GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Marinobacter adhaerens HP15

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate GFF249 HP15_248 diaminopimelate epimerase

Query= SwissProt::P0A6K1
         (274 letters)



>FitnessBrowser__Marino:GFF249
          Length = 304

 Score =  335 bits (858), Expect = 9e-97
 Identities = 166/274 (60%), Positives = 203/274 (74%)

Query: 1   MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60
           ++F+KMHGLGNDFMVVDA++Q     PE+IR LA+R+ G+GFDQLLVVEPP  P++DF Y
Sbjct: 12  LRFTKMHGLGNDFMVVDAISQPFRLRPEMIRELANRNFGIGFDQLLVVEPPGLPDVDFRY 71

Query: 61  RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120
           RIFNADGSEV QCGNGARCFARFVR + LTNK+ IRV TA G + L V  + +V VNMG 
Sbjct: 72  RIFNADGSEVEQCGNGARCFARFVRDQRLTNKKVIRVQTAKGVIELRVGREGMVMVNMGV 131

Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180
           P F P A+PF A++ +  Y +    QT+    +SMGNPH V+ V+DVD A VETLGP LE
Sbjct: 132 PEFNPPAIPFAADRRKDVYTVDVDGQTVELSALSMGNPHGVLLVEDVDQAPVETLGPKLE 191

Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240
            H RFP RANIGF+Q++ R H+RLRV+ERG+GET ACGSGACAAV  G  +GLL   V V
Sbjct: 192 RHPRFPARANIGFLQILDRTHVRLRVFERGSGETLACGSGACAAVVAGCLRGLLDARVEV 251

Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274
           EL GG L I W+G G P+ M GPA  V++G + L
Sbjct: 252 ELRGGPLVIEWQGEGTPVMMEGPATSVFEGQLRL 285


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: 300
Number of extensions: 8
Number of successful extensions: 2
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: 304
Length adjustment: 26
Effective length of query: 248
Effective length of database: 278
Effective search space:    68944
Effective search space used:    68944
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: 48 (23.1 bits)

Align candidate GFF249 HP15_248 (diaminopimelate epimerase)
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.19056.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
      6e-95  303.7   0.0    6.9e-95  303.5   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF249  HP15_248 diaminopimelate epimera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF249  HP15_248 diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.5   0.0   6.9e-95   6.9e-95       2     269 ..      13     284 ..      12     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 303.5 bits;  conditional E-value: 6.9e-95
                          TIGR00652   2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemCGNg 76 
                                        +F+kmhGlgNdF++vd + + +   ++e++r++++r++g+g+D++l+vep + ++ d+++rifN+DGSe+e+CGNg
  lcl|FitnessBrowser__Marino:GFF249  13 RFTKMHGLGNDFMVVDAISQPFRL-RPEMIRELANRNFGIGFDQLLVVEPpGLPDVDFRYRIFNADGSEVEQCGNG 87 
                                        8*****************965555.5***********************9899*********************** PP

                          TIGR00652  77 iRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeell.alevl... 148
                                        +Rcfa+fv+++ l++kk ++v+t +g+i++ v +e+  v v+mg p+f++ +ip+ ++  +  +++    +++   
  lcl|FitnessBrowser__Marino:GFF249  88 ARCFARFVRDQRLTNKKVIRVQTAKGVIELRVGREG-MVMVNMGVPEFNPPAIPFAADRRKDVYTVDvDGQTVels 162
                                        ************************************.******************965544433332022222345 PP

                          TIGR00652 149 vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAsavv 224
                                        ++++GnPH v+ vedv+++++e+lg++le h++fp++ N+ f++++++ +++lrv+ERG+geTlaCG+Ga+A++v+
  lcl|FitnessBrowser__Marino:GFF249 163 ALSMGNPHGVLLVEDVDQAPVETLGPKLERHPRFPARANIGFLQILDRTHVRLRVFERGSGETLACGSGACAAVVA 238
                                        **************************************************************************** PP

                          TIGR00652 225 alklgktkkkvtvhleggeLeievkedg.kvyltGpavlvlegela 269
                                        +   g+++ +v+v+l+gg L+ie++ +g  v+++Gpa+ v+eg+l 
  lcl|FitnessBrowser__Marino:GFF249 239 GCLRGLLDARVEVELRGGPLVIEWQGEGtPVMMEGPATSVFEGQLR 284
                                        ****************************9**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (304 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.21
//
[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:

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