Alignments for a candidate for dapE in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Dinoroseobacter shibae DFL-12

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate 3606580 Dshi_0012 succinyl-diaminopimelate desuccinylase (RefSeq)

Query= curated2:Q3IYS2
         (380 letters)



>FitnessBrowser__Dino:3606580
          Length = 379

 Score =  582 bits (1500), Expect = e-171
 Identities = 285/377 (75%), Positives = 316/377 (83%)

Query: 4   DPVALTADLVRCPSVTPEEGGALDLIERILSGAGFDCTRVDRNGVPNLFARWGRKGANRT 63
           DPVALTADL+RCPSVTPEEGGAL L+E  LS AGF CTRVDRNG+ NLFARWG KG  R+
Sbjct: 3   DPVALTADLIRCPSVTPEEGGALSLLEARLSAAGFACTRVDRNGIANLFARWGEKGHARS 62

Query: 64  FGFNGHTDVVPVGDAAAWTRDPFGGEIADGWLWGRGATDMKSGVAAFVAAAVDFVQETPP 123
           FGFNGHTDVVPVG  A W  DPFG ++   W++GRGA DMKS VAAF AAA+DFV +TPP
Sbjct: 63  FGFNGHTDVVPVGARADWRFDPFGAQVEGDWMYGRGAVDMKSAVAAFAAAAMDFVADTPP 122

Query: 124 DGAVVLTITGDEEGDSTDGTVALLDWMAAEGEAMSVCLVGEPTCPERLGEMMKIGRRGSM 183
           DGAV+L ITGDEEGD+ DGTVALLDWMAA+GEAM VCLVGEPTCP+ +GEMMKIGRRGSM
Sbjct: 123 DGAVILAITGDEEGDAKDGTVALLDWMAAQGEAMDVCLVGEPTCPDEMGEMMKIGRRGSM 182

Query: 184 TAFFTARGVQGHSAYPHRAKNPVAALARLIDRLSSHDLDYGTEHFDASTLAVTTFDTGNP 243
           T FF A GVQGHSAYPHRAKNP+ ALA+L+DRL+  +LD GT+HFD STLAVTTFDTGNP
Sbjct: 183 TFFFEALGVQGHSAYPHRAKNPLPALAKLVDRLAGLELDTGTDHFDPSTLAVTTFDTGNP 242

Query: 244 ATNVIPALCRATVNIRFNDAHSGASLTRWLEEEAARVAADTGVEIALSAKISGESFLTPP 303
           A NVIPA CRATVNIRFNDAHS  SLT  +   AA VAA+TG+EI     +SGESF+TPP
Sbjct: 243 ANNVIPAACRATVNIRFNDAHSSESLTAMVRGIAAEVAAETGIEITDRVSVSGESFITPP 302

Query: 304 GELSELVARAVEAETGLRPEPSTSGGTSDARFVRAHCPVVEFGLVGKTMHQVDERVEVAQ 363
           G LS+LVA AVE ETG  P  STSGGTSDARFV+ HCPVVEFGLVGK+MHQVDERV +AQ
Sbjct: 303 GRLSDLVAAAVETETGRVPVLSTSGGTSDARFVQHHCPVVEFGLVGKSMHQVDERVAIAQ 362

Query: 364 IEPLKAIYLRILKDYFA 380
           I  LKAIY RIL+DYFA
Sbjct: 363 IPQLKAIYTRILRDYFA 379


Lambda     K      H
   0.318    0.135    0.408 

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: 582
Number of extensions: 14
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: 380
Length of database: 379
Length adjustment: 30
Effective length of query: 350
Effective length of database: 349
Effective search space:   122150
Effective search space used:   122150
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 3606580 Dshi_0012 (succinyl-diaminopimelate desuccinylase (RefSeq))
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.18083.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-115  372.1   0.0   1.7e-115  371.9   0.0    1.0  1  lcl|FitnessBrowser__Dino:3606580  Dshi_0012 succinyl-diaminopimela


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3606580  Dshi_0012 succinyl-diaminopimelate desuccinylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.9   0.0  1.7e-115  1.7e-115       3     368 ..       6     375 ..       4     377 .. 0.96

  Alignments for each domain:
  == domain 1  score: 371.9 bits;  conditional E-value: 1.7e-115
                         TIGR01246   3 elakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt..eepvlvfaGhtDvvPaGelekWss 77 
                                       +l+ +Li+ +svtP++ ga++l+++rL++ gf++ ++  ++++nl+a+ g   ++  + f GhtDvvP+G   +W+ 
  lcl|FitnessBrowser__Dino:3606580   6 ALTADLIRCPSVTPEEGGALSLLEARLSAAGFACTRVDRNGIANLFARWGEkgHARSFGFNGHTDVVPVGARADWRF 82 
                                       6899*******************************************99886677899******************* PP

                         TIGR01246  78 dpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkkvvetlkerdelidy 154
                                       dpf ++++   +ygrGa+Dmk+++aaf +aa +fv++ +   G + l it Deeg+a+dGt+++++++ ++ e +d 
  lcl|FitnessBrowser__Dino:3606580  83 DPFGAQVEGDWMYGRGAVDMKSAVAAFAAAAMDFVADTPP-DGAVILAITGDEEGDAKDGTVALLDWMAAQGEAMDV 158
                                       ***********************************99875.8*********************************** PP

                         TIGR01246 155 avvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffppsslqia 231
                                       ++vgeP++ +++G+++kiGrrGs+t+ ++  G+qGh aYPh+a+nP++ +++++ +l+  +lD G+++f ps l ++
  lcl|FitnessBrowser__Dino:3606580 159 CLVGEPTCPDEMGEMMKIGRRGSMTFFFEALGVQGHSAYPHRAKNPLPALAKLVDRLAGLELDTGTDHFDPSTLAVT 235
                                       ***************************************************************************** PP

                         TIGR01246 232 nieagtgasnviPgelkvkfnlrfssevseeelkskvekildkh....kldYelewklsgepfltkegklikkvaea 304
                                         ++g+ a+nviP++ +++ n+rf+  +s+e+l   v+ i  +     +++ + + ++sge+f+t  g+l + va+a
  lcl|FitnessBrowser__Dino:3606580 236 TFDTGNPANNVIPAACRATVNIRFNDAHSSESLTAMVRGIAAEVaaetGIEITDRVSVSGESFITPPGRLSDLVAAA 312
                                       *********************************999988776654444888888899******************** PP

                         TIGR01246 305 ieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklle 368
                                       +e  +++ p lstsGGtsDarf+++  + vve+Glv +++h+v+e+v i+++ +l+++y+++l+
  lcl|FitnessBrowser__Dino:3606580 313 VETETGRVPVLSTSGGTSDARFVQHH-CPVVEFGLVGKSMHQVDERVAIAQIPQLKAIYTRILR 375
                                       ***********************998.*********************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (379 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.84
//
[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