GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Echinicola vietnamensis KMM 6221, DSM 17526

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate Echvi_3959 Echvi_3959 dihydrodipicolinate synthase

Query= SwissProt::Q9JZR4
         (291 letters)



>FitnessBrowser__Cola:Echvi_3959
          Length = 286

 Score =  221 bits (562), Expect = 2e-62
 Identities = 116/279 (41%), Positives = 175/279 (62%), Gaps = 4/279 (1%)

Query: 4   GSLVALITPMNQDGSIHYEQLRDLIDWHIENGTDGIVAVGTTGESATLSVEEHTAVIEAV 63
           G+ VAL+TP +++G+I Y  L  +I+  I+ G D +V +GTTGE++T+S +E   ++ A 
Sbjct: 6   GTGVALVTPFDEEGNIDYNGLDKVIEHVIQGGADYLVVMGTTGEASTMSRKEKHDILAAA 65

Query: 64  VKHVAKRVPVIAGTGANNTVEAIALSQAAEKAGADYTLSVVPYYNKPSQEGIYQHFKTIA 123
           VK    R+P++ G GANNT  AI      + +G    LSV PYYNKP+QEGIYQH+  +A
Sbjct: 66  VKTNNGRLPIVYGIGANNTQAAIDEIDETDLSGVAALLSVSPYYNKPTQEGIYQHYIKVA 125

Query: 124 EATSIPMIIYNVPGRTVVSMTNDTILRLAEIPNIVGVKEASGNIGSNIELINRAPEGFVV 183
           +A+ +P+I+YNVPGRT+ ++T  T LRL+E P I+GVKEASG++   +++I + P  F++
Sbjct: 126 DASPVPIILYNVPGRTMSNITAATTLRLSEHPKIIGVKEASGDMVQCMDIIRKKPSDFLL 185

Query: 184 LSGDDHTALPFMLCGGHGVITVAANAAPKLFADMCRAALQGDIALARELNDRLIPIYDTM 243
           +SGDD         GGHG I+V ANA P +F  +C  + +  +A       RL+ I   M
Sbjct: 186 ISGDDMLTTSLKAIGGHGAISVLANAYPDIFKTICHGSAEESLA----ATFRLLDINAWM 241

Query: 244 FCEPSPAAPKWAVSALGRCEPHVRLPLVPLTENGQAKVR 282
           + E +P   K  +  +G C   VRLPL+  TE+   K++
Sbjct: 242 YVESNPVGVKNLLKHMGVCGDQVRLPLLRATESLDKKIK 280


Lambda     K      H
   0.317    0.133    0.386 

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: 226
Number of extensions: 8
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: 291
Length of database: 286
Length adjustment: 26
Effective length of query: 265
Effective length of database: 260
Effective search space:    68900
Effective search space used:    68900
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 Echvi_3959 Echvi_3959 (dihydrodipicolinate 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.1323874.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
    1.1e-93  299.2   0.1    1.2e-93  299.0   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_3959  Echvi_3959 dihydrodipicolinate s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3959  Echvi_3959 dihydrodipicolinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.0   0.1   1.2e-93   1.2e-93       4     283 ..       9     283 ..       6     286 .] 0.97

  Alignments for each domain:
  == domain 1  score: 299.0 bits;  conditional E-value: 1.2e-93
                            TIGR00674   4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsn 77 
                                          +Al+TPf+e+g++d++ l+k+ie+ i+ g d +vv+GtTGE+ t+s +Ek++++  av+++++r+p++ G+g+n
  lcl|FitnessBrowser__Cola:Echvi_3959   9 VALVTPFDEEGNIDYNGLDKVIEHVIQGGADYLVVMGTTGEASTMSRKEKHDILAAAVKTNNGRLPIVYGIGAN 82 
                                          7************************************************************************* PP

                            TIGR00674  78 ateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaee 151
                                          +t+ ai+ ++e++ +gv+++l+v+PyYnkPtqeG+y+h+ ++a+++ +PiilYnvP+Rt  +++  t++rL+e+
  lcl|FitnessBrowser__Cola:Echvi_3959  83 NTQAAIDEIDETDLSGVAALLSVSPYYNKPTQEGIYQHYIKVADASPVPIILYNVPGRTMSNITAATTLRLSEH 156
                                          ************************************************************************** PP

                            TIGR00674 152 veivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdtee 225
                                          ++i+++Keasgd+ +++ i+++++ df + sGdD lt+++ a+G++G iSV++n  p+ +k +++  +e++ + 
  lcl|FitnessBrowser__Cola:Echvi_3959 157 PKIIGVKEASGDMVQCMDIIRKKPSDFLLISGDDMLTTSLKAIGGHGAISVLANAYPDIFKTICHGSAEESLAA 230
                                          **********************************************************9999999877777766 PP

                            TIGR00674 226 areihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevl 283
                                                +ll++  ++++e+NP++vK +l+ +g++   ++RlPL  ++e+  +k+ke  
  lcl|FitnessBrowser__Cola:Echvi_3959 231 T----FRLLDINAWMYVESNPVGVKNLLKHMGVCGD-QVRLPLLRATESLDKKIKELA 283
                                          6....9****************************98.***************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (286 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: 19.93
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

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:

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