GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Epibacterium ulvae U95

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_090220024.1 CV091_RS15865 4-hydroxy-tetrahydrodipicolinate synthase

Query= BRENDA::Q8UGL3
         (294 letters)



>NCBI__GCF_002796795.1:WP_090220024.1
          Length = 290

 Score =  392 bits (1008), Expect = e-114
 Identities = 206/293 (70%), Positives = 235/293 (80%), Gaps = 3/293 (1%)

Query: 1   MFKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVV 60
           MFKGS+PAL+TPF  NG +D  A    VEWQI EGS  LVPVGTTGESPTLS +EH+ VV
Sbjct: 1   MFKGSMPALVTPFR-NGELDLDALKHLVEWQIGEGSTALVPVGTTGESPTLSLEEHETVV 59

Query: 61  ELCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTPYYNKPTQKGLFAHFS 120
           E  ++ AA RVPVIAGAGSNNT +AI L   A +AGADA LVVTPYYNKPTQ+G+ AH+ 
Sbjct: 60  EEVVKAAAGRVPVIAGAGSNNTVDAIRLVEFAAKAGADAALVVTPYYNKPTQRGMLAHYK 119

Query: 121 AVAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHKNIIGVKDATGKLDRVSEQRISCGK 180
           A+ +   LPIVIYNIP RS+VDMSP TMG L K  + IIGVKDATG + RVS+QR +CG 
Sbjct: 120 ALHDCADLPIVIYNIPGRSIVDMSPATMGELAKLPR-IIGVKDATGDIARVSQQRATCGA 178

Query: 181 DFVQLSGEDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALEYQDRLMPL 240
           DF+QLSGED +ALGFNAHGGVGCISVTANVAPRLC+EFQAA LAGDYAKALEYQDRLMPL
Sbjct: 179 DFMQLSGEDASALGFNAHGGVGCISVTANVAPRLCAEFQAATLAGDYAKALEYQDRLMPL 238

Query: 241 HRAIFMEPGVCGTKYALSKTRGGNRRVRSPLMSTLEPATEAAIDAALKHAGLM 293
           H AIF EPGV G KYALSK    +  VR PL + LE +T+AA+DAA+KHAGL+
Sbjct: 239 HEAIFTEPGVAGAKYALSKLGLCSDEVRLPL-TGLEDSTKAALDAAMKHAGLL 290


Lambda     K      H
   0.317    0.133    0.384 

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: 347
Number of extensions: 13
Number of successful extensions: 4
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: 294
Length of database: 290
Length adjustment: 26
Effective length of query: 268
Effective length of database: 264
Effective search space:    70752
Effective search space used:    70752
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_090220024.1 CV091_RS15865 (4-hydroxy-tetrahydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

# 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/TIGR00674.hmm
# target sequence database:        /tmp/gapView.771019.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00674  [M=286]
Accession:   TIGR00674
Description: dapA: 4-hydroxy-tetrahydrodipicolinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-100  321.4   0.0   2.1e-100  321.2   0.0    1.0  1  NCBI__GCF_002796795.1:WP_090220024.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002796795.1:WP_090220024.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.2   0.0  2.1e-100  2.1e-100       2     285 ..       5     286 ..       4     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: 321.2 bits;  conditional E-value: 2.1e-100
                             TIGR00674   2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGt 74 
                                           +++Al+TPf++ + +d++al++l+e qi +g+ a+v+vGtTGEs+tLsleE+++v+e +v+ +++rvpviaG+
  NCBI__GCF_002796795.1:WP_090220024.1   5 SMPALVTPFRNGE-LDLDALKHLVEWQIGEGSTALVPVGTTGESPTLSLEEHETVVEEVVKAAAGRVPVIAGA 76 
                                           789******9988.*********************************************************** PP

                             TIGR00674  75 gsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkr 147
                                           gsn+t +ai+l+++a+k+g+d++lvvtPyYnkPtq+G+++h+ka++++++lPi++Yn+P+R+ v+++p t+ +
  NCBI__GCF_002796795.1:WP_090220024.1  77 GSNNTVDAIRLVEFAAKAGADAALVVTPYYNKPTQRGMLAHYKALHDCADLPIVIYNIPGRSIVDMSPATMGE 149
                                           ************************************************************************* PP

                             TIGR00674 148 LaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaale 220
                                           La+ ++i+++K+a+gd++rvs+ +a+ ++df  lsG+Da +l + a G+ G iSV++nvap++++e+ +a+l+
  NCBI__GCF_002796795.1:WP_090220024.1 150 LAKLPRIIGVKDATGDIARVSQQRATCGADFMQLSGEDASALGFNAHGGVGCISVTANVAPRLCAEFQAATLA 222
                                           ************************************************************************* PP

                             TIGR00674 221 gdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285
                                           gd+++a+e + +l++l++a+f+e+   + K+al  lgl+   e+RlPLt l++++k  l++++k+
  NCBI__GCF_002796795.1:WP_090220024.1 223 GDYAKALEYQDRLMPLHEAIFTEPGVAGAKYALSKLGLCSD-EVRLPLTGLEDSTKAALDAAMKH 286
                                           ***************************************99.***************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (290 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: 00:00:00.00
# Mc/sec: 15.45
//
[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