Alignments for a candidate for dapE in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Pseudomonas putida KT2440

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate PP_1525 PP_1525 Succinyl-diaminopimelate desuccinylase

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__Putida:PP_1525
          Length = 383

 Score =  463 bits (1191), Expect = e-135
 Identities = 233/375 (62%), Positives = 280/375 (74%), Gaps = 2/375 (0%)

Query: 4   SPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQS-PL 62
           SP L LA +LI R SVTP DA CQ  M+ RL A+GF++E M  ED  NFWA  G+Q  P+
Sbjct: 8   SPTLQLACDLIRRPSVTPVDADCQAQMMNRLGAVGFQLEPMRIEDVDNFWATHGSQDGPV 67

Query: 63  FVFAGHTDVVPAGPLSQWHTPPFEPTV-IDGFLHGRGAADMKGSLACMIVAVERFIAEHP 121
             FAGHTDVVP GP+ QW   PFE  +  DG L GRGAADMKGSLA M++A ERF+ ++P
Sbjct: 68  LCFAGHTDVVPTGPVQQWQHEPFEALIDADGMLCGRGAADMKGSLASMVIASERFVQDYP 127

Query: 122 DHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRG 181
           +H+G + FLITSDEEGP  +GT  VVE L ARNE +D CIVGEPSST  +GDVVKNGRRG
Sbjct: 128 NHRGKVAFLITSDEEGPAHHGTKAVVERLKARNERLDWCIVGEPSSTTLLGDVVKNGRRG 187

Query: 182 SITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAG 241
           S+   L ++G QGHVAYPHLA NP+H A PALAELAA  WDEGNA+FPPTSFQI NL +G
Sbjct: 188 SLGAKLTIRGKQGHVAYPHLARNPIHLAAPALAELAAEHWDEGNAFFPPTSFQISNLNSG 247

Query: 242 TGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGE 301
           TGA+NV+PGE    FNFRFSTE T E ++ RV ++LD H LD+ V W LSG PFLT+ GE
Sbjct: 248 TGATNVVPGELTALFNFRFSTESTVEGLQARVSAILDKHELDWSVDWALSGLPFLTEPGE 307

Query: 302 LLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADL 361
           LL AV A+++ V  +     T+GGTSDGRFIA MG QVVELGPVNATIH+V+E +  +DL
Sbjct: 308 LLDAVAASIKGVTGRDTQPSTSGGTSDGRFIATMGTQVVELGPVNATIHQVDERILASDL 367

Query: 362 EKLTDMYQKTLNHLL 376
           + LT++Y +TL  LL
Sbjct: 368 DLLTEIYYQTLVRLL 382


Lambda     K      H
   0.318    0.135    0.403 

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: 498
Number of extensions: 20
Number of successful extensions: 3
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: 377
Length of database: 383
Length adjustment: 30
Effective length of query: 347
Effective length of database: 353
Effective search space:   122491
Effective search space used:   122491
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate PP_1525 PP_1525 (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.1097818.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.8e-164  532.0   0.0   4.3e-164  531.8   0.0    1.0  1  FitnessBrowser__Putida:PP_1525  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Putida:PP_1525  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.8   0.0  4.3e-164  4.3e-164       2     370 .]      11     381 ..      10     381 .. 0.99

  Alignments for each domain:
  == domain 1  score: 531.8 bits;  conditional E-value: 4.3e-164
                       TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt.eepvlvfaGhtDvvPaGelekWssdp 79 
                                     l+la++Li+r+svtP da++q+ +++rL ++gf+ e +++ed+ n+wat+g  + pvl+faGhtDvvP+G++++W+ +p
  FitnessBrowser__Putida:PP_1525  11 LQLACDLIRRPSVTPVDADCQAQMMNRLGAVGFQLEPMRIEDVDNFWATHGSqDGPVLCFAGHTDVVPTGPVQQWQHEP 89 
                                     689***********************************************98678************************ PP

                       TIGR01246  80 fepee.rdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdelidyavv 157
                                     fe+ +  dG+l grGaaDmkgsla++v+a+erfv+++++h+G++++litsDeeg a +Gtk+vve lk+r+e +d+++v
  FitnessBrowser__Putida:PP_1525  90 FEALIdADGMLCGRGAADMKGSLASMVIASERFVQDYPNHRGKVAFLITSDEEGPAHHGTKAVVERLKARNERLDWCIV 168
                                     *987527************************************************************************ PP

                       TIGR01246 158 gePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffppsslqianieag 236
                                     gePss+  lGDv+k+GrrGs+ +kl+i+G+qGhvaYPh+a+nP+h a+p+l+el+a+++DeGn+ffpp+s+qi+n+++g
  FitnessBrowser__Putida:PP_1525 169 GEPSSTTLLGDVVKNGRRGSLGAKLTIRGKQGHVAYPHLARNPIHLAAPALAELAAEHWDEGNAFFPPTSFQISNLNSG 247
                                     ******************************************************************************* PP

                       TIGR01246 237 tgasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklikkvaeaieevlkkkpel 315
                                     tga+nv+Pgel++ fn+rfs+e+++e l+ +v++ildkh+ld++++w lsg pflt+ g+l+++va++i+ v+++ ++ 
  FitnessBrowser__Putida:PP_1525 248 TGATNVVPGELTALFNFRFSTESTVEGLQARVSAILDKHELDWSVDWALSGLPFLTEPGELLDAVAASIKGVTGRDTQP 326
                                     ******************************************************************************* PP

                       TIGR01246 316 stsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                     stsGGtsD+rfia++g++vvelG+vn+tih+v+e++  +dl+ l+e+y+++l +l
  FitnessBrowser__Putida:PP_1525 327 STSGGTSDGRFIATMGTQVVELGPVNATIHQVDERILASDLDLLTEIYYQTLVRL 381
                                     **************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (383 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.78
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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