GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapD in Pseudomonas stutzeri RCH2

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 GFF1428 Psest_1465 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= SwissProt::G3XD76
         (344 letters)



>lcl|FitnessBrowser__psRCH2:GFF1428 Psest_1465
           2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
           N-succinyltransferase
          Length = 344

 Score =  587 bits (1514), Expect = e-172
 Identities = 298/344 (86%), Positives = 318/344 (92%)

Query: 1   MSQSLFSLAFGVGTQNRQEAWLEVFYALPLLKPSSEIVAAVAPILGYAAGNQALTFTSQQ 60
           MS +LFSLAFGVGTQNRQ  WLEVFYA PLLKP+ E+VAAVAP+LGYA GNQA+T T+ Q
Sbjct: 1   MSATLFSLAFGVGTQNRQGDWLEVFYAQPLLKPAGELVAAVAPLLGYAGGNQAITITTSQ 60

Query: 61  AYQLADALKGIDAAQSALLSRLAESQKPLVATLLAEDAAPSSTAEAYLKLHLLSHRLVKP 120
           A QLADALK +DA Q ALL+RLAESQ+PLVATLLAEDA  SST EAYLKLHLLSHRL KP
Sbjct: 61  AAQLADALKPLDATQYALLTRLAESQRPLVATLLAEDAPLSSTPEAYLKLHLLSHRLAKP 120

Query: 121 HAVNLSGIFPLLPNVAWTNIGAVDLAELAELQLEARLKGKLLEVFSVDKFPKMTDYVVPA 180
           H +NL+GIFPLLPNVAWTN GAVDL ELAE QLEARLKG LLEVFSVDKFPKMTDYVVPA
Sbjct: 121 HGLNLTGIFPLLPNVAWTNQGAVDLGELAERQLEARLKGDLLEVFSVDKFPKMTDYVVPA 180

Query: 181 GVRIADTARVRLGAYIGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC 240
           GVRIADTARVRLGAY+GEGTTVMHEGF+NFNAGT+GPGMIEGRVSAGVFVGKGSDLGGGC
Sbjct: 181 GVRIADTARVRLGAYVGEGTTVMHEGFINFNAGTQGPGMIEGRVSAGVFVGKGSDLGGGC 240

Query: 241 STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNIVEAGLYITAGTKVALLDEQNALV 300
           STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRN VE+GLYITAGTKV+LLDE + LV
Sbjct: 241 STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNTVESGLYITAGTKVSLLDENDQLV 300

Query: 301 KVVKARDLAGQPDLLFRRNSQNGAVECKTNKTAIELNEALHAHN 344
           KVVKAR+LAGQ DLLFRRNSQ GAVECKT+K+AIELNEALHAHN
Sbjct: 301 KVVKARELAGQSDLLFRRNSQTGAVECKTHKSAIELNEALHAHN 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: 473
Number of extensions: 17
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 GFF1428 Psest_1465 (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.4908.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-191  622.0   0.4   1.2e-191  621.9   0.4    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1428  Psest_1465 2,3,4,5-tetrahydropyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1428  Psest_1465 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 !  621.9   0.4  1.2e-191  1.2e-191       1     341 []       5     344 .]       5     344 .] 0.99

  Alignments for each domain:
  == domain 1  score: 621.9 bits;  conditional E-value: 1.2e-191
                           TIGR03536   1 llslalGvgtknrkgewlevffptpllnpdeelveavaealgyegGnqaieltaeklealaaalkeagleeqael 75 
                                         l+sla+Gvgt+nr+g+wlevf+++pll p+ elv+ava  lgy+gGnqai++t++++++la alk   +++q +l
  lcl|FitnessBrowser__psRCH2:GFF1428   5 LFSLAFGVGTQNRQGDWLEVFYAQPLLKPAGELVAAVAPLLGYAGGNQAITITTSQAAQLADALKPL-DATQYAL 78 
                                         59**************************************************************999.6778889 PP

                           TIGR03536  76 aaklkeskrplvavlleedaapasvpeaylklqllshrlvkphgvnleGifgllknvawtneGaidleelaerql 150
                                         +++l+es+rplva+ll+eda  +s+peaylkl+llshrl+kphg+nl+Gif+ll+nvawtn+Ga+dl elaerql
  lcl|FitnessBrowser__psRCH2:GFF1428  79 LTRLAESQRPLVATLLAEDAPLSSTPEAYLKLHLLSHRLAKPHGLNLTGIFPLLPNVAWTNQGAVDLGELAERQL 153
                                         9************************************************************************** PP

                           TIGR03536 151 earlnGevlevdsvdkfpkmtdyvvpkGvriadtarvrlGayvGeGttvmheGfvnfnaGteGasmveGrisaGv 225
                                         earl+G++lev+svdkfpkmtdyvvp+GvriadtarvrlGayvGeGttvmheGf+nfnaGt+G++m+eGr+saGv
  lcl|FitnessBrowser__psRCH2:GFF1428 154 EARLKGDLLEVFSVDKFPKMTDYVVPAGVRIADTARVRLGAYVGEGTTVMHEGFINFNAGTQGPGMIEGRVSAGV 228
                                         *************************************************************************** PP

                           TIGR03536 226 lvGkGsdlGGGastmGtlsGGGnivisvGeecllGanaGiGiplGdrctveaGlyitaGtkvallddkgelvevv 300
                                         +vGkGsdlGGG+stmGtlsGGGnivisvGe+cl+GanaGiGiplGdr+tve+GlyitaGtkv+lld++++lv+vv
  lcl|FitnessBrowser__psRCH2:GFF1428 229 FVGKGSDLGGGCSTMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNTVESGLYITAGTKVSLLDENDQLVKVV 303
                                         *************************************************************************** PP

                           TIGR03536 301 kardlaGksdllfrrnslnGavecltnksaielneelhann 341
                                         kar+laG+sdllfrrns++Gavec+t+ksaielne+lha+n
  lcl|FitnessBrowser__psRCH2:GFF1428 304 KARELAGQSDLLFRRNSQTGAVECKTHKSAIELNEALHAHN 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: 6.98
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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