Alignments for a candidate for dapF in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapF in Phaeobacter inhibens BS107

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate GFF3342 PGA1_c33950 diaminopimelate epimerase DapF

Query= curated2:Q3IZB6
         (279 letters)



>FitnessBrowser__Phaeo:GFF3342
          Length = 281

 Score =  298 bits (763), Expect = 9e-86
 Identities = 143/275 (52%), Positives = 193/275 (70%), Gaps = 2/275 (0%)

Query: 2   MDMGASSGLGFMKMHGAGNDFVVIDSRGRGGALVTAGLARALGDRHRGVGFDQLAEIRDQ 61
           M +G+ + L FMKMHG GNDFVV+D+R +    +T  +A  +  R  G+GFDQL  I   
Sbjct: 4   MTIGSDTRLPFMKMHGLGNDFVVVDARDQTWD-ITPAMAEGIAHRQMGIGFDQLTVITKG 62

Query: 62  EGADCALDFWNSDGSRSGTCGNATRCVSDYLMRDLGRDEVNLVTARGRLHARRREDGLVA 121
           +  D  L F+N+DGS S  CGNATRC++ +L+ + G+  + L T RG L A    +GL +
Sbjct: 63  D-EDAHLTFYNADGSTSAACGNATRCIARHLLDESGKTHLRLTTDRGLLLAEDAGNGLTS 121

Query: 122 VNMGAPQLLWSEIPLARAMETDSLPLEGTPSAVGMGNPHCIYFVEDAEAVDLAGRGAAVE 181
           VNMG PQL W +IPLA  ++T  LP+EG P+A GMGNPHC +FV++AE + LA  GA  E
Sbjct: 122 VNMGEPQLDWQDIPLAEDVDTLELPIEGAPTATGMGNPHCTFFVDNAEVIPLAEFGARYE 181

Query: 182 TDPLFPERTNVEFASLIGPDRLRLRVWERGAGITLACGSGACATAVAAARRGLTGRQVRL 241
             PL+PERTNV+ A ++ PD LR+RVWERG GITLA GS +CATAVAAARRGLT R+V++
Sbjct: 182 HHPLYPERTNVQVAHVVAPDHLRMRVWERGVGITLASGSSSCATAVAAARRGLTSRKVQI 241

Query: 242 EMDGGVLEVDWRDEGVWLSGPVARVFEGHLSPEMM 276
           ++DGG L +DWR +GVW++GP   V +GH + + +
Sbjct: 242 DLDGGTLWIDWRKDGVWMTGPTMHVADGHFTRQFL 276


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: 310
Number of extensions: 11
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: 279
Length of database: 281
Length adjustment: 26
Effective length of query: 253
Effective length of database: 255
Effective search space:    64515
Effective search space used:    64515
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 GFF3342 PGA1_c33950 (diaminopimelate epimerase DapF)
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.17078.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    6.6e-75  238.0   0.0    7.6e-75  237.8   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3342  PGA1_c33950 diaminopimelate epim


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3342  PGA1_c33950 diaminopimelate epimerase DapF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.8   0.0   7.6e-75   7.6e-75       3     268 ..      14     271 ..      12     273 .. 0.95

  Alignments for each domain:
  == domain 1  score: 237.8 bits;  conditional E-value: 7.6e-75
                          TIGR00652   3 FlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeaemCGNgiR 78 
                                        F+kmhGlgNdFv+vd +d++   + +++++ +++r++g+g+D++ +++  + ++d++l+++N+DGS  + CGN+ R
  lcl|FitnessBrowser__Phaeo:GFF3342  14 FMKMHGLGNDFVVVDARDQTWDIT-PAMAEGIAHRQMGIGFDQLTVIT--KGDEDAHLTFYNADGSTSAACGNATR 86 
                                        9*****************888777.9*********************9..5999********************** PP

                          TIGR00652  79 cfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalevlvvdvGn 154
                                        c+a+++ ++ +k  ++l++ t++gl+ +e   ++   +v+mgep++  ++ipl ++ ++ +  + + +  +  +Gn
  lcl|FitnessBrowser__Phaeo:GFF3342  87 CIARHLLDESGK--THLRLTTDRGLLLAEDAGNG-LTSVNMGEPQLDWQDIPLAEDVDTLELPI-EGAPTATGMGN 158
                                        ***********9..8**************99999.*******************8777774333.334479***** PP

                          TIGR00652 155 PHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGavAsavvalklgk 230
                                        PH+ +fv++ e ++l e g+  e+h+ +pe++Nv++++v+ +d++++rv+ERG+g+Tla G+ ++A+av+a++ g+
  lcl|FitnessBrowser__Phaeo:GFF3342 159 PHCTFFVDNAEVIPLAEFGARYEHHPLYPERTNVQVAHVVAPDHLRMRVWERGVGITLASGSSSCATAVAAARRGL 234
                                        **************************************************************************** PP

                          TIGR00652 231 tkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268
                                        t +kv++ l+gg L i++++dg v++tGp  +v++g+ 
  lcl|FitnessBrowser__Phaeo:GFF3342 235 TSRKVQIDLDGGTLWIDWRKDG-VWMTGPTMHVADGHF 271
                                        *********************8.************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (281 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: 00:00:00.00
# Mc/sec: 10.66
//
[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