Alignments for a candidate for dapE in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Pseudomonas fluorescens FW300-N2E3

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate AO353_16410 AO353_16410 succinyl-diaminopimelate desuccinylase

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_16410
          Length = 383

 Score =  451 bits (1159), Expect = e-131
 Identities = 230/375 (61%), Positives = 272/375 (72%), Gaps = 2/375 (0%)

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

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

Query: 122 DHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRG 181
           DH+G + FLITSDEEGP  +GT  VVE L AR E +D CIVGEPSST  VGDVVKNGRRG
Sbjct: 128 DHKGKVAFLITSDEEGPAHHGTKAVVERLAARKERLDWCIVGEPSSTTLVGDVVKNGRRG 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+ V W LSG PFLT+ G 
Sbjct: 248 TGATNVIPGDLVAVFNFRFSTESTVEGLQQRVADILDKHGLDWHVDWALSGLPFLTEPGA 307

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

Query: 362 EKLTDMYQKTLNHLL 376
           + LT++Y +TL  LL
Sbjct: 368 DLLTEIYYQTLIKLL 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: 505
Number of extensions: 27
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 AO353_16410 AO353_16410 (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.4193.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.5e-164  533.3   0.0   1.8e-164  533.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_16410  AO353_16410 succinyl-diaminopime


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_16410  AO353_16410 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  533.1   0.0  1.8e-164  1.8e-164       2     370 .]      11     381 ..      10     381 .. 0.98

  Alignments for each domain:
  == domain 1  score: 533.1 bits;  conditional E-value: 1.8e-164
                                     TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt.eepvlvfaGhtD 65 
                                                   l+la++Li+r+svtP da++q+ +++rL   gf+ e +++ed+ n+wat+g  e pvl+faGhtD
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_16410  11 LQLAIDLIRRPSVTPVDADCQKQMMQRLGDAGFALEPMRIEDVDNFWATHGKhEGPVLCFAGHTD 75 
                                                   5899**********************************************98789********** PP

                                     TIGR01246  66 vvPaGelekWssdpfepeerd.GklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsD 129
                                                   vvP+G++++W+ dpf++++ + G+l grGaaDmkgsla++ vaaerfv++++dhkG++++litsD
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_16410  76 VVPTGPVQAWQIDPFDAVIDEhGMLCGRGAADMKGSLASMTVAAERFVADFPDHKGKVAFLITSD 140
                                                   ***************9987544******************************************* PP

                                     TIGR01246 130 eegeaidGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYP 194
                                                   eeg a +Gtk+vve l +r+e +d+++vgePss+  +GDv+k+GrrGs+ +kl+++G+qGhvaYP
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_16410 141 EEGPAHHGTKAVVERLAARKERLDWCIVGEPSSTTLVGDVVKNGRRGSLGAKLTVRGVQGHVAYP 205
                                                   ***************************************************************** PP

                                     TIGR01246 195 hkaenPvhkavpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssev 259
                                                   h+a+nP+h a+p+l+el+a+++D+Gn+ffpp+s+qi+n+++gtga+nviPg+l + fn+rfs+e+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_16410 206 HLAKNPIHLAAPALAELAAEHWDHGNDFFPPTSFQISNVNSGTGATNVIPGDLVAVFNFRFSTES 270
                                                   ***************************************************************** PP

                                     TIGR01246 260 seeelkskvekildkhkldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDa 324
                                                   ++e l+++v++ildkh+ld++++w lsg pflt+ g l+++v ++i+ ++++++++stsGGtsD+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_16410 271 TVEGLQQRVADILDKHGLDWHVDWALSGLPFLTEPGALLDAVSASIKTITGRETKASTSGGTSDG 335
                                                   ***************************************************************** PP

                                     TIGR01246 325 rfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                                   rfia++g++vvelG+vn+tih+vne+v  +dl+ l+e+y+++l++l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_16410 336 RFIATMGTQVVELGPVNATIHQVNERVLASDLDLLTEIYYQTLIKL 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: 7.45
//
[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