Alignments for a candidate for dapE in Pseudomonas benzenivorans DSM 8628

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Pseudomonas benzenivorans DSM 8628

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate WP_090443146.1 BLS63_RS09295 succinyl-diaminopimelate desuccinylase

Query= BRENDA::Q9KQ52
         (377 letters)



>NCBI__GCF_900100495.1:WP_090443146.1
          Length = 384

 Score =  476 bits (1225), Expect = e-139
 Identities = 241/375 (64%), Positives = 281/375 (74%), Gaps = 2/375 (0%)

Query: 4   SPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQS-PL 62
           S  L LA ELI R SVTP D GCQ+LM+ RL+ALGF IE M  E+  NFWA  G Q  P+
Sbjct: 9   SATLELACELIRRPSVTPVDEGCQELMMRRLQALGFRIEPMRIEEVENFWASHGEQDGPV 68

Query: 63  FVFAGHTDVVPAGPLSQWHTPPFEPTV-IDGFLHGRGAADMKGSLACMIVAVERFIAEHP 121
             FAGHTDVVP GPL  W   PF+  +   G L GRGAADMKGSLA MI+AVERF+A+HP
Sbjct: 69  LCFAGHTDVVPTGPLQAWQHQPFDALIDAQGMLCGRGAADMKGSLAAMIIAVERFVADHP 128

Query: 122 DHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRG 181
            H+G I FLITSDEEGP  +GT  V+E L ARNE +D CIVGEPSST  VGDVVKNGRRG
Sbjct: 129 KHKGRIAFLITSDEEGPAQHGTKAVIERLAARNERLDWCIVGEPSSTALVGDVVKNGRRG 188

Query: 182 SITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAG 241
           S+   L V+G QGHVAYPHLA NP+H A PALAELAA  WD+GNA+FPPTSFQ+ NL AG
Sbjct: 189 SLGATLTVRGVQGHVAYPHLARNPIHLAAPALAELAAEHWDDGNAFFPPTSFQVSNLNAG 248

Query: 242 TGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGE 301
           TGA+NVIPGE    FNFRFSTE T E +++RV ++LD HGLDY V+W LSG PFLT+ G 
Sbjct: 249 TGATNVIPGELRAVFNFRFSTESTVEGLQKRVEAILDRHGLDYHVEWALSGLPFLTEPGA 308

Query: 302 LLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADL 361
           LL AV A+++ V  +     T+GGTSDGRFIA +G QVVELGPVNATIH++NE V  +DL
Sbjct: 309 LLDAVAASIKAVTGRETTPSTSGGTSDGRFIATLGTQVVELGPVNATIHQINERVLASDL 368

Query: 362 EKLTDMYQKTLNHLL 376
           E LT++Y +TL  LL
Sbjct: 369 EVLTEIYYQTLVKLL 383


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: 18
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: 384
Length adjustment: 30
Effective length of query: 347
Effective length of database: 354
Effective search space:   122838
Effective search space used:   122838
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 WP_090443146.1 BLS63_RS09295 (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.31125.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-167  541.9   0.0   4.1e-167  541.7   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090443146.1  BLS63_RS09295 succinyl-diaminopi


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090443146.1  BLS63_RS09295 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  541.7   0.0  4.1e-167  4.1e-167       2     370 .]      12     382 ..      11     382 .. 0.98

  Alignments for each domain:
  == domain 1  score: 541.7 bits;  conditional E-value: 4.1e-167
                                 TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt.eepvlvfaGhtDvvPa 69 
                                               lela+eLi+r+svtP d+g+qel+++rL++lgf+ie +++e+++n+wa +g  + pvl+faGhtDvvP+
  lcl|NCBI__GCF_900100495.1:WP_090443146.1  12 LELACELIRRPSVTPVDEGCQELMMRRLQALGFRIEPMRIEEVENFWASHGEqDGPVLCFAGHTDVVPT 80 
                                               689***********************************************98578************** PP

                                 TIGR01246  70 GelekWssdpfepee.rdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidG 137
                                               G+l++W+ +pf++ +  +G+l grGaaDmkgslaa+++a+erfv+++++hkG++++litsDeeg a +G
  lcl|NCBI__GCF_900100495.1:WP_090443146.1  81 GPLQAWQHQPFDALIdAQGMLCGRGAADMKGSLAAMIIAVERFVADHPKHKGRIAFLITSDEEGPAQHG 149
                                               ***********9875279*************************************************** PP

                                 TIGR01246 138 tkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavp 206
                                               tk+v+e l +r+e +d+++vgePss+  +GDv+k+GrrGs+ ++l+++G+qGhvaYPh+a+nP+h a+p
  lcl|NCBI__GCF_900100495.1:WP_090443146.1 150 TKAVIERLAARNERLDWCIVGEPSSTALVGDVVKNGRRGSLGATLTVRGVQGHVAYPHLARNPIHLAAP 218
                                               ********************************************************************* PP

                                 TIGR01246 207 vlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkh 275
                                               +l+el+a+++D+Gn+ffpp+s+q++n++agtga+nviPgel++ fn+rfs+e+++e l+++ve+ild+h
  lcl|NCBI__GCF_900100495.1:WP_090443146.1 219 ALAELAAEHWDDGNAFFPPTSFQVSNLNAGTGATNVIPGELRAVFNFRFSTESTVEGLQKRVEAILDRH 287
                                               ********************************************************************* PP

                                 TIGR01246 276 kldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndti 344
                                               +ldY++ew lsg pflt+ g l+++va++i+ v++++++ stsGGtsD+rfia+lg++vvelG+vn+ti
  lcl|NCBI__GCF_900100495.1:WP_090443146.1 288 GLDYHVEWALSGLPFLTEPGALLDAVAASIKAVTGRETTPSTSGGTSDGRFIATLGTQVVELGPVNATI 356
                                               ********************************************************************* PP

                                 TIGR01246 345 hkvneavkiedleklsevyeklleel 370
                                               h++ne+v  +dle l+e+y+++l +l
  lcl|NCBI__GCF_900100495.1:WP_090443146.1 357 HQINERVLASDLEVLTEIYYQTLVKL 382
                                               *********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (384 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: 00:00:00.01
# Mc/sec: 11.67
//
[ok]

This GapMind analysis is from Apr 10 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