Alignments for a candidate for dapF in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapF in Pseudomonas fluorescens GW456-L13

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate PfGW456L13_844 Diaminopimelate epimerase (EC 5.1.1.7)

Query= SwissProt::P0A6K1
         (274 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_844
          Length = 276

 Score =  315 bits (808), Expect = 5e-91
 Identities = 150/274 (54%), Positives = 194/274 (70%)

Query: 1   MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60
           ++F+KMHGLGNDFMV+D V+Q+    P+  ++  DRH G+GFDQLL+VE P +P++DF Y
Sbjct: 3   LRFTKMHGLGNDFMVLDLVSQHAHILPKHAKQWGDRHTGIGFDQLLIVEAPSNPDVDFRY 62

Query: 61  RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120
           RIFN+DGSEV QCGNGARCFARFV  K LT KR IRV T +G + L V +D  + VNMG 
Sbjct: 63  RIFNSDGSEVEQCGNGARCFARFVLDKRLTAKRVIRVETKSGVIELDVRNDGQISVNMGA 122

Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180
           P   P+ +PF+A +  K+Y +      +    VSMGNPH V++V D++ A V  LGP +E
Sbjct: 123 PRLVPADIPFQAPEQAKSYQVDVDGTPVDLAAVSMGNPHAVLRVSDINNAPVHELGPKIE 182

Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240
            H RFP R N+GF+QV+ R   +LRV+ERGAGETQACG+GACAA    I QG +   + +
Sbjct: 183 HHPRFPARVNVGFLQVIDRSRAQLRVWERGAGETQACGTGACAAAVAAISQGWMDSPLLI 242

Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274
           +LPGGRL I W GPG P+ MTGPAV VY+G + L
Sbjct: 243 DLPGGRLSIEWAGPGQPVMMTGPAVRVYEGQVRL 276


Lambda     K      H
   0.323    0.140    0.425 

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: 259
Number of extensions: 7
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: 274
Length of database: 276
Length adjustment: 25
Effective length of query: 249
Effective length of database: 251
Effective search space:    62499
Effective search space used:    62499
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)

Align candidate PfGW456L13_844 (Diaminopimelate epimerase (EC 5.1.1.7))
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

# 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/TIGR00652.hmm
# target sequence database:        /tmp/gapView.23687.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00652  [M=270]
Accession:   TIGR00652
Description: DapF: diaminopimelate epimerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
    1.2e-96  309.2   0.0    1.4e-96  309.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_844  Diaminopimelate epimerase (EC 5.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_844  Diaminopimelate epimerase (EC 5.1.1.7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.1   0.0   1.4e-96   1.4e-96       2     268 ..       4     274 ..       3     276 .] 0.94

  Alignments for each domain:
  == domain 1  score: 309.1 bits;  conditional E-value: 1.4e-96
                                              TIGR00652   2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseea 56 
                                                            +F+kmhGlgNdF+++d v ++     ++ +++  drhtg+g+D++l+ve+ s+++ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_844   4 RFTKMHGLGNDFMVLDLVSQHAHIL-PKHAKQWGDRHTGIGFDQLLIVEApSNPDV 58 
                                                            8******************999988.9*********************9878999* PP

                                              TIGR00652  57 dvklrifNsDGSeaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeen 112
                                                            d+++rifNsDGSe+e+CGNg+Rcfa+fv +k l+ k+ ++vet++g+i++ v +++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_844  59 DFRYRIFNSDGSEVEQCGNGARCFARFVLDKRLTAKRVIRVETKSGVIELDVRNDG 114
                                                            ******************************************************** PP

                                              TIGR00652 113 kkvkvdmgepkfkkeeipltvekeeekeellalev....lvvdvGnPHlvvfvedv 164
                                                             +++v+mg p++ +++ip+++ ++++++++    +     +v++GnPH+v+ v+d+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_844 115 -QISVNMGAPRLVPADIPFQAPEQAKSYQVDVDGTpvdlAAVSMGNPHAVLRVSDI 169
                                                            .*******************65555545444433343425**************** PP

                                              TIGR00652 165 ekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavA 220
                                                            ++++++elg+++e+h++fp++vNv f++v ++++ +lrv+ERGageT+aCGtGa+A
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_844 170 NNAPVHELGPKIEHHPRFPARVNVGFLQVIDRSRAQLRVWERGAGETQACGTGACA 225
                                                            ******************************************************** PP

                                              TIGR00652 221 savvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegel 268
                                                            +av+a+ +g +++ + + l+gg+L ie+   g  v++tGpav+v+eg++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_844 226 AAVAAISQGWMDSPLLIDLPGGRLSIEWAGPGqPVMMTGPAVRVYEGQV 274
                                                            ********************************99*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (276 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: 6.85
//
[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