Alignments for a candidate for dapE in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Dyella japonica UNC79MFTsu3.2

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate N515DRAFT_0745 N515DRAFT_0745 succinyldiaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0745
          Length = 377

 Score =  424 bits (1089), Expect = e-123
 Identities = 209/371 (56%), Positives = 257/371 (69%), Gaps = 2/371 (0%)

Query: 8   ELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAPVVCFAG 67
           +L  ELI R SVTPDD  CQ LLA RL ++GF  E L +G+  N+W   G   P++ F G
Sbjct: 6   DLTAELIRRRSVTPDDAGCQALLAGRLARVGFKVEHLRYGEVDNLWATHGEGGPLLMFLG 65

Query: 68  HTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNHQGSI 127
           HTDVVPTGP E W S PFEPA RDG LYGRGAADMK S+A    A E FV  HP+H+G +
Sbjct: 66  HTDVVPTGPAESWRSDPFEPAVRDGYLYGRGAADMKGSVAAMAVALEAFVTAHPDHRGRV 125

Query: 128 ALLITSDEEGDA-LDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSLSGN 186
             L+TSDEEG   LDG  KV +  +A  E ID+C+VGEP++ ++LGD+I+ GRRGSLS  
Sbjct: 126 GFLMTSDEEGPTNLDGVRKVAEHFRASGERIDWCVVGEPSSKERLGDLIRVGRRGSLSAT 185

Query: 187 LTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGATN 246
           LTV+G QGH+AYP  A NP+H FAPAL EL  E WDEGN  FPPTSFQ+SN+N GTGATN
Sbjct: 186 LTVRGIQGHVAYPEKAKNPIHAFAPALAELAAERWDEGNVDFPPTSFQVSNLNAGTGATN 245

Query: 247 VIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQA-GKLTDV 305
           VIPG L    NFR+ST S    L++RV  ILD+H + Y L W+ SG+PFL  A G L D 
Sbjct: 246 VIPGALVALVNFRYSTASRAEALRERVERILDRHKLDYALDWNLSGEPFLCPAGGALRDT 305

Query: 306 ARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDIPKLS 365
             +   + CG+E E ST GGTSDGRFI  +  E++ELGP NATIH+++E V + D+ KL 
Sbjct: 306 VVSVCRDLCGVEPEQSTGGGTSDGRFIAPLGAEVVELGPVNATIHKVDECVAVADLDKLP 365

Query: 366 AVYEGILARLL 376
           ++Y  I  RLL
Sbjct: 366 SLYRAICERLL 376


Lambda     K      H
   0.317    0.135    0.400 

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: 434
Number of extensions: 16
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: 381
Length of database: 377
Length adjustment: 30
Effective length of query: 351
Effective length of database: 347
Effective search space:   121797
Effective search space used:   121797
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate N515DRAFT_0745 N515DRAFT_0745 (succinyldiaminopimelate 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.32582.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.1e-162  526.3   0.0   2.4e-162  526.1   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0745  N515DRAFT_0745 succinyldiaminopi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0745  N515DRAFT_0745 succinyldiaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.1   0.0  2.4e-162  2.4e-162       2     370 .]       5     375 ..       4     375 .. 0.98

  Alignments for each domain:
  == domain 1  score: 526.1 bits;  conditional E-value: 2.4e-162
                                    TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvv 67 
                                                  ++l+ eLi+r+svtP+dag+q+l+a rL ++gf++e+l+++++ nlwat+g + p l+f GhtDvv
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0745   5 FDLTAELIRRRSVTPDDAGCQALLAGRLARVGFKVEHLRYGEVDNLWATHGEGGPLLMFLGHTDVV 70 
                                                  7899************************************************************** PP

                                    TIGR01246  68 PaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeege 133
                                                  P+G+ e+W+sdpfep++rdG+lygrGaaDmkgs+aa+ va e fv++++dh+G++++l+tsDeeg 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0745  71 PTGPAESWRSDPFEPAVRDGYLYGRGAADMKGSVAAMAVALEAFVTAHPDHRGRVGFLMTSDEEGP 136
                                                  *****************************************************************6 PP

                                    TIGR01246 134 .aidGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkae 198
                                                    +dG++kv+e +++  e id++vvgePss+++lGD+i++GrrGs++++l+++GiqGhvaYP+ka+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0745 137 tNLDGVRKVAEHFRASGERIDWCVVGEPSSKERLGDLIRVGRRGSLSATLTVRGIQGHVAYPEKAK 202
                                                  268*************************************************************** PP

                                    TIGR01246 199 nPvhkavpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeel 264
                                                  nP+h ++p+l+el+a+++DeGn  fpp+s+q++n++agtga+nviPg+l +  n+r+s+ + +e l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0745 203 NPIHAFAPALAELAAERWDEGNVDFPPTSFQVSNLNAGTGATNVIPGALVALVNFRYSTASRAEAL 268
                                                  ****************************************************************** PP

                                    TIGR01246 265 kskvekildkhkldYelewklsgepfltk.egklikkvaeaieevlkkkpelstsGGtsDarfiak 329
                                                  +++ve+ild+hkldY l+w+lsgepfl    g l ++v+++ + +++ +pe st+GGtsD+rfia 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0745 269 RERVERILDRHKLDYALDWNLSGEPFLCPaGGALRDTVVSVCRDLCGVEPEQSTGGGTSDGRFIAP 334
                                                  ****************************96789999****************************** PP

                                    TIGR01246 330 lgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                                  lgaevvelG+vn+tihkv+e+v ++dl+kl ++y+ + e+l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0745 335 LGAEVVELGPVNATIHKVDECVAVADLDKLPSLYRAICERL 375
                                                  ***********************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (377 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: 10.58
//
[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