Alignments for a candidate for dapE in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Pseudomonas fluorescens GW456-L13

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate PfGW456L13_4721 N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18)

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4721
          Length = 383

 Score =  448 bits (1153), Expect = e-130
 Identities = 228/375 (60%), Positives = 272/375 (72%), Gaps = 2/375 (0%)

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

Query: 63  FVFAGHTDVVPAGPLSQWHTPPFEPTVID-GFLHGRGAADMKGSLACMIVAVERFIAEHP 121
             FAGHTDVVP GP++ W   PF   + + G L GRGAADMKGSLA M VA ERF+ ++P
Sbjct: 68  LCFAGHTDVVPTGPVAAWQIEPFNALIDEHGMLCGRGAADMKGSLAAMTVASERFVTDYP 127

Query: 122 DHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRG 181
           +H+G + FLITSDEEGP  +GT  VVE L AR E +D CIVGEPSST  VGDVVKNGRRG
Sbjct: 128 NHKGKVAFLITSDEEGPAHHGTKAVVERLAARKERLDWCIVGEPSSTTLVGDVVKNGRRG 187

Query: 182 SITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAG 241
           S+   L V+G QGHVAYPHLA NP+H A PALAELAA  WD GN +FPPTSFQI N+ +G
Sbjct: 188 SLGAKLTVRGVQGHVAYPHLAKNPIHLAAPALAELAAEHWDHGNDFFPPTSFQISNVNSG 247

Query: 242 TGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGE 301
           TGA+NVIPG+    FNFRFSTE T E +++RV  +LD HGLD+ + W LSG PFLT+ G 
Sbjct: 248 TGATNVIPGDLVAVFNFRFSTESTVEGLQKRVADILDKHGLDWHIDWALSGLPFLTEPGA 307

Query: 302 LLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADL 361
           LL AV A+++++  +     T+GGTSDGRFIA MG QVVELGPVNATIH+VNE V  ADL
Sbjct: 308 LLDAVSASIKDITGRETKASTSGGTSDGRFIATMGTQVVELGPVNATIHQVNERVLAADL 367

Query: 362 EKLTDMYQKTLNHLL 376
           + LT++Y +TL  LL
Sbjct: 368 DVLTEIYYQTLIKLL 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: 515
Number of extensions: 26
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 PfGW456L13_4721 (N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18))
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.1133.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.9e-163  529.7   0.0   2.2e-163  529.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4721  N-succinyl-L,L-diaminopimelate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4721  N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  529.5   0.0  2.2e-163  2.2e-163       2     370 .]      11     381 ..      10     381 .. 0.98

  Alignments for each domain:
  == domain 1  score: 529.5 bits;  conditional E-value: 2.2e-163
                                               TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt.ee 55 
                                                             l+la++Li+r+svtP da++q+ +++rL   gf+ e +++ed+ n+wat+g+ + 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4721  11 LQLAIDLIRRPSVTPIDADCQKQMMQRLGDAGFTLEPMRIEDVDNFWATHGQdDG 65 
                                                             5899***********************************************9789 PP

                                               TIGR01246  56 pvlvfaGhtDvvPaGelekWssdpfepee.rdGklygrGaaDmkgslaafvvaae 109
                                                             pvl+faGhtDvvP+G++ +W+ +pf++ + ++G+l grGaaDmkgslaa+ va+e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4721  66 PVLCFAGHTDVVPTGPVAAWQIEPFNALIdEHGMLCGRGAADMKGSLAAMTVASE 120
                                                             *************************9976256*********************** PP

                                               TIGR01246 110 rfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdelidyavvgePssvk 164
                                                             rfv+++++hkG++++litsDeeg a +Gtk+vve l +r+e +d+++vgePss+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4721 121 RFVTDYPNHKGKVAFLITSDEEGPAHHGTKAVVERLAARKERLDWCIVGEPSSTT 175
                                                             ******************************************************* PP

                                               TIGR01246 165 klGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeG 219
                                                              +GDv+k+GrrGs+ +kl+++G+qGhvaYPh+a+nP+h a+p+l+el+a+++D+G
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4721 176 LVGDVVKNGRRGSLGAKLTVRGVQGHVAYPHLAKNPIHLAAPALAELAAEHWDHG 230
                                                             ******************************************************* PP

                                               TIGR01246 220 neffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildk 274
                                                             n+ffpp+s+qi+n+++gtga+nviPg+l + fn+rfs+e+++e l+++v++ildk
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4721 231 NDFFPPTSFQISNVNSGTGATNVIPGDLVAVFNFRFSTESTVEGLQKRVADILDK 285
                                                             ******************************************************* PP

                                               TIGR01246 275 hkldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiak 329
                                                             h+ld++++w lsg pflt+ g l+++v ++i+ ++++++++stsGGtsD+rfia+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4721 286 HGLDWHIDWALSGLPFLTEPGALLDAVSASIKDITGRETKASTSGGTSDGRFIAT 340
                                                             ******************************************************* PP

                                               TIGR01246 330 lgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                                             +g++vvelG+vn+tih+vne+v  +dl+ l+e+y+++l++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4721 341 MGTQVVELGPVNATIHQVNERVLAADLDVLTEIYYQTLIKL 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.74
//
[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