GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapE in Marinobacter adhaerens HP15

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; Aspartyl peptidase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate GFF1182 HP15_1159 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q8ZN75
         (375 letters)



>lcl|FitnessBrowser__Marino:GFF1182 HP15_1159
           succinyl-diaminopimelate desuccinylase
          Length = 378

 Score =  472 bits (1215), Expect = e-138
 Identities = 233/373 (62%), Positives = 284/373 (76%), Gaps = 2/373 (0%)

Query: 4   PVIELTQQLIRRPSLSPDDAGCQALMIERLRKIGFTIEHMDFGDTQNFWAWRG-RGETLA 62
           P +EL   LIRRPS++PDDAGCQ LM+ RL  +GFT E++ FGDT N WA +G  G  LA
Sbjct: 7   PTLELAVDLIRRPSVTPDDAGCQELMMSRLAPLGFTGENLRFGDTDNLWARKGSEGPVLA 66

Query: 63  FAGHTDVVPAGDVDRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVAAERFVAQHPHHR 122
           FAGHTDVVP G    W +PPF+P IRDG L GRGAADMKGSLAA V A ERFVA +P HR
Sbjct: 67  FAGHTDVVPTGPEKNWSHPPFDPVIRDGYLLGRGAADMKGSLAAFVTACERFVASYPDHR 126

Query: 123 GRLAFLITSDEEASAKNGTVKVVEALMARNERLDYCLVGEPSSTEIVGDVVKNGRRGSLT 182
           G +A LITSDEE  A++GTVKVVE L ARNE++D+CL+GEPSST  VGDV+KNGRRGSL 
Sbjct: 127 GSIALLITSDEEGPAQHGTVKVVETLEARNEKIDWCLIGEPSSTREVGDVIKNGRRGSLH 186

Query: 183 CNLTIHGVQGHVAYPHLADNPVHRAAPFLNELVAIEWDRGNDFFPATSMQVANIQAGTGS 242
             LT+HGVQGHVAYPHLA+NPVH  AP L+ L    WD GNDFFP T+ Q+  ++AGTGS
Sbjct: 187 GYLTVHGVQGHVAYPHLAENPVHLVAPALDALAKEFWDNGNDFFPPTTFQITKLEAGTGS 246

Query: 243 NNVIPGELFVQFNFRFSTELTDEMIKERVHALLEKHQLRYTVDWWLSGQPFLTARGKLVD 302
            N+IPGE  V FNFR+ TE T E ++ERV A+L++H L+Y + W LSG+PFLT +G LV 
Sbjct: 247 -NIIPGECLVHFNFRYCTENTAESLEERVVAILDRHNLKYDLQWHLSGRPFLTDKGALVS 305

Query: 303 AVVNAIEHYNEIKPQLLTTGGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQLL 362
           A  +AI      + +L T+GGTSDGRFIA  GAQVVELGP+NATIHK++ECV A DL  L
Sbjct: 306 ASQSAIRTVTGRETELSTSGGTSDGRFIAPTGAQVVELGPINATIHKVDECVKADDLNTL 365

Query: 363 ARMYQRIMEQLVA 375
           + +Y++I+ +L+A
Sbjct: 366 SEIYEQILIELLA 378


Lambda     K      H
   0.322    0.136    0.415 

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: 445
Number of extensions: 8
Number of successful extensions: 4
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: 375
Length of database: 378
Length adjustment: 30
Effective length of query: 345
Effective length of database: 348
Effective search space:   120060
Effective search space used:   120060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate GFF1182 HP15_1159 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

# 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/TIGR01246.hmm
# target sequence database:        /tmp/gapView.15594.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01246  [M=370]
Accession:   TIGR01246
Description: dapE_proteo: succinyl-diaminopimelate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.4e-170  551.2   0.0   6.2e-170  551.0   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF1182  HP15_1159 succinyl-diaminopimela


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1182  HP15_1159 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  551.0   0.0  6.2e-170  6.2e-170       2     370 .]       9     376 ..       8     376 .. 0.99

  Alignments for each domain:
  == domain 1  score: 551.0 bits;  conditional E-value: 6.2e-170
                           TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaGelekWs 76 
                                         lela +Li+r+svtP+dag+qel+++rL  lgf+ e l+f+dt nlwa++g e pvl+faGhtDvvP+G++++Ws
  lcl|FitnessBrowser__Marino:GFF1182   9 LELAVDLIRRPSVTPDDAGCQELMMSRLAPLGFTGENLRFGDTDNLWARKGSEGPVLAFAGHTDVVPTGPEKNWS 83 
                                         689************************************************************************ PP

                           TIGR01246  77 sdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdel 151
                                          +pf+p++rdG+l grGaaDmkgslaafv+a+erfv++++dh+Gs++llitsDeeg a +Gt+kvvetl++r+e+
  lcl|FitnessBrowser__Marino:GFF1182  84 HPPFDPVIRDGYLLGRGAADMKGSLAAFVTACERFVASYPDHRGSIALLITSDEEGPAQHGTVKVVETLEARNEK 158
                                         *************************************************************************** PP

                           TIGR01246 152 idyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffpps 226
                                         id++++gePss++++GDvik+GrrGs+ g l+++G+qGhvaYPh+aenPvh ++p+l +l+++ +D+Gn+ffpp+
  lcl|FitnessBrowser__Marino:GFF1182 159 IDWCLIGEPSSTREVGDVIKNGRRGSLHGYLTVHGVQGHVAYPHLAENPVHLVAPALDALAKEFWDNGNDFFPPT 233
                                         *************************************************************************** PP

                           TIGR01246 227 slqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklikkv 301
                                          +qi+ +eagtg sn+iPge  v+fn+r+++e ++e+l+++v++ild+h+l+Y+l+w+lsg+pflt++g l+++ 
  lcl|FitnessBrowser__Marino:GFF1182 234 TFQITKLEAGTG-SNIIPGECLVHFNFRYCTENTAESLEERVVAILDRHNLKYDLQWHLSGRPFLTDKGALVSAS 307
                                         ***********9.69************************************************************ PP

                           TIGR01246 302 aeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                         ++ai+ v+++++elstsGGtsD+rfia  ga+vvelG++n+tihkv+e+vk +dl+ lse+ye++l+el
  lcl|FitnessBrowser__Marino:GFF1182 308 QSAIRTVTGRETELSTSGGTSDGRFIAPTGAQVVELGPINATIHKVDECVKADDLNTLSEIYEQILIEL 376
                                         *****************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (378 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: 8.90
//
[ok]

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

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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 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