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.23632.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: 6.62
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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:

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:

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:

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