Alignments for a candidate for dapE in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Dechlorosoma suillum PS

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate Dsui_2711 Dsui_2711 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__PS:Dsui_2711
          Length = 383

 Score =  493 bits (1270), Expect = e-144
 Identities = 243/375 (64%), Positives = 286/375 (76%)

Query: 2   TETQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAP 61
           T   +L+LA +LISR SVTP+D  C  L++ RL  +GF  E ++ G+T N+W RRG+ AP
Sbjct: 8   TSDPTLDLAAQLISRRSVTPEDGGCMDLISARLKPLGFTLEAINQGNTVNLWARRGSAAP 67

Query: 62  VVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHP 121
           +VC AGHTDVVPTGPVE+W S PF P  RDG LYGRGAADMK S+A FVTA E FVA+HP
Sbjct: 68  LVCLAGHTDVVPTGPVEQWASDPFTPTLRDGMLYGRGAADMKGSLAAFVTAVETFVARHP 127

Query: 122 NHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRG 181
            HQGSIA L+TSDEEGDA DGT  VV+ L+AR E ID CIVGEPT V++LGDM+KNGRRG
Sbjct: 128 QHQGSIAFLLTSDEEGDATDGTVAVVEALQARGEGIDCCIVGEPTCVNRLGDMVKNGRRG 187

Query: 182 SLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGG 241
           SLSG LTVKG QGHIAYPHLA NP+H  APA+ EL    WD+GNEYFPPT++Q+SNI GG
Sbjct: 188 SLSGRLTVKGIQGHIAYPHLAKNPIHLAAPAIAELAATEWDQGNEYFPPTTWQVSNIRGG 247

Query: 242 TGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGK 301
           TGATNVIPG +++ FNFRFST ST  GLK R+ A+L KHG+ YDL W+   +PFLT  G 
Sbjct: 248 TGATNVIPGTVDILFNFRFSTASTPEGLKSRLEAVLAKHGIDYDLAWTLGAKPFLTGRGP 307

Query: 302 LTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDI 361
           L D A AAI E   IE ELSTTGGTSDGRFI  I  ++IELGP NATIH+I+E V    +
Sbjct: 308 LVDAAMAAIREELNIETELSTTGGTSDGRFIAEICPQVIELGPVNATIHKIDECVEAAAL 367

Query: 362 PKLSAVYEGILARLL 376
           P+LSA Y  IL +LL
Sbjct: 368 PRLSATYCRILEKLL 382


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: 486
Number of extensions: 13
Number of successful extensions: 1
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: 383
Length adjustment: 30
Effective length of query: 351
Effective length of database: 353
Effective search space:   123903
Effective search space used:   123903
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 Dsui_2711 Dsui_2711 (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.13869.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     5e-166  538.2   0.0   5.7e-166  538.0   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_2711  Dsui_2711 succinyl-diaminopimela


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2711  Dsui_2711 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  538.0   0.0  5.7e-166  5.7e-166       2     370 .]      13     381 ..      12     381 .. 0.99

  Alignments for each domain:
  == domain 1  score: 538.0 bits;  conditional E-value: 5.7e-166
                         TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaGelekWssd 78 
                                       l+la +Lisr+svtP+d g+++li +rLk lgf+ e ++ ++t nlwa+rg  +p +++aGhtDvvP+G++e+W sd
  lcl|FitnessBrowser__PS:Dsui_2711  13 LDLAAQLISRRSVTPEDGGCMDLISARLKPLGFTLEAINQGNTVNLWARRGSAAPLVCLAGHTDVVPTGPVEQWASD 89 
                                       6899************************************************************************* PP

                         TIGR01246  79 pfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdelidya 155
                                       pf+p+ rdG+lygrGaaDmkgslaafv+a+e fv+++++h+Gs+++l+tsDeeg+a dGt++vve l++r e id +
  lcl|FitnessBrowser__PS:Dsui_2711  90 PFTPTLRDGMLYGRGAADMKGSLAAFVTAVETFVARHPQHQGSIAFLLTSDEEGDATDGTVAVVEALQARGEGIDCC 166
                                       ***************************************************************************** PP

                         TIGR01246 156 vvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffppsslqian 232
                                       +vgeP++v++lGD++k+GrrGs++g+l++kGiqGh+aYPh+a+nP+h a+p+++el+a+++D+Gne+fpp+  q++n
  lcl|FitnessBrowser__PS:Dsui_2711 167 IVGEPTCVNRLGDMVKNGRRGSLSGRLTVKGIQGHIAYPHLAKNPIHLAAPAIAELAATEWDQGNEYFPPTTWQVSN 243
                                       ***************************************************************************** PP

                         TIGR01246 233 ieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklikkvaeaieevl 309
                                       i++gtga+nviPg +++ fn+rfs+ ++ e lks++e++l kh++dY+l w+l ++pflt +g l++++++ai+e l
  lcl|FitnessBrowser__PS:Dsui_2711 244 IRGGTGATNVIPGTVDILFNFRFSTASTPEGLKSRLEAVLAKHGIDYDLAWTLGAKPFLTGRGPLVDAAMAAIREEL 320
                                       ***************************************************************************** PP

                         TIGR01246 310 kkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                       ++++elst+GGtsD+rfia++  +v+elG+vn+tihk++e+v+ + l +ls+ y ++le+l
  lcl|FitnessBrowser__PS:Dsui_2711 321 NIETELSTTGGTSDGRFIAEICPQVIELGPVNATIHKIDECVEAAALPRLSATYCRILEKL 381
                                       *********************************************************9986 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: 7.73
//
[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