GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Epibacterium ulvae U95

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_090219124.1 CV091_RS12385 4-hydroxy-tetrahydrodipicolinate reductase

Query= BRENDA::Q2YJN7
         (268 letters)



>NCBI__GCF_002796795.1:WP_090219124.1
          Length = 269

 Score =  313 bits (801), Expect = 3e-90
 Identities = 156/265 (58%), Positives = 196/265 (73%), Gaps = 1/265 (0%)

Query: 2   GLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDDP 61
           G+V+ GA GRMGQ LI+T+   + A+LVGA+ER G  ++G+D G   G   +GV +T D 
Sbjct: 6   GIVITGASGRMGQMLIKTVLDSDKARLVGAVEREGHDWVGQDIGAAMGGADVGVTVTSDA 65

Query: 62  LPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVKS 121
           L  FAKA  V+DFT+PAA++EF+ LAAQAR VHVIGTTG + E+  ++  +ARHA IV++
Sbjct: 66  LEAFAKAQAVIDFTAPAATIEFSKLAAQARAVHVIGTTGMTEEEIAQLEPSARHAVIVRA 125

Query: 122 GNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDIA 181
           GNMSLGVNLL  L +K A AL  +DFDIE++E HH HKVDAPSGTAL+LGEAAA GR ++
Sbjct: 126 GNMSLGVNLLVQLTKKVAAALD-DDFDIEVIEAHHHHKVDAPSGTALMLGEAAAEGRGVS 184

Query: 182 LADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFAR 241
           L D     RDG TG R+ G IGF  +RGG ++G+H V+ A  GER+VL H A DR+IFAR
Sbjct: 185 LKDVRDSGRDGITGARKKGDIGFTAIRGGDIVGEHDVLFAAAGERIVLRHMATDRAIFAR 244

Query: 242 GAIKAALWAHGKKPGLYSMLDVLGL 266
           GA+KAALW  GK PG Y MLDVLGL
Sbjct: 245 GALKAALWGQGKTPGEYDMLDVLGL 269


Lambda     K      H
   0.318    0.136    0.387 

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: 273
Number of extensions: 12
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: 268
Length of database: 269
Length adjustment: 25
Effective length of query: 243
Effective length of database: 244
Effective search space:    59292
Effective search space used:    59292
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: 47 (22.7 bits)

Align candidate WP_090219124.1 CV091_RS12385 (4-hydroxy-tetrahydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

# 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/TIGR00036.hmm
# target sequence database:        /tmp/gapView.3550664.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00036  [M=270]
Accession:   TIGR00036
Description: dapB: 4-hydroxy-tetrahydrodipicolinate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.4e-83  265.7   7.8    2.9e-83  265.5   7.8    1.0  1  NCBI__GCF_002796795.1:WP_090219124.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002796795.1:WP_090219124.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.5   7.8   2.9e-83   2.9e-83       4     270 .]       7     268 ..       5     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 265.5 bits;  conditional E-value: 2.9e-83
                             TIGR00036   4 vavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvl 76 
                                           ++++Ga+GrmG+ +ik+v ++++ +lv+a+er+g++ +g+DiG  +g + vgv+v++d   +      ka+ +
  NCBI__GCF_002796795.1:WP_090219124.1   7 IVITGASGRMGQMLIKTVLDSDKARLVGAVEREGHDWVGQDIGAAMGGADVGVTVTSDALEA----FAKAQAV 75 
                                           89*****************************************************9876544....5788899 PP

                             TIGR00036  77 iDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvl 149
                                           iDft p a+ e  k+a+++    V+GTTG++ee++++l+  a +  + +v a N+++Gvnll++l++k+a  l
  NCBI__GCF_002796795.1:WP_090219124.1  76 IDFTAPAATIEFSKLAAQARAVHVIGTTGMTEEEIAQLEPSARH--AVIVRAGNMSLGVNLLVQLTKKVAAAL 146
                                           ******************************************99..999************************ PP

                             TIGR00036 150 edv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgeh 221
                                           +d  DiE+iE+HH+hK+DaPSGTAl l+e+ a+ rg  lk++  ++r+g+tG+rkk +iG++a+Rggd+vgeh
  NCBI__GCF_002796795.1:WP_090219124.1 147 DDDfDIEVIEAHHHHKVDAPSGTALMLGEAAAEGRGVSLKDVRDSGRDGITGARKKGDIGFTAIRGGDIVGEH 219
                                           8766********************************************************************* PP

                             TIGR00036 222 tvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                            vlFa  Ger+ ++H a++Ra+fa+G+++a+ w + k  + yd+ dvl+
  NCBI__GCF_002796795.1:WP_090219124.1 220 DVLFAAAGERIVLRHMATDRAIFARGALKAALWGQGKTPGEYDMLDVLG 268
                                           ***********************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (269 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: 22.16
//
[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