Alignments for a candidate for dapF in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapF in Shewanella oneidensis MR-1

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate 203387 SO4308 diaminopimelate epimerase (NCBI ptt file)

Query= SwissProt::P0A6K1
         (274 letters)



>FitnessBrowser__MR1:203387
          Length = 275

 Score =  394 bits (1011), Expect = e-114
 Identities = 189/274 (68%), Positives = 217/274 (79%)

Query: 1   MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60
           +QF+KMHGLGNDFMVVD +TQNVFFSPE IRRLADR+ GVGFDQLL+VEPPYDP+LDFHY
Sbjct: 2   IQFTKMHGLGNDFMVVDGITQNVFFSPEQIRRLADRNFGVGFDQLLLVEPPYDPDLDFHY 61

Query: 61  RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120
           RIFNADG EV  CGNGARCFARFVR KGLTNK  IRVST+ G+M L +  D  V VNMG 
Sbjct: 62  RIFNADGGEVENCGNGARCFARFVRNKGLTNKNKIRVSTSAGKMTLRLERDGTVTVNMGV 121

Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180
           P  EPS +PF+A KAEKTY+++  +QT LCG  SMGNPHCV+ V+DV  A V  +G +L 
Sbjct: 122 PVLEPSQIPFKAKKAEKTYLLQTPQQTFLCGAASMGNPHCVLDVEDVANANVAEIGALLT 181

Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240
            HERFP   N+GFMQVV   HI+LRVYERGA ET ACG+GACAAV VG  QG L ++V+V
Sbjct: 182 KHERFPRGVNVGFMQVVNAGHIKLRVYERGAAETLACGTGACAAVVVGQIQGKLDQQVQV 241

Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274
           +LPGG L I W+G G PL+MTGPA HVYDG I L
Sbjct: 242 DLPGGSLTINWEGEGKPLWMTGPAQHVYDGQIQL 275


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: 281
Number of extensions: 6
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: 275
Length adjustment: 25
Effective length of query: 249
Effective length of database: 250
Effective search space:    62250
Effective search space used:    62250
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 203387 SO4308 (diaminopimelate epimerase (NCBI ptt file))
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.503.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.9e-102  327.7   0.0   3.3e-102  327.5   0.0    1.0  1  lcl|FitnessBrowser__MR1:203387  SO4308 diaminopimelate epimerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203387  SO4308 diaminopimelate epimerase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.5   0.0  3.3e-102  3.3e-102       1     269 [.       2     274 ..       2     275 .] 0.96

  Alignments for each domain:
  == domain 1  score: 327.5 bits;  conditional E-value: 3.3e-102
                       TIGR00652   1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemCGNgiR 78 
                                     ++F+kmhGlgNdF++vd ++++++++ +e++r+++dr++gvg+D++llvep ++++ d+++rifN+DG e+e+CGNg+R
  lcl|FitnessBrowser__MR1:203387   2 IQFTKMHGLGNDFMVVDGITQNVFFS-PEQIRRLADRNFGVGFDQLLLVEPpYDPDLDFHYRIFNADGGEVENCGNGAR 79 
                                     69***********************9.9**********************999************************** PP

                       TIGR00652  79 cfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalev..l...vvdv 152
                                     cfa+fv++kgl++k++++v+t ag++++ +e+++ +v+v+mg p +++++ip++++k+e+ ++ll++    +   + ++
  lcl|FitnessBrowser__MR1:203387  80 CFARFVRNKGLTNKNKIRVSTSAGKMTLRLERDG-TVTVNMGVPVLEPSQIPFKAKKAEK-TYLLQTPQqtFlcgAASM 156
                                     **********************************.********************99888.55555554453579**** PP

                       TIGR00652 153 GnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAsavvalklgkt 231
                                     GnPH+v+ vedv ++++ e+g+ll +he+fp gvNv f++v++  +iklrvyERGa eTlaCGtGa+A++vv+  +gk+
  lcl|FitnessBrowser__MR1:203387 157 GNPHCVLDVEDVANANVAEIGALLTKHERFPRGVNVGFMQVVNAGHIKLRVYERGAAETLACGTGACAAVVVGQIQGKL 235
                                     ******************************************************************************* PP

                       TIGR00652 232 kkkvtvhleggeLeievkedg.kvyltGpavlvlegela 269
                                     +++v+v l+gg+L+i+++ +g  +++tGpa++v++g+++
  lcl|FitnessBrowser__MR1:203387 236 DQQVQVDLPGGSLTINWEGEGkPLWMTGPAQHVYDGQIQ 274
                                     *********************99*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (275 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.03
//
[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