Alignments for a candidate for dapB in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Dinoroseobacter shibae DFL-12

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate 3609657 Dshi_3040 Dihydrodipicolinate reductase (RefSeq)

Query= BRENDA::Q2YJN7
         (268 letters)



>FitnessBrowser__Dino:3609657
          Length = 269

 Score =  312 bits (799), Expect = 5e-90
 Identities = 159/265 (60%), Positives = 191/265 (72%), Gaps = 1/265 (0%)

Query: 2   GLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDDP 61
           G+VV G  GRMG+ LI T++  + A+LVG  ER G  ++G D G   G   +GV +TDDP
Sbjct: 6   GIVVTGGSGRMGRMLIETVRGSDAARLVGVTERPGHDWIGADIGVALGGAAIGVTVTDDP 65

Query: 62  LPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVKS 121
           L  FA A  V+DFTSPAA+V  A L AQAR VHVIGTTG S  D   + AAARHA IV++
Sbjct: 66  LEAFATAQAVIDFTSPAATVAHAELTAQARAVHVIGTTGFSPADLAHLEAAARHAVIVRA 125

Query: 122 GNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDIA 181
           GNMSLGVNLL  L +K A AL   D+DIE++E HHRHKVDAPSGTAL+LGEAAA GR +A
Sbjct: 126 GNMSLGVNLLVKLTEKVAAALDA-DYDIEVIEAHHRHKVDAPSGTALMLGEAAAAGRGVA 184

Query: 182 LADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFAR 241
           LAD S R RDG TG R+ G IGF+ +RGG ++G+H V+ A  GER+ L H A DRS+FAR
Sbjct: 185 LADVSDRGRDGITGERKRGDIGFSAIRGGDIVGEHDVLFAAEGERITLRHVASDRSVFAR 244

Query: 242 GAIKAALWAHGKKPGLYSMLDVLGL 266
           GA+KAALW   K PG Y M+DVLGL
Sbjct: 245 GALKAALWGQDKGPGAYDMMDVLGL 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: 280
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: 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 3609657 Dshi_3040 (Dihydrodipicolinate reductase (RefSeq))
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.8304.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    5.7e-82  261.2   5.1      7e-82  261.0   5.1    1.0  1  lcl|FitnessBrowser__Dino:3609657  Dshi_3040 Dihydrodipicolinate re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609657  Dshi_3040 Dihydrodipicolinate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.0   5.1     7e-82     7e-82       4     270 .]       7     268 ..       6     268 .. 0.97

  Alignments for each domain:
  == domain 1  score: 261.0 bits;  conditional E-value: 7e-82
                         TIGR00036   4 vavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvliDft 80 
                                       ++v+G +GrmGr +i++v  ++  +lv++ er+g++  g DiG   g + +gv+v+dd   +      +a+ +iDft
  lcl|FitnessBrowser__Dino:3609657   7 IVVTGGSGRMGRMLIETVRGSDAARLVGVTERPGHDWIGADIGVALGGAAIGVTVTDDPLEA----FATAQAVIDFT 79 
                                       89*****************************************************9986544....4677889**** PP

                         TIGR00036  81 tpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvle.dvDiEi 156
                                        p a++ ++++++++    V+GTTGfs +dl++l+++a +  + +v a N+++Gvnll+kl+ek+a  l+ d+DiE+
  lcl|FitnessBrowser__Dino:3609657  80 SPAATVAHAELTAQARAVHVIGTTGFSPADLAHLEAAARH--AVIVRAGNMSLGVNLLVKLTEKVAAALDaDYDIEV 154
                                       **************************************99..999********************99996599**** PP

                         TIGR00036 157 iElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgehtvlFasdGerle 233
                                       iE+HHrhK+DaPSGTAl l+e+ a+ rg  l ++   +r+g+tGerk+ +iG++a+Rggd+vgeh vlFa +Ger++
  lcl|FitnessBrowser__Dino:3609657 155 IEAHHRHKVDAPSGTALMLGEAAAAGRGVALADVSDRGRDGITGERKRGDIGFSAIRGGDIVGEHDVLFAAEGERIT 231
                                       *****************************9*********************************************** PP

                         TIGR00036 234 itHkassRaafakGvvrairwledkeekvydledvld 270
                                       ++H as+R++fa+G+++a+ w +dk  + yd+ dvl+
  lcl|FitnessBrowser__Dino:3609657 232 LRHVASDRSVFARGALKAALWGQDKGPGAYDMMDVLG 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.59
//
[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