Alignments for a candidate for dapF in Phyllobacterium brassicacearum STM 196

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapF in Phyllobacterium brassicacearum STM 196

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_106712694.1 CU102_RS19150 diaminopimelate epimerase

Query= curated2:Q8YJF0
         (303 letters)



>NCBI__GCF_003010955.1:WP_106712694.1
          Length = 296

 Score =  469 bits (1207), Expect = e-137
 Identities = 226/295 (76%), Positives = 248/295 (84%)

Query: 1   MATKAAFARMNGLGNQIIVADMRGRADSITSAAAIRLASDSETAFDQIMAIHDPRTPGTD 60
           M   A FA+MNGLGN+IIVADMRGRAD IT  AAI L  D+ T FDQIMAIH  RT GT+
Sbjct: 1   MVAHAQFAKMNGLGNEIIVADMRGRADRITPEAAIALDRDTATKFDQIMAIHSARTDGTE 60

Query: 61  YYIAIINCDGTQAQACGNGTRCVVQALAAETGRHAFTFETRAGILTATEHDDGLISVDMG 120
            YI IIN DGTQAQACGNG RCVVQAL++ETG+H FTFET AGILTA EH DG ISVDMG
Sbjct: 61  AYIEIINSDGTQAQACGNGMRCVVQALSSETGKHEFTFETIAGILTAQEHPDGQISVDMG 120

Query: 121 TPRFDWQDIPLAQAVADTRKIELQVDPADAPVLHSPSIASMGNPHAVFWVDKDVWSYELD 180
            PRFDWQDIPLA+   DTRKIELQ+ P DAPVLHSPS+ASMGNPHA+FWVD+DVW+Y+++
Sbjct: 121 MPRFDWQDIPLAEPFHDTRKIELQIGPIDAPVLHSPSVASMGNPHAIFWVDQDVWTYDME 180

Query: 181 KFGPLLENHPIFPERANISIAHVTSSDTIDLRTWERGAGLTRACGSAACAAAVSAARTGR 240
           +FGPLLENHPIFPERANISIAHVTS   I LRTWERGAGLTRACGSAACAAAVSA RTGR
Sbjct: 181 RFGPLLENHPIFPERANISIAHVTSRHAITLRTWERGAGLTRACGSAACAAAVSAVRTGR 240

Query: 241 TGRKVTVNVPGGPLLIEWRDDDHVMMTGPAEWEFSGTFDPATGEWSRDTQGLQGS 295
           T R VTV VPGGPLLIEW ++DHV+MTGPAEWEFSG+ DP TG W RD    QG+
Sbjct: 241 TDRTVTVTVPGGPLLIEWLENDHVIMTGPAEWEFSGSLDPQTGAWQRDETPSQGA 295


Lambda     K      H
   0.318    0.132    0.408 

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: 425
Number of extensions: 13
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: 303
Length of database: 296
Length adjustment: 27
Effective length of query: 276
Effective length of database: 269
Effective search space:    74244
Effective search space used:    74244
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: 48 (23.1 bits)

Align candidate WP_106712694.1 CU102_RS19150 (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.619865.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.8e-68  216.3   0.0    3.4e-68  216.0   0.0    1.0  1  NCBI__GCF_003010955.1:WP_106712694.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106712694.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.0   0.0   3.4e-68   3.4e-68       2     268 ..       6     278 ..       5     279 .. 0.90

  Alignments for each domain:
  == domain 1  score: 216.0 bits;  conditional E-value: 3.4e-68
                             TIGR00652   2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemC 73 
                                           +F+km+GlgN+ ++ d + +    + +e + +  dr t +++D+++ ++    + ++++++i NsDG +a+ C
  NCBI__GCF_003010955.1:WP_106712694.1   6 QFAKMNGLGNEIIVADMRGRADRIT-PEAAIA-LDRDTATKFDQIMAIHSaRTDGTEAYIEIINSDGTQAQAC 76 
                                           8**********99999998777666.565555.699************987788999**************** PP

                             TIGR00652  74 GNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeiplt...vekeeekeell 143
                                           GNg+Rc+++ + ++++k  +e+++et ag+++++ + ++ +++vdmg p+f  ++ipl    +++ + + ++ 
  NCBI__GCF_003010955.1:WP_106712694.1  77 GNGMRCVVQALSSETGK--HEFTFETIAGILTAQEHPDG-QISVDMGMPRFDWQDIPLAepfHDTRKIELQIG 146
                                           **************999..7**************99999.******************944333333333443 PP

                             TIGR00652 144 alev....l....vvdvGnPHlvvfved.vekldleelgklleaheefpegvNvefvevkkedeiklrvyERG 207
                                              +    l    v ++GnPH+++ v++ v + d+e+ g+lle+h+ fpe+ N+ +++v+++++i+lr++ERG
  NCBI__GCF_003010955.1:WP_106712694.1 147 P--IdapvLhspsVASMGNPHAIFWVDQdVWTYDMERFGPLLENHPIFPERANISIAHVTSRHAITLRTWERG 217
                                           3..2557625677***********99876******************************************** PP

                             TIGR00652 208 ageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268
                                           ag T+aCG+ a+A+av a+++g+t++ vtv+++gg L ie+ e+++v++tGpa+  ++g l
  NCBI__GCF_003010955.1:WP_106712694.1 218 AGLTRACGSAACAAAVSAVRTGRTDRTVTVTVPGGPLLIEWLENDHVIMTGPAEWEFSGSL 278
                                           *****************************************************99888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (296 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: 19.33
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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 original 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