GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapF in Burkholderia phytofirmans PsJN

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate BPHYT_RS01665 BPHYT_RS01665 diaminopimelate epimerase

Query= SwissProt::P0A6K1
         (274 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS01665 BPHYT_RS01665
           diaminopimelate epimerase
          Length = 299

 Score =  282 bits (721), Expect = 7e-81
 Identities = 149/283 (52%), Positives = 182/283 (64%), Gaps = 9/283 (3%)

Query: 1   MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60
           ++F+KMHG GNDF+V+D  TQ V  +P  +R LADRH GVG DQLL+VE P    +DF Y
Sbjct: 3   LKFTKMHGAGNDFVVLDGYTQPVNLTPAQVRALADRHFGVGADQLLLVEKPTVAGVDFRY 62

Query: 61  RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120
           RIFN DG EV  CGNGARCF +FVR  GLT++R +RV    G + LT+ ++  V V+MG 
Sbjct: 63  RIFNCDGGEVEHCGNGARCFVKFVRDSGLTDQRSVRVQVQKGTITLTMQENGEVLVDMGT 122

Query: 121 PNFEPSAVPF-------RANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVE 173
           P F+P  VPF       R   A+  + +     T    VVSMGNPH V  VDDV+   V 
Sbjct: 123 PVFDPERVPFATKGLQGRGEGADTLWPLDVNGTTRWISVVSMGNPHAVQVVDDVEAFPVL 182

Query: 174 TLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGL 233
             GPV+E H RFP+R N GFMQ+V R  I+LRVYERGAGET ACG+GACAAVA GI++GL
Sbjct: 183 VEGPVIERHARFPQRVNAGFMQIVGRSEIKLRVYERGAGETLACGTGACAAVAAGIRRGL 242

Query: 234 LAEEVRVELPGGRLDIAWKG--PGHPLYMTGPAVHVYDGFIHL 274
           L   V V   GG+L I W       PL M GPA  V++G I L
Sbjct: 243 LDAPVLVHTHGGKLTITWDAAQADQPLLMAGPAATVFEGEIEL 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: 254
Number of extensions: 6
Number of successful extensions: 4
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: 299
Length adjustment: 26
Effective length of query: 248
Effective length of database: 273
Effective search space:    67704
Effective search space used:    67704
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 BPHYT_RS01665 BPHYT_RS01665 (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.10716.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    1.5e-91  292.5   0.0    1.7e-91  292.3   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS01665  BPHYT_RS01665 diaminopimelate ep


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS01665  BPHYT_RS01665 diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.3   0.0   1.7e-91   1.7e-91       2     268 ..       4     283 ..       3     285 .. 0.92

  Alignments for each domain:
  == domain 1  score: 292.3 bits;  conditional E-value: 1.7e-91
                                TIGR00652   2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSea 70 
                                              +F+kmhG+gNdFv++d  ++ +  + +++vr+++drh+gvgaD++llve+ +    d+++rifN DG e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS01665   4 KFTKMHGAGNDFVVLDGYTQPVNLT-PAQVRALADRHFGVGADQLLLVEKpTVAGVDFRYRIFNCDGGEV 72 
                                              8******************766666.**********************9889999*************** PP

                                TIGR00652  71 emCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeeke 140
                                              e CGNg+Rcf+kfv+++gl+++++++v++++g+i+++++e++ +v vdmg+p f +e +p+ +++ + + 
  lcl|FitnessBrowser__BFirm:BPHYT_RS01665  73 EHCGNGARCFVKFVRDSGLTDQRSVRVQVQKGTITLTMQENG-EVLVDMGTPVFDPERVPFATKGLQGRG 141
                                              ******************************************.******************976665555 PP

                                TIGR00652 141 ellalev.........l..vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedei 199
                                              e + +           +  vv++GnPH+v +v+dve +++   g+++e h +fp++vN  f+++++++ei
  lcl|FitnessBrowser__BFirm:BPHYT_RS01665 142 EGADTLWpldvngttrWisVVSMGNPHAVQVVDDVEAFPVLVEGPVIERHARFPQRVNAGFMQIVGRSEI 211
                                              5544322445577766268*************************************************** PP

                                TIGR00652 200 klrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg...kvyltGpavlvleg 266
                                              klrvyERGageTlaCGtGa+A+++++++ g+++  v vh++gg+L+i++  ++    +++ Gpa +v+eg
  lcl|FitnessBrowser__BFirm:BPHYT_RS01665 212 KLRVYERGAGETLACGTGACAAVAAGIRRGLLDAPVLVHTHGGKLTITWDAAQadqPLLMAGPAATVFEG 281
                                              *************************************************87665569************* PP

                                TIGR00652 267 el 268
                                              e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS01665 282 EI 283
                                              97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (299 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.47
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see 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