Alignments for a candidate for dapE in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Polaromonas naphthalenivorans CJ2

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate WP_011801201.1 PNAP_RS09060 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>NCBI__GCF_000015505.1:WP_011801201.1
          Length = 406

 Score =  434 bits (1115), Expect = e-126
 Identities = 226/402 (56%), Positives = 272/402 (67%), Gaps = 31/402 (7%)

Query: 4   TQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEEL-----HFGDTKNIWLR--- 55
           +++L LA++LISRPSVTPDD  CQ LL  RL  +GF  E +     HF  T N+W +   
Sbjct: 2   SRTLHLAEQLISRPSVTPDDAGCQALLIARLAPLGFKCETIVSGPEHFRVT-NLWAKFEG 60

Query: 56  ----------------------RGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGR 93
                                    K   + FAGHTDVVPTGP+ +W S PF P+ R G+
Sbjct: 61  FSPSAQAALAQPAIESIANTELSQAKVKTLVFAGHTDVVPTGPLAQWHSHPFTPSHRAGK 120

Query: 94  LYGRGAADMKTSIACFVTACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKAR 153
           LYGRG ADMKTSIA  V A E F+A HP    S+A LITSDEEG  +DGT  V D L AR
Sbjct: 121 LYGRGTADMKTSIAAMVVAVEEFLAAHPRPALSMAFLITSDEEGPGIDGTVVVCDRLLAR 180

Query: 154 DELIDYCIVGEPTAVDKLGDMIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPAL 213
            E++DYCIVGEPT+V +LGDMIKNGRRG+LSG L+VKG QGHIAYPHLA NP+H FAPAL
Sbjct: 181 GEVLDYCIVGEPTSVKQLGDMIKNGRRGTLSGKLSVKGVQGHIAYPHLAKNPIHLFAPAL 240

Query: 214 LELTQEVWDEGNEYFPPTSFQISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRV 273
            EL    WD+GN++FP TS+Q+SNI+ GTGA+NVIPG+L V FNFRF TEST   L+QR+
Sbjct: 241 AELVATQWDQGNDFFPATSWQVSNIHAGTGASNVIPGDLVVDFNFRFCTESTPESLQQRL 300

Query: 274 HAILDKHGVQYDLQWSCSGQPFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIK 333
            AIL KH  +Y+L+W+  G PFLT  G L D  R AI    G++ ELSTTGGTSDGRFI 
Sbjct: 301 LAILSKHQFEYELKWTLGGLPFLTTPGTLVDAVRGAILAETGVQTELSTTGGTSDGRFIA 360

Query: 334 AIAQELIELGPSNATIHQINENVRLNDIPKLSAVYEGILARL 375
            I  ++IELGP NATIHQINE V    +  L  +Y+G+L RL
Sbjct: 361 KICPQVIELGPVNATIHQINECVDTASLDPLKNIYKGVLERL 402


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: 482
Number of extensions: 20
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 381
Length of database: 406
Length adjustment: 31
Effective length of query: 350
Effective length of database: 375
Effective search space:   131250
Effective search space used:   131250
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_011801201.1 PNAP_RS09060 (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.23989.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.1e-152  491.8   0.0   7.3e-151  488.3   0.0    1.9  1  lcl|NCBI__GCF_000015505.1:WP_011801201.1  PNAP_RS09060 succinyl-diaminopim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011801201.1  PNAP_RS09060 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  488.3   0.0  7.3e-151  7.3e-151       2     370 .]       5     402 ..       4     402 .. 0.97

  Alignments for each domain:
  == domain 1  score: 488.3 bits;  conditional E-value: 7.3e-151
                                 TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefe....dtknlwatrgt............. 53 
                                               l+la++Lisr+svtP+dag+q+l+++rL  lgf++e++  +     ++nlwa+ +              
  lcl|NCBI__GCF_000015505.1:WP_011801201.1   5 LHLAEQLISRPSVTPDDAGCQALLIARLAPLGFKCETIVSGpehfRVTNLWAKFEGfspsaqaalaqpa 73 
                                               689**********************************9877333357899997544599999******* PP

                                 TIGR01246  54 ............eepvlvfaGhtDvvPaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaer 110
                                                           + ++lvfaGhtDvvP+G+l +W+s+pf+p++r GklygrG+aDmk+s+aa+vva+e+
  lcl|NCBI__GCF_000015505.1:WP_011801201.1  74 iesiantelsqaKVKTLVFAGHTDVVPTGPLAQWHSHPFTPSHRAGKLYGRGTADMKTSIAAMVVAVEE 142
                                               ********99887889***************************************************** PP

                                 TIGR01246 111 fvkknadhkGslsllitsDeegeaidGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsit 179
                                               f+++++    s+++litsDeeg  idGt+ v + l +r e +dy++vgeP+svk+lGD+ik+GrrG ++
  lcl|NCBI__GCF_000015505.1:WP_011801201.1 143 FLAAHPRPALSMAFLITSDEEGPGIDGTVVVCDRLLARGEVLDYCIVGEPTSVKQLGDMIKNGRRGTLS 211
                                               ********************************************************************* PP

                                 TIGR01246 180 gklkikGiqGhvaYPhkaenPvhkavpvlkeliaiklDeGneffppsslqianieagtgasnviPgelk 248
                                               gkl++kG+qGh+aYPh+a+nP+h ++p+l+el+a+++D+Gn+ffp++s q++ni+agtgasnviPg+l 
  lcl|NCBI__GCF_000015505.1:WP_011801201.1 212 GKLSVKGVQGHIAYPHLAKNPIHLFAPALAELVATQWDQGNDFFPATSWQVSNIHAGTGASNVIPGDLV 280
                                               ********************************************************************* PP

                                 TIGR01246 249 vkfnlrfssevseeelkskvekildkhkldYelewklsgepfltkegklikkvaeaieevlkkkpelst 317
                                               v fn+rf++e++ e+l++++ +il kh+ +Yel+w+l g pflt  g l+++v+ ai   ++ ++elst
  lcl|NCBI__GCF_000015505.1:WP_011801201.1 281 VDFNFRFCTESTPESLQQRLLAILSKHQFEYELKWTLGGLPFLTTPGTLVDAVRGAILAETGVQTELST 349
                                               ********************************************************************* PP

                                 TIGR01246 318 sGGtsDarfiaklgaevvelGlvndtihkvneavkiedleklsevyeklleel 370
                                               +GGtsD+rfiak+  +v+elG+vn+tih++ne+v  + l+ l+++y+ +le+l
  lcl|NCBI__GCF_000015505.1:WP_011801201.1 350 TGGTSDGRFIAKICPQVIELGPVNATIHQINECVDTASLDPLKNIYKGVLERL 402
                                               **************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (406 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 3.39
//
[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