Alignments for a candidate for dapB in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Burkholderia phytofirmans PsJN

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate BPHYT_RS16800 BPHYT_RS16800 4-hydroxy-tetrahydrodipicolinate reductase

Query= BRENDA::Q9K1F1
         (269 letters)



>FitnessBrowser__BFirm:BPHYT_RS16800
          Length = 265

 Score =  322 bits (826), Expect = 4e-93
 Identities = 163/264 (61%), Positives = 201/264 (76%), Gaps = 1/264 (0%)

Query: 4   LKIAIAGANGRMGRVLVEAVNNHPDTVLSGALEHSGSEALGLDAGYAVGLKTGIAISDDV 63
           +KIAIAGA+GRMGR+L+E V N  D  LSGAL+ +GS  LG DAG  +G +TG+ ++DDV
Sbjct: 1   MKIAIAGASGRMGRMLIETVLNDSDATLSGALDRAGSPQLGQDAGAFLGKQTGVVLTDDV 60

Query: 64  DAVLAQSDVLIDFTRPEPTLKHLQKCVEKQVNIIIGTTGFDDTGKAAIHTAAEKTGIVFA 123
           + V A+SD LIDFTRPE TL HL+      V ++IGTTGFD+  KA +  AA+K  I+F+
Sbjct: 61  ERVFAESDYLIDFTRPEGTLMHLEAAQRHNVKMVIGTTGFDNEQKAQLRAAADKIAIMFS 120

Query: 124 ANFSVGVNLTFHILDTVARVLNEGYDIEIIEGHHRHKVDAPSGTALRMGEVIAGALGRDL 183
           AN SVGVN+T  +L+  A+    GYDIEIIE HHRHKVDAPSGTAL MGEVIA ALGR+L
Sbjct: 121 ANMSVGVNVTLKLLEFAAKHFATGYDIEIIEAHHRHKVDAPSGTALVMGEVIANALGRNL 180

Query: 184 KQCAVYGREGHTGPRDPSTIGFATVRAGDIVGDHTALFATDGERVEITHKASSRMTFAAG 243
             CAVY REG TG RDPSTIGF+ +R GDIVGDHT LFA  GER+EITHK++SR+++A G
Sbjct: 181 DDCAVYSREGVTGERDPSTIGFSAIRGGDIVGDHTVLFAGIGERIEITHKSASRLSYAQG 240

Query: 244 AVRAAVWVNG-KTGLYDMQDVLGL 266
           A+RA  ++    TG +DMQDVLGL
Sbjct: 241 ALRAVRFLESHATGFFDMQDVLGL 264


Lambda     K      H
   0.318    0.136    0.392 

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: 278
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: 269
Length of database: 265
Length adjustment: 25
Effective length of query: 244
Effective length of database: 240
Effective search space:    58560
Effective search space used:    58560
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 BPHYT_RS16800 BPHYT_RS16800 (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.19117.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    1.1e-99  319.4   2.8    1.2e-99  319.2   2.8    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS16800  BPHYT_RS16800 4-hydroxy-tetrahyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS16800  BPHYT_RS16800 4-hydroxy-tetrahydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.2   2.8   1.2e-99   1.2e-99       2     270 .]       1     263 [.       1     263 [. 0.98

  Alignments for each domain:
  == domain 1  score: 319.2 bits;  conditional E-value: 1.2e-99
                                TIGR00036   2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaek 71 
                                              +k+a+aGa+GrmGr +i++v +  d  l++al+r gs++ g+D+G + g  ++gv ++dd+e v      
  lcl|FitnessBrowser__BFirm:BPHYT_RS16800   1 MKIAIAGASGRMGRMLIETVLNDSDATLSGALDRAGSPQLGQDAGAFLGK-QTGVVLTDDVERV----FA 65 
                                              89**********************************************96.678889***9988....78 PP

                                TIGR00036  72 kadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkl 141
                                              + d liDft+pe++l ++++a +++v++V+GTTGf++e++++l+++a+k  +a+++++N+++Gvn+ lkl
  lcl|FitnessBrowser__BFirm:BPHYT_RS16800  66 ESDYLIDFTRPEGTLMHLEAAQRHNVKMVIGTTGFDNEQKAQLRAAADK--IAIMFSANMSVGVNVTLKL 133
                                              89***********************************************..******************* PP

                                TIGR00036 142 lekaakvled.vDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGia 210
                                              le aak +   +DiEiiE+HHrhK+DaPSGTAl ++e+ia+a g++l+++av++reg+tGer  ++iG++
  lcl|FitnessBrowser__BFirm:BPHYT_RS16800 134 LEFAAKHFATgYDIEIIEAHHRHKVDAPSGTALVMGEVIANALGRNLDDCAVYSREGVTGERDPSTIGFS 203
                                              *******97627********************************************************** PP

                                TIGR00036 211 avRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                              a+Rggd+vg+htvlFa++Ger+eitHk+ sR ++a+G++ra+r+le  +++++d++dvl+
  lcl|FitnessBrowser__BFirm:BPHYT_RS16800 204 AIRGGDIVGDHTVLFAGIGERIEITHKSASRLSYAQGALRAVRFLESHATGFFDMQDVLG 263
                                              **********************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (265 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: 6.41
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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