Alignments for a candidate for dapB in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Sinorhizobium fredii NGR234

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate YP_002827965.1 NGR_c34880 4-hydroxy-tetrahydrodipicolinate reductase

Query= BRENDA::Q2YJN7
         (268 letters)



>NCBI__GCF_000018545.1:YP_002827965.1
          Length = 272

 Score =  393 bits (1010), Expect = e-114
 Identities = 198/267 (74%), Positives = 223/267 (83%)

Query: 1   MGLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDD 60
           M LVVVGA GRMGQTLIRT+    G +L  AIERS SPF+G+DAGE+ G+G +GV ITD 
Sbjct: 6   MKLVVVGAAGRMGQTLIRTVHEAAGVRLHAAIERSNSPFIGRDAGELAGLGPIGVPITDK 65

Query: 61  PLPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVK 120
           PL  F +A GVLDFT+PA +VEFAGLAAQARIVHVIGTTGCSA+D+ KIRAAARHA +VK
Sbjct: 66  PLEAFVEAEGVLDFTAPAGTVEFAGLAAQARIVHVIGTTGCSADDEAKIRAAARHARVVK 125

Query: 121 SGNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDI 180
           SGNMSLGVNLL VL + AA AL  +D+DIEILEMHHRHKVDAPSGTALLLGEAAA+GR I
Sbjct: 126 SGNMSLGVNLLGVLTETAARALSAKDWDIEILEMHHRHKVDAPSGTALLLGEAAAKGRGI 185

Query: 181 ALADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFA 240
            LAD +V+VRDG+TGPR  G IGFATLRGG V+G+HSVILAG GE V LSH A DRSIFA
Sbjct: 186 DLADQAVKVRDGHTGPRPQGTIGFATLRGGLVVGEHSVILAGEGELVTLSHSATDRSIFA 245

Query: 241 RGAIKAALWAHGKKPGLYSMLDVLGLN 267
           RGA+ AALW   +KPG Y+MLDVLGLN
Sbjct: 246 RGAVAAALWGRSQKPGFYTMLDVLGLN 272


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: 306
Number of extensions: 10
Number of successful extensions: 1
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: 272
Length adjustment: 25
Effective length of query: 243
Effective length of database: 247
Effective search space:    60021
Effective search space used:    60021
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 YP_002827965.1 NGR_c34880 (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.20869.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      2e-82  262.7   0.8    2.3e-82  262.5   0.8    1.0  1  lcl|NCBI__GCF_000018545.1:YP_002827965.1  NGR_c34880 4-hydroxy-tetrahydrod


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002827965.1  NGR_c34880 4-hydroxy-tetrahydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.5   0.8   2.3e-82   2.3e-82       2     270 .]       6     270 ..       5     270 .. 0.96

  Alignments for each domain:
  == domain 1  score: 262.5 bits;  conditional E-value: 2.3e-82
                                 TIGR00036   2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlae 70 
                                               +k++v GaaGrmG+ +i++v+ea +++l aa+er +s+  g+D+Gelag+g++gvp++d+   +     
  lcl|NCBI__GCF_000018545.1:YP_002827965.1   6 MKLVVVGAAGRMGQTLIRTVHEAAGVRLHAAIERSNSPFIGRDAGELAGLGPIGVPITDKPLEA----F 70 
                                               89*******************************************************9985533....3 PP

                                 TIGR00036  71 kkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlll 139
                                                +a+ ++Dft p +++e + +a+++ +  V+GTTG s +d ++++++a +  +++v + N+++Gvnll 
  lcl|NCBI__GCF_000018545.1:YP_002827965.1  71 VEAEGVLDFTAPAGTVEFAGLAAQARIVHVIGTTGCSADDEAKIRAAARH--ARVVKSGNMSLGVNLLG 137
                                               5667778******************************************9..9**************** PP

                                 TIGR00036 140 kllekaakvl..edvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkee 206
                                                l+e+aa+ l  +d+DiEi+E+HHrhK+DaPSGTAl l+e+ ak rg dl ++av+ r+g+tG r + +
  lcl|NCBI__GCF_000018545.1:YP_002827965.1 138 VLTETAARALsaKDWDIEILEMHHRHKVDAPSGTALLLGEAAAKGRGIDLADQAVKVRDGHTGPRPQGT 206
                                               *******99844699****************************************************** PP

                                 TIGR00036 207 iGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                               iG+a++Rgg vvgeh+v+ a++Ge ++++H a++R++fa+G+v a+ w   ++ ++y++ dvl+
  lcl|NCBI__GCF_000018545.1:YP_002827965.1 207 IGFATLRGGLVVGEHSVILAGEGELVTLSHSATDRSIFARGAVAAALWGRSQKPGFYTMLDVLG 270
                                               **************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (272 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: 00:00:00.01
# Mc/sec: 6.92
//
[ok]

This GapMind analysis is from Apr 10 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