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.7019.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.84
//
[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