Alignments for a candidate for dapB in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Paraburkholderia bryophila 376MFSha3.1

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate H281DRAFT_06318 H281DRAFT_06318 dihydrodipicolinate reductase

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__Burk376:H281DRAFT_06318
          Length = 265

 Score =  301 bits (772), Expect = 7e-87
 Identities = 158/265 (59%), Positives = 193/265 (72%), Gaps = 1/265 (0%)

Query: 6   IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65
           +++AIAGA GRMGR LI+  L      L  AL+R GS  LG DAG   G  +TGV +   
Sbjct: 1   MKIAIAGASGRMGRMLIETVLNDSDATLSGALDRAGSPQLGQDAGAFLGK-QTGVMLTDD 59

Query: 66  LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125
           ++ V  + D  IDFTRPEGTL HL   ++H   MVIGTTGFD   K  +R AA +IAI+F
Sbjct: 60  IERVFAESDYLIDFTRPEGTLMHLEAAQRHNVKMVIGTTGFDNEQKAQLRAAADNIAIMF 119

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           A+N SVGVNV LKLLE AAK      DIEIIEAHHRHKVDAPSGTAL MGE IA+AL ++
Sbjct: 120 ASNMSVGVNVTLKLLEYAAKHFATGYDIEIIEAHHRHKVDAPSGTALTMGEVIANALGRN 179

Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245
           L DCAVYSREG TGER P TIGF+ +R GDIVG+HT +FA IGER+EITHK++SR+++A 
Sbjct: 180 LDDCAVYSREGVTGERDPSTIGFSAIRGGDIVGDHTVLFAGIGERIEITHKSASRLSYAQ 239

Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270
           GA+R+  +L G ++G FDM+DVL L
Sbjct: 240 GALRAVRFLEGHQTGFFDMQDVLGL 264


Lambda     K      H
   0.319    0.135    0.383 

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: 255
Number of extensions: 7
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: 273
Length of database: 265
Length adjustment: 25
Effective length of query: 248
Effective length of database: 240
Effective search space:    59520
Effective search space used:    59520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate H281DRAFT_06318 H281DRAFT_06318 (dihydrodipicolinate 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.8039.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.9e-100  321.9   2.3   2.1e-100  321.7   2.3    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06318  H281DRAFT_06318 dihydrodipicolin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06318  H281DRAFT_06318 dihydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.7   2.3  2.1e-100  2.1e-100       2     270 .]       1     263 [.       1     263 [. 0.98

  Alignments for each domain:
  == domain 1  score: 321.7 bits;  conditional E-value: 2.1e-100
                                    TIGR00036   2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkv 67 
                                                  +k+a+aGa+GrmGr +i++v +  d  l++al+r gs++ g+D+G + g  ++gv ++dd+e v  
  lcl|FitnessBrowser__Burk376:H281DRAFT_06318   1 MKIAIAGASGRMGRMLIETVLNDSDATLSGALDRAGSPQLGQDAGAFLGK-QTGVMLTDDIERV-- 63 
                                                  89**********************************************96.78999******88.. PP

                                    TIGR00036  68 laekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfai 133
                                                      + d liDft+pe++l ++++a +++v++V+GTTGf++e++++l+++a++  +a+++a+N+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06318  64 --FAESDYLIDFTRPEGTLMHLEAAQRHNVKMVIGTTGFDNEQKAQLRAAADN--IAIMFASNMSV 125
                                                  ..7889*********************************************99..*********** PP

                                    TIGR00036 134 Gvnlllkllekaakvled.vDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregl 198
                                                  Gvn+ lklle+aak +   +DiEiiE+HHrhK+DaPSGTAl ++e+ia+a g++l+++av++reg+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06318 126 GVNVTLKLLEYAAKHFATgYDIEIIEAHHRHKVDAPSGTALTMGEVIANALGRNLDDCAVYSREGV 191
                                                  ***************97627********************************************** PP

                                    TIGR00036 199 tGerkkeeiGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvyd 264
                                                  tGer  ++iG++a+Rggd+vg+htvlFa++Ger+eitHk+ sR ++a+G++ra+r+le  +++++d
  lcl|FitnessBrowser__Burk376:H281DRAFT_06318 192 TGERDPSTIGFSAIRGGDIVGDHTVLFAGIGERIEITHKSASRLSYAQGALRAVRFLEGHQTGFFD 257
                                                  ****************************************************************** PP

                                    TIGR00036 265 ledvld 270
                                                  ++dvl+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06318 258 MQDVLG 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.66
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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