Alignments for a candidate for dapE in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Halomonas desiderata SP1

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate WP_086509351.1 BZY95_RS07630 succinyl-diaminopimelate desuccinylase

Query= BRENDA::Q9KQ52
         (377 letters)



>NCBI__GCF_002151265.1:WP_086509351.1
          Length = 390

 Score =  476 bits (1224), Expect = e-139
 Identities = 234/373 (62%), Positives = 280/373 (75%), Gaps = 1/373 (0%)

Query: 4   SPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLF 63
           SP L LA ELI R SVTP D GCQ LMIERL+ LGF IE + F D  NFWA  G   P+ 
Sbjct: 10  SPTLQLAMELIRRPSVTPDDLGCQALMIERLERLGFHIERLPFGDVENFWATHGHHGPVL 69

Query: 64  VFAGHTDVVPAGPLSQWHTPPFEPTVID-GFLHGRGAADMKGSLACMIVAVERFIAEHPD 122
            FAGHTDVVP+GP + W  PPFEP + D G L GRG+ADMKGSLA MI AVERF+  HPD
Sbjct: 70  AFAGHTDVVPSGPHTYWEYPPFEPCIDDDGMLRGRGSADMKGSLAAMITAVERFVTAHPD 129

Query: 123 HQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGS 182
           H G I FLITSDEEGP ++GT  VVE L  R+E +D CIVGEPSST  +GDV+KNGRRGS
Sbjct: 130 HHGRIAFLITSDEEGPAVDGTRAVVEHLRERHERLDYCIVGEPSSTDVLGDVIKNGRRGS 189

Query: 183 ITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAGT 242
           + G L +KG QGHVAYPHLA NP+H+A+PAL  L    WD GNA+FP TSFQI N++AGT
Sbjct: 190 LGGVLHIKGIQGHVAYPHLARNPIHQAMPALDALVREHWDSGNAFFPATSFQISNIRAGT 249

Query: 243 GASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGEL 302
           GA+NVIPG+ +V FNFRFSTE+T E+++ R  ++LDAHGL+Y + WTL+G+PFLT  GEL
Sbjct: 250 GATNVIPGDVEVVFNFRFSTEVTHEQLRERTQAILDAHGLEYQLDWTLNGEPFLTAEGEL 309

Query: 303 LAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLE 362
           + A +  VE V  + P L T+GGTSDGRFIA +G+QVVELGP NATIH+ NE VR ADL+
Sbjct: 310 VDAALHGVEAVLGRRPKLSTSGGTSDGRFIATLGSQVVELGPRNATIHQTNERVRAADLD 369

Query: 363 KLTDMYQKTLNHL 375
            L+ +Y+  L  L
Sbjct: 370 DLSRIYEAILGKL 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: 509
Number of extensions: 15
Number of successful extensions: 2
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: 390
Length adjustment: 30
Effective length of query: 347
Effective length of database: 360
Effective search space:   124920
Effective search space used:   124920
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_086509351.1 BZY95_RS07630 (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.27306.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-168  546.8   0.0   1.4e-168  546.6   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509351.1  BZY95_RS07630 succinyl-diaminopi


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509351.1  BZY95_RS07630 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  546.6   0.0  1.4e-168  1.4e-168       2     370 .]      13     382 ..      12     382 .. 0.99

  Alignments for each domain:
  == domain 1  score: 546.6 bits;  conditional E-value: 1.4e-168
                                 TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaG 70 
                                               l+la+eLi+r+svtP+d g+q+l++erL++lgf+ie+l f+d++n+wat+g + pvl+faGhtDvvP+G
  lcl|NCBI__GCF_002151265.1:WP_086509351.1  13 LQLAMELIRRPSVTPDDLGCQALMIERLERLGFHIERLPFGDVENFWATHGHHGPVLAFAGHTDVVPSG 81 
                                               5899***************************************************************** PP

                                 TIGR01246  71 elekWssdpfepee.rdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGt 138
                                               ++  W+ +pfep +  dG+l grG+aDmkgslaa+++a+erfv++++dh+G++++litsDeeg a+dGt
  lcl|NCBI__GCF_002151265.1:WP_086509351.1  82 PHTYWEYPPFEPCIdDDGMLRGRGSADMKGSLAAMITAVERFVTAHPDHHGRIAFLITSDEEGPAVDGT 150
                                               ************87258**************************************************** PP

                                 TIGR01246 139 kkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpv 207
                                               ++vve l+er+e +dy++vgePss++ lGDvik+GrrGs+ g l+ikGiqGhvaYPh+a+nP+h+a+p+
  lcl|NCBI__GCF_002151265.1:WP_086509351.1 151 RAVVEHLRERHERLDYCIVGEPSSTDVLGDVIKNGRRGSLGGVLHIKGIQGHVAYPHLARNPIHQAMPA 219
                                               ********************************************************************* PP

                                 TIGR01246 208 lkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhk 276
                                               l +l+ +++D+Gn+ffp++s+qi+ni+agtga+nviPg+++v fn+rfs+ev++e+l+++ ++ild+h+
  lcl|NCBI__GCF_002151265.1:WP_086509351.1 220 LDALVREHWDSGNAFFPATSFQISNIRAGTGATNVIPGDVEVVFNFRFSTEVTHEQLRERTQAILDAHG 288
                                               ********************************************************************* PP

                                 TIGR01246 277 ldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtih 345
                                               l+Y+l+w+l gepflt eg+l++++ + +e vl+++p+lstsGGtsD+rfia+lg++vvelG+ n+tih
  lcl|NCBI__GCF_002151265.1:WP_086509351.1 289 LEYQLDWTLNGEPFLTAEGELVDAALHGVEAVLGRRPKLSTSGGTSDGRFIATLGSQVVELGPRNATIH 357
                                               ********************************************************************* PP

                                 TIGR01246 346 kvneavkiedleklsevyeklleel 370
                                               + ne+v+ +dl+ ls++ye +l +l
  lcl|NCBI__GCF_002151265.1:WP_086509351.1 358 QTNERVRAADLDDLSRIYEAILGKL 382
                                               ********************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (390 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: 00:00:00.02
# Mc/sec: 6.05
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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