Alignments for a candidate for dapD in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_3078 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117)

Query= SwissProt::G3XD76
         (344 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3078
          Length = 344

 Score =  593 bits (1529), Expect = e-174
 Identities = 297/344 (86%), Positives = 322/344 (93%)

Query: 1   MSQSLFSLAFGVGTQNRQEAWLEVFYALPLLKPSSEIVAAVAPILGYAAGNQALTFTSQQ 60
           MS +LFSLAFGVGTQNRQ AWLEVFYA PLL PS++I+ A+APILGY+ GNQA+TFT+ Q
Sbjct: 1   MSTTLFSLAFGVGTQNRQGAWLEVFYAQPLLNPSADIIKAIAPILGYSEGNQAITFTTTQ 60

Query: 61  AYQLADALKGIDAAQSALLSRLAESQKPLVATLLAEDAAPSSTAEAYLKLHLLSHRLVKP 120
           A QLA+ALKG+DAAQ+ALL+RLAES KPLVATLLAEDA  SST EAYLKLHLLSHRLVKP
Sbjct: 61  ASQLAEALKGVDAAQAALLTRLAESHKPLVATLLAEDAQLSSTPEAYLKLHLLSHRLVKP 120

Query: 121 HAVNLSGIFPLLPNVAWTNIGAVDLAELAELQLEARLKGKLLEVFSVDKFPKMTDYVVPA 180
           H +NL+GIFPLLPNVAWT+ GA+DLAELAE QLEARL+G+LLEVFSVDKFPKMTDYVVPA
Sbjct: 121 HGLNLAGIFPLLPNVAWTSQGAIDLAELAEHQLEARLRGELLEVFSVDKFPKMTDYVVPA 180

Query: 181 GVRIADTARVRLGAYIGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC 240
           GVRIAD AR+RLGAY+GEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC
Sbjct: 181 GVRIADAARIRLGAYVGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC 240

Query: 241 STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNIVEAGLYITAGTKVALLDEQNALV 300
           STMGTLSGGGNIVI VGEGCLIGANAGIGIPLGDRN VE+GLY+TAGTKV LLDE N LV
Sbjct: 241 STMGTLSGGGNIVIKVGEGCLIGANAGIGIPLGDRNTVESGLYVTAGTKVKLLDENNQLV 300

Query: 301 KVVKARDLAGQPDLLFRRNSQNGAVECKTNKTAIELNEALHAHN 344
           KVVKARDLAGQPDLLFRRNS+ GAVECKT+K+AIELNEALHAHN
Sbjct: 301 KVVKARDLAGQPDLLFRRNSETGAVECKTHKSAIELNEALHAHN 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: 465
Number of extensions: 14
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 Pf6N2E2_3078 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))
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.11517.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   5.6e-193  626.2   0.8   6.3e-193  626.1   0.8    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3078  2,3,4,5-tetrahydropyridine-2,6-d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3078  2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  626.1   0.8  6.3e-193  6.3e-193       1     341 []       5     344 .]       5     344 .] 0.99

  Alignments for each domain:
  == domain 1  score: 626.1 bits;  conditional E-value: 6.3e-193
                                      TIGR03536   1 llslalGvgtknrkgewlevffptpllnpdeelveavaealgyegGnqaieltaeklealaaal 64 
                                                    l+sla+Gvgt+nr+g+wlevf+++pllnp++++++a+a  lgy++Gnqai++t++++++la+al
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3078   5 LFSLAFGVGTQNRQGAWLEVFYAQPLLNPSADIIKAIAPILGYSEGNQAITFTTTQASQLAEAL 68 
                                                    59************************************************************** PP

                                      TIGR03536  65 keagleeqaelaaklkeskrplvavlleedaapasvpeaylklqllshrlvkphgvnleGifgl 128
                                                    k + +++qa+l+++l+es++plva+ll+eda+ +s+peaylkl+llshrlvkphg+nl+Gif+l
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3078  69 KGV-DAAQAALLTRLAESHKPLVATLLAEDAQLSSTPEAYLKLHLLSHRLVKPHGLNLAGIFPL 131
                                                    *99.8899******************************************************** PP

                                      TIGR03536 129 lknvawtneGaidleelaerqlearlnGevlevdsvdkfpkmtdyvvpkGvriadtarvrlGay 192
                                                    l+nvawt++Gaidl elae+qlearl+Ge+lev+svdkfpkmtdyvvp+Gvriad+ar+rlGay
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3078 132 LPNVAWTSQGAIDLAELAEHQLEARLRGELLEVFSVDKFPKMTDYVVPAGVRIADAARIRLGAY 195
                                                    **************************************************************** PP

                                      TIGR03536 193 vGeGttvmheGfvnfnaGteGasmveGrisaGvlvGkGsdlGGGastmGtlsGGGnivisvGee 256
                                                    vGeGttvmheGfvnfnaGteG++m+eGr+saGv+vGkGsdlGGG+stmGtlsGGGnivi+vGe+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3078 196 VGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGCSTMGTLSGGGNIVIKVGEG 259
                                                    **************************************************************** PP

                                      TIGR03536 257 cllGanaGiGiplGdrctveaGlyitaGtkvallddkgelvevvkardlaGksdllfrrnslnG 320
                                                    cl+GanaGiGiplGdr+tve+Gly+taGtkv+lld++++lv+vvkardlaG+ dllfrrns++G
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3078 260 CLIGANAGIGIPLGDRNTVESGLYVTAGTKVKLLDENNQLVKVVKARDLAGQPDLLFRRNSETG 323
                                                    **************************************************************** PP

                                      TIGR03536 321 avecltnksaielneelhann 341
                                                    avec+t+ksaielne+lha+n
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3078 324 AVECKTHKSAIELNEALHAHN 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.62
//
[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