Alignments for a candidate for dapD in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Pseudomonas putida KT2440

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 PP_1530 PP_1530 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= SwissProt::G3XD76
         (344 letters)



>FitnessBrowser__Putida:PP_1530
          Length = 344

 Score =  598 bits (1541), Expect = e-176
 Identities = 304/344 (88%), Positives = 322/344 (93%)

Query: 1   MSQSLFSLAFGVGTQNRQEAWLEVFYALPLLKPSSEIVAAVAPILGYAAGNQALTFTSQQ 60
           MS +LFSLAFGVG+QNRQ AWLEVFYA PLL PS+E+VAAVAP+LGY  GNQA+ F++ Q
Sbjct: 1   MSNTLFSLAFGVGSQNRQGAWLEVFYAQPLLNPSAELVAAVAPVLGYEGGNQAIAFSNAQ 60

Query: 61  AYQLADALKGIDAAQSALLSRLAESQKPLVATLLAEDAAPSSTAEAYLKLHLLSHRLVKP 120
           A QLA+ALKG+DAAQ+ALL+RLAES KPLVATLLAEDAA SST EAYLKLHLLSHRLVKP
Sbjct: 61  AAQLAEALKGVDAAQAALLTRLAESHKPLVATLLAEDAALSSTPEAYLKLHLLSHRLVKP 120

Query: 121 HAVNLSGIFPLLPNVAWTNIGAVDLAELAELQLEARLKGKLLEVFSVDKFPKMTDYVVPA 180
           H V+L+GIFPLLPNVAWTN GAVDL ELAELQLEARLKG+LLEVFSVDKFPKMTDYVVPA
Sbjct: 121 HGVSLAGIFPLLPNVAWTNQGAVDLGELAELQLEARLKGELLEVFSVDKFPKMTDYVVPA 180

Query: 181 GVRIADTARVRLGAYIGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC 240
           GVRIADTARVRLGAYIGEGTT+MHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC
Sbjct: 181 GVRIADTARVRLGAYIGEGTTIMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC 240

Query: 241 STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNIVEAGLYITAGTKVALLDEQNALV 300
           STMGTLSGGGNIVI VGEGCLIGANAGIGIPLGDRN VEAGLYITAGTKV LLDE N LV
Sbjct: 241 STMGTLSGGGNIVIKVGEGCLIGANAGIGIPLGDRNTVEAGLYITAGTKVNLLDENNELV 300

Query: 301 KVVKARDLAGQPDLLFRRNSQNGAVECKTNKTAIELNEALHAHN 344
           KVVKARDLAGQ DLLFRRNS NGAVECKT+K+AIELNEALHAHN
Sbjct: 301 KVVKARDLAGQTDLLFRRNSLNGAVECKTHKSAIELNEALHAHN 344


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: 474
Number of extensions: 16
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: 344
Length of database: 344
Length adjustment: 29
Effective length of query: 315
Effective length of database: 315
Effective search space:    99225
Effective search space used:    99225
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 PP_1530 PP_1530 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase)
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.9459.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   9.5e-197  638.6   2.4   1.1e-196  638.5   2.4    1.0  1  lcl|FitnessBrowser__Putida:PP_1530  PP_1530 2,3,4,5-tetrahydropyridi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1530  PP_1530 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  638.5   2.4  1.1e-196  1.1e-196       1     341 []       5     344 .]       5     344 .] 0.99

  Alignments for each domain:
  == domain 1  score: 638.5 bits;  conditional E-value: 1.1e-196
                           TIGR03536   1 llslalGvgtknrkgewlevffptpllnpdeelveavaealgyegGnqaieltaeklealaaalkeagleeqael 75 
                                         l+sla+Gvg++nr+g+wlevf+++pllnp++elv+ava +lgyegGnqai+++++++++la+alk + +++qa+l
  lcl|FitnessBrowser__Putida:PP_1530   5 LFSLAFGVGSQNRQGAWLEVFYAQPLLNPSAELVAAVAPVLGYEGGNQAIAFSNAQAAQLAEALKGV-DAAQAAL 78 
                                         59***************************************************************99.8899*** PP

                           TIGR03536  76 aaklkeskrplvavlleedaapasvpeaylklqllshrlvkphgvnleGifgllknvawtneGaidleelaerql 150
                                         +++l+es++plva+ll+edaa +s+peaylkl+llshrlvkphgv+l+Gif+ll+nvawtn+Ga+dl elae ql
  lcl|FitnessBrowser__Putida:PP_1530  79 LTRLAESHKPLVATLLAEDAALSSTPEAYLKLHLLSHRLVKPHGVSLAGIFPLLPNVAWTNQGAVDLGELAELQL 153
                                         *************************************************************************** PP

                           TIGR03536 151 earlnGevlevdsvdkfpkmtdyvvpkGvriadtarvrlGayvGeGttvmheGfvnfnaGteGasmveGrisaGv 225
                                         earl+Ge+lev+svdkfpkmtdyvvp+GvriadtarvrlGay+GeGtt+mheGfvnfnaGteG++m+eGr+saGv
  lcl|FitnessBrowser__Putida:PP_1530 154 EARLKGELLEVFSVDKFPKMTDYVVPAGVRIADTARVRLGAYIGEGTTIMHEGFVNFNAGTEGPGMIEGRVSAGV 228
                                         *************************************************************************** PP

                           TIGR03536 226 lvGkGsdlGGGastmGtlsGGGnivisvGeecllGanaGiGiplGdrctveaGlyitaGtkvallddkgelvevv 300
                                         +vGkGsdlGGG+stmGtlsGGGnivi+vGe+cl+GanaGiGiplGdr+tveaGlyitaGtkv+lld+++elv+vv
  lcl|FitnessBrowser__Putida:PP_1530 229 FVGKGSDLGGGCSTMGTLSGGGNIVIKVGEGCLIGANAGIGIPLGDRNTVEAGLYITAGTKVNLLDENNELVKVV 303
                                         *************************************************************************** PP

                           TIGR03536 301 kardlaGksdllfrrnslnGavecltnksaielneelhann 341
                                         kardlaG++dllfrrnslnGavec+t+ksaielne+lha+n
  lcl|FitnessBrowser__Putida:PP_1530 304 KARDLAGQTDLLFRRNSLNGAVECKTHKSAIELNEALHAHN 344
                                         ****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (341 nodes)
Target sequences:                          1  (344 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 10.80
//
[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