Alignments for a candidate for dapF in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapF in Pseudomonas fluorescens FW300-N2E2

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate Pf6N2E2_6030 Diaminopimelate epimerase (EC 5.1.1.7)

Query= curated2:Q3IZB6
         (279 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6030
          Length = 267

 Score =  246 bits (628), Expect = 4e-70
 Identities = 129/264 (48%), Positives = 167/264 (63%), Gaps = 2/264 (0%)

Query: 10  LGFMKMHGAGNDFVVIDSRGRGGALVTAGLARALGDRHRGVGFDQLAEIRDQEGADCALD 69
           L F KMH  G+DFV++DSR      VT+ +A+ +GDR+RGVGF+QLA + D + AD  + 
Sbjct: 3   LNFQKMHANGDDFVIVDSRHSANP-VTSAMAQRMGDRNRGVGFNQLAVLLDCDDADARVM 61

Query: 70  FWNSDGSRSGTCGNATRCVSDYLMRDLGRDEVNLVTARGRLHARRREDGLVAVNMGAPQL 129
           FWN+DGS    CG+ATR  +D LMR+     V L T RG L   R   G ++V+MG P  
Sbjct: 62  FWNADGSALDVCGSATRGAADMLMREANVASVALRTNRGLLTCERTPTGDISVDMGVPLF 121

Query: 130 LWSEIPLARAMETDSLPLEGTPSAVGMGNPHCIYFVEDAEAVDLAGRGAAVETDPLFPER 189
            WS+IPLA+ ++T  LPL G+P A  MGNPHC YFV+D   VD+A  G A+ET+ LFP +
Sbjct: 122 DWSDIPLAQELDTTVLPLAGSPVACSMGNPHCTYFVDDLATVDIATIGPAIETNALFPLK 181

Query: 190 TNVEFASLIGPDRLRLRVWERGAGITLACGSGACATAVAAARRGLTGRQVRLEMDGGVLE 249
           TNV F  +I    +RLR+WERGAGI L  GS +C   V   RRGL   +V +E DGG + 
Sbjct: 182 TNVHFVQIIDRTHIRLRIWERGAGIALGSGSCSCGAVVNGIRRGLLDPRVEVECDGGSVT 241

Query: 250 VDWRDEG-VWLSGPVARVFEGHLS 272
           V W   G V+L GPV   F G +S
Sbjct: 242 VQWDGVGAVFLIGPVEVSFSGTMS 265


Lambda     K      H
   0.321    0.138    0.423 

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: 276
Number of extensions: 11
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: 279
Length of database: 267
Length adjustment: 25
Effective length of query: 254
Effective length of database: 242
Effective search space:    61468
Effective search space used:    61468
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate Pf6N2E2_6030 (Diaminopimelate epimerase (EC 5.1.1.7))
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.28259.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
    5.6e-62  195.6   0.0    6.3e-62  195.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6030  Diaminopimelate epimerase (EC 5.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6030  Diaminopimelate epimerase (EC 5.1.1.7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.4   0.0   6.3e-62   6.3e-62       2     268 ..       4     264 ..       3     266 .. 0.95

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 6.3e-62
                                      TIGR00652   2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNs 65 
                                                    +F kmh++g dFv+vd++++  + + +++++++ dr+ gvg+ ++ ++  + ++ad+++ ++N+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6030   4 NFQKMHANGDDFVIVDSRHSANPVT-SAMAQRMGDRNRGVGFNQLAVLL-DCDDADARVMFWNA 65 
                                                    7******************999998.79*****************9999.59************ PP

                                      TIGR00652  66 DGSeaemCGNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeei 129
                                                    DGS+ + CG + R +a  ++ ++ +   ++ + t++gl+++e + ++ +++vdmg p f  ++i
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6030  66 DGSALDVCGSATRGAADMLMREANV--ASVALRTNRGLLTCERTPTG-DISVDMGVPLFDWSDI 126
                                                    ********************99999..79******************.**************** PP

                                      TIGR00652 130 pltvekeeekeellalev..lvvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefv 191
                                                    pl +e +++   +l l+   ++ ++GnPH+  fv+d+ ++d+ ++g+++e++  fp ++Nv+fv
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6030 127 PLAQELDTT---VLPLAGspVACSMGNPHCTYFVDDLATVDIATIGPAIETNALFPLKTNVHFV 187
                                                    **9965555...555444348******************************************* PP

                                      TIGR00652 192 evkkedeiklrvyERGageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedgkvy 255
                                                    ++ ++ +i+lr++ERGag+ l  G+ ++ ++v +++ g+++ +v+v+ +gg++++++   g v+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6030 188 QIIDRTHIRLRIWERGAGIALGSGSCSCGAVVNGIRRGLLDPRVEVECDGGSVTVQWDGVGAVF 251
                                                    **************************************************************** PP

                                      TIGR00652 256 ltGpavlvlegel 268
                                                    l Gp+++ ++g++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6030 252 LIGPVEVSFSGTM 264
                                                    *******999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (267 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.68
//
[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