ +al+y+gGnqai+ tae+l++la+al++ g++ qa+la
  lcl|FitnessBrowser__Marino:GFF1183   3 FAFGIGIGTQNNQGEWLEVFYQQPVMTPDNTLMDVISNALDYKGGNQAISATAEQLSQLANALRQIGQTGQASLA 77 
                                         89************************************************************************* PP

                           TIGR03536  77 aklkeskrplvavlleedaapasvpeaylklqllshrlvkphgvnleGifgllknvawtneGaidleelaerqle 151
                                          k+++skrp+v+++le+d+ ++s+pe+ylkl+l+shr++kphg++l+Gifgll+n+awt+eGaidl+el++rql+
  lcl|FitnessBrowser__Marino:GFF1183  78 DKAAASKRPVVVTVLETDDTASSTPEVYLKLHLISHRMAKPHGLKLDGIFGLLPNLAWTSEGAIDLNELSDRQLQ 152
                                         *************************************************************************** PP

                           TIGR03536 152 arlnGevlevdsvdkfpkmtdyvvpkGvriadtarvrlGayvGeGttvmheGfvnfnaGteGasmveGrisaGvl 226
                                         arl+G++lev+svdkfp+mtdyvvpkGvriadtarvrlGayvGeGttvmheGf+nfnaGteG+sm+eGrisaGv+
  lcl|FitnessBrowser__Marino:GFF1183 153 ARLEGRTLEVKSVDKFPQMTDYVVPKGVRIADTARVRLGAYVGEGTTVMHEGFINFNAGTEGTSMIEGRISAGVM 227
                                         *************************************************************************** PP

                           TIGR03536 227 vGkGsdlGGGastmGtlsGGGnivisvGeecllGanaGiGiplGdrctveaGlyitaGtkvallddkgelvevvk 301
                                         vGkGsdlGGG+stmGtlsGGGni+i vGe+cl+GanaGiGiplGdrc+veaGlyitaGtkvalldd++elvev+k
  lcl|FitnessBrowser__Marino:GFF1183 228 VGKGSDLGGGCSTMGTLSGGGNIIIAVGENCLIGANAGIGIPLGDRCKVEAGLYITAGTKVALLDDNNELVEVIK 302
                                         *************************************************************************** PP

                           TIGR03536 302 ardlaGksdllfrrnslnGavecltnksaielneelhann 341
                                         ardla ++dllfrrns++Gavec+tnksaielneelhann
  lcl|FitnessBrowser__Marino:GFF1183 303 ARDLANQTDLLFRRNSQTGAVECKTNKSAIELNEELHANN 342
                                         **************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (341 nodes)
Target sequences:                          1  (342 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.30
//
[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