GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Lentibacillus jeotgali Grbi

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_029329001.1 ON01_RS05555 diaminopimelate epimerase

Query= SwissProt::Q81XR2
         (288 letters)



>NCBI__GCF_000224785.1:WP_029329001.1
          Length = 287

 Score =  288 bits (738), Expect = 7e-83
 Identities = 137/284 (48%), Positives = 194/284 (68%), Gaps = 4/284 (1%)

Query: 1   MSQFSFTKMHGLGNSYIYVNMFEEQ---IPEEDLALVAEKVSNINTGIGADGMILICPSD 57
           M +  FTKM GLGN+Y+  +        +PE D   +A +VS+++ GIG+DG+ILI  S+
Sbjct: 1   MGELMFTKMQGLGNNYVVFDQLGHSANILPENDYPELARRVSDMSFGIGSDGIILIGASE 60

Query: 58  VAPVKMRMFNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEE-G 116
            A  KMR+FN DGSE K+CGNGLRCVAK+ Y+++  +D  F+IETL G+VT +VTV    
Sbjct: 61  QADFKMRIFNKDGSEAKNCGNGLRCVAKFLYDNQYPKDPRFSIETLGGVVTVDVTVNHHN 120

Query: 117 KVTLAKIDMGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDV 176
           +     +DMG PRL +  IPM G+ +   ++E + + +  Y  T +SMGNPHA+IFVDDV
Sbjct: 121 QAAYVTVDMGKPRLAKKMIPMQGDPDETAVKEVYTFGDKSYQLTCLSMGNPHAIIFVDDV 180

Query: 177 EQAPLTTLGPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVA 236
           ++ PL T+GP++E   +FPERVN+  + + N++E+N+RVWERGSG+T ACGTGACA+V A
Sbjct: 181 DKVPLETIGPIIEHSSLFPERVNIGVVHVKNQQEINYRVWERGSGITMACGTGACASVAA 240

Query: 237 SILNGKMERGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRG 280
           + LN  +   +   VHL GGDL I   + G++LM+G A  IC G
Sbjct: 241 AALNNLLNTTQPTLVHLPGGDLTIELADNGHILMQGKACYICHG 284


Lambda     K      H
   0.318    0.136    0.398 

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: 269
Number of extensions: 10
Number of successful extensions: 3
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: 288
Length of database: 287
Length adjustment: 26
Effective length of query: 262
Effective length of database: 261
Effective search space:    68382
Effective search space used:    68382
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_029329001.1 ON01_RS05555 (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.983538.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.6e-93  299.0   0.0    1.8e-93  298.9   0.0    1.0  1  NCBI__GCF_000224785.1:WP_029329001.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_029329001.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.9   0.0   1.8e-93   1.8e-93       2     268 ..       5     286 ..       4     287 .] 0.90

  Alignments for each domain:
  == domain 1  score: 298.9 bits;  conditional E-value: 1.8e-93
                             TIGR00652   2 eFlkmhGlgNdFvlvdevd..eelvkee..aelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSea 70 
                                            F+km+GlgN++v+ d++   ++++ e+  +el+r+v+d+ +g+g+Dg++l+ + se+ad+k+rifN DGSea
  NCBI__GCF_000224785.1:WP_029329001.1   5 MFTKMQGLGNNYVVFDQLGhsANILPENdyPELARRVSDMSFGIGSDGIILIGA-SEQADFKMRIFNKDGSEA 76 
                                           6****************9865666666679***********************5.****************** PP

                             TIGR00652  71 emCGNgiRcfakfvyekglkekkelsvetlaglikveveeen....kkvkvdmgepkfkkeeipltvekee.. 137
                                           ++CGNg+Rc+akf+y++++ +  ++s+etl g+++v v+ +     + v+vdmg+p++ k+ ip++++++e  
  NCBI__GCF_000224785.1:WP_029329001.1  77 KNCGNGLRCVAKFLYDNQYPKDPRFSIETLGGVVTVDVTVNHhnqaAYVTVDMGKPRLAKKMIPMQGDPDEta 149
                                           *********************9***********998776555558999******************6655511 PP

                             TIGR00652 138 ekeellalev...l.vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyER 206
                                           +ke+ ++ +    l ++++GnPH+++fv+dv+k++le++g+ +e++  fpe+vN+ +v+vk+++ei  rv+ER
  NCBI__GCF_000224785.1:WP_029329001.1 150 VKEVYTFGDKsyqLtCLSMGNPHAIIFVDDVDKVPLETIGPIIEHSSLFPERVNIGVVHVKNQQEINYRVWER 222
                                           445555555465527********************************************************** PP

                             TIGR00652 207 GageTlaCGtGavAsavvalk..lgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268
                                           G+g+T+aCGtGa+As+++a+   l +t +   vhl+gg+L+ie+ ++g+++++G+a ++++gel
  NCBI__GCF_000224785.1:WP_029329001.1 223 GSGITMACGTGACASVAAAALnnLLNTTQPTLVHLPGGDLTIELADNGHILMQGKACYICHGEL 286
                                           ****************99987445555666*******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (287 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: 00:00:00.00
# Mc/sec: 13.54
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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