Alignments for a candidate for dapE in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Sulfurimonas denitrificans DSM 1251

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate WP_011373074.1 SUDEN_RS07550 succinyl-diaminopimelate desuccinylase

Query= BRENDA::O25002
         (383 letters)



>NCBI__GCF_000012965.1:WP_011373074.1
          Length = 365

 Score =  332 bits (851), Expect = 1e-95
 Identities = 172/381 (45%), Positives = 250/381 (65%), Gaps = 22/381 (5%)

Query: 1   MDALEITQKLISYPTITPKECGIFEYIKSLFPHFKTLECGENGVKNLFLYRIFNPPKDHA 60
           M  +E+ + +IS  + TP + G+ ++I++    F+ +     GVKNLFLY+ F+      
Sbjct: 1   MKTIELFKFMISAKSQTPDDGGLLDFIQNYLDDFEAIRVDVEGVKNLFLYKKFSQGD--- 57

Query: 61  EEKHAKENTKPLHFCFAGHIDVVPPGNHWQSDPFKPVIKEGFLYGRGAQDMKGGVGAFLS 120
                       H CFAGH+DVVP G+ W SDP+    ++G++YGRGAQDMK GV AF+ 
Sbjct: 58  ------------HLCFAGHVDVVPAGDGWDSDPYIATERDGYIYGRGAQDMKSGVAAFVQ 105

Query: 121 A---SLNFNPKTPFLLSILLTSDEEGPGIFGTRLMLEKLKEKDLLPHMAIVAEPTCEKVL 177
           A   + +FN      LS+LLTSDEEG G +GT  +L  L++K +LP  A+VAEPTCE V 
Sbjct: 106 AIKDTKHFNGT----LSLLLTSDEEGEGTYGTIEVLNYLRDKSMLPDFAVVAEPTCEMVF 161

Query: 178 GDSIKIGRRGSINGKLILKGVQGHVAYPQKCQNPIDTLASVLPLISGVNLDNGDEYFDPS 237
           GD+IK+GRRGSING + L+G QGH AYP+K  NPI+ +A  L  ++GV+LDNGDE+F PS
Sbjct: 162 GDAIKVGRRGSINGYITLRGKQGHAAYPEKSINPINLIAPKLANMAGVDLDNGDEFFSPS 221

Query: 238 KLVITNLHAGLGANNITPASVEIIFNARHSLKTTKESLKEYLEKVLKDLPYTLELESSSS 297
           K VIT++ AG+   N+TP  ++++FN R++  T+++ ++E++EK L+DL Y L L   S 
Sbjct: 222 KFVITDIRAGMQVTNVTPNELKMMFNVRNTTLTSQKEIREFVEKNLEDLDYDLRLTQGSY 281

Query: 298 PFITASHSKLTSVLKENILKTCHTTPLLNTKGGTSDARFFSAHGIEVVEFGVINDRIHAI 357
           PF T + +KL   +  +I +     P  +T GGTSDAR  +  GI+V+EFGVIND IHAI
Sbjct: 282 PFKTDTKTKLVKNIDASIEQISGIKPKHSTAGGTSDARHMAPLGIDVIEFGVINDTIHAI 341

Query: 358 DERVSLKELELLEKVFLGVLE 378
           +ER +  E++ L +VF  +++
Sbjct: 342 NERTTKDEVKKLYEVFKHLID 362


Lambda     K      H
   0.318    0.138    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: 380
Number of extensions: 11
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: 383
Length of database: 365
Length adjustment: 30
Effective length of query: 353
Effective length of database: 335
Effective search space:   118255
Effective search space used:   118255
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 WP_011373074.1 SUDEN_RS07550 (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.10786.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-133  429.5   0.1   6.1e-133  429.3   0.1    1.0  1  lcl|NCBI__GCF_000012965.1:WP_011373074.1  SUDEN_RS07550 succinyl-diaminopi


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012965.1:WP_011373074.1  SUDEN_RS07550 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.3   0.1  6.1e-133  6.1e-133       3     368 ..       5     362 ..       3     364 .. 0.98

  Alignments for each domain:
  == domain 1  score: 429.3 bits;  conditional E-value: 6.1e-133
                                 TIGR01246   3 elakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgt.eepvlvfaGhtDvvPaG 70 
                                               el k +is ks tP+d g +++i++ L   +fe+ ++ +e++knl++ +++ + ++l+faGh+DvvPaG
  lcl|NCBI__GCF_000012965.1:WP_011373074.1   5 ELFKFMISAKSQTPDDGGLLDFIQNYLD--DFEAIRVDVEGVKNLFLYKKFsQGDHLCFAGHVDVVPAG 71 
                                               788899**********************..*****************99997889************** PP

                                 TIGR01246  71 elekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtk 139
                                                 + W+sdp+ ++erdG++ygrGa+Dmk+++aafv+a +    +   ++G+lsll+tsDeege  +Gt+
  lcl|NCBI__GCF_000012965.1:WP_011373074.1  72 --DGWDSDPYIATERDGYIYGRGAQDMKSGVAAFVQAIK----DTKHFNGTLSLLLTSDEEGEGTYGTI 134
                                               ..99********************************977....8999********************** PP

                                 TIGR01246 140 kvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvl 208
                                               +v+++l+++++l+d+avv+eP+++   GD ik+GrrGsi+g ++++G+qGh aYP+k++nP++ ++p l
  lcl|NCBI__GCF_000012965.1:WP_011373074.1 135 EVLNYLRDKSMLPDFAVVAEPTCEMVFGDAIKVGRRGSINGYITLRGKQGHAAYPEKSINPINLIAPKL 203
                                               ********************************************************************* PP

                                 TIGR01246 209 keliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkl 277
                                               ++++ ++lD+G+eff+ps++ i++i+ag++++nv+P+elk++fn+r+++ +s++e+++ vek l++  l
  lcl|NCBI__GCF_000012965.1:WP_011373074.1 204 ANMAGVDLDNGDEFFSPSKFVITDIRAGMQVTNVTPNELKMMFNVRNTTLTSQKEIREFVEKNLED--L 270
                                               **************************************************************9998..* PP

                                 TIGR01246 278 dYelewklsgepfltk.egklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtih 345
                                               dY+l++++ + pf t+ + kl+k++ ++ie+++++kp+ st+GGtsDar++a lg +v+e+G++ndtih
  lcl|NCBI__GCF_000012965.1:WP_011373074.1 271 DYDLRLTQGSYPFKTDtKTKLVKNIDASIEQISGIKPKHSTAGGTSDARHMAPLGIDVIEFGVINDTIH 339
                                               ***************9899************************************************** PP

                                 TIGR01246 346 kvneavkiedleklsevyeklle 368
                                               ++ne+++ ++++kl+ev+++l+ 
  lcl|NCBI__GCF_000012965.1:WP_011373074.1 340 AINERTTKDEVKKLYEVFKHLID 362
                                               *******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (365 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.59
//
[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