Alignments for a candidate for dapB in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Marinobacter adhaerens HP15

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate GFF3137 HP15_3079 dihydrodipicolinate reductase

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__Marino:GFF3137
          Length = 266

 Score =  333 bits (853), Expect = 3e-96
 Identities = 167/265 (63%), Positives = 203/265 (76%)

Query: 6   IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65
           +RVAI GA GRMG+ LI+A    EG++LGAA+   GSSL+G+DAGE+ G GKTGV +  S
Sbjct: 1   MRVAIIGAAGRMGKVLIEAVDGTEGLELGAAVVEPGSSLIGADAGEMTGIGKTGVKMAGS 60

Query: 66  LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125
           L  VKDDFDV +DFT P+ TL +  FC+ +GK +VIGTTG  +A KQ +  AA   A+VF
Sbjct: 61  LADVKDDFDVLVDFTFPDLTLENAEFCKANGKMLVIGTTGMSDAEKQQLALAAESTAVVF 120

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           A N SVGVNV+L LL  AA  +GD  D+EIIEAHHRHK DAPSGTAL MGE +A AL +D
Sbjct: 121 APNMSVGVNVVLNLLRTAAATLGDDYDVEIIEAHHRHKKDAPSGTALRMGEVVADALGRD 180

Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245
           LK+CAVY REG TGER    IGF T+RAGD+VG+HT +FA  GER+E+THKASSRMTFA 
Sbjct: 181 LKECAVYGREGFTGERTRKEIGFETIRAGDVVGDHTVLFATEGERIEVTHKASSRMTFAK 240

Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270
           GA+R+ALWL  K +GL+DM+DVLDL
Sbjct: 241 GAMRAALWLKDKPAGLYDMQDVLDL 265


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: 271
Number of extensions: 9
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: 273
Length of database: 266
Length adjustment: 25
Effective length of query: 248
Effective length of database: 241
Effective search space:    59768
Effective search space used:    59768
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 GFF3137 HP15_3079 (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.14206.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-106  342.3   4.3   1.2e-106  342.1   4.3    1.0  1  lcl|FitnessBrowser__Marino:GFF3137  HP15_3079 dihydrodipicolinate re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3137  HP15_3079 dihydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.1   4.3  1.2e-106  1.2e-106       2     270 .]       1     264 [.       1     264 [. 0.98

  Alignments for each domain:
  == domain 1  score: 342.1 bits;  conditional E-value: 1.2e-106
                           TIGR00036   2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvl 76 
                                         ++va+ GaaGrmG+ +i+av  +e+lel+aa+  +gss+ g D+Ge++gigk+gv++  +l  v    ++++dvl
  lcl|FitnessBrowser__Marino:GFF3137   1 MRVAIIGAAGRMGKVLIEAVDGTEGLELGAAVVEPGSSLIGADAGEMTGIGKTGVKMAGSLADV----KDDFDVL 71 
                                         89*****************************************************999999877....******* PP

                           TIGR00036  77 iDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvle. 150
                                         +Dft p+ +len++++ ++g+ lV+GTTG+s++++++l+ +ae   +a+v+apN+++Gvn++l ll++aa +l+ 
  lcl|FitnessBrowser__Marino:GFF3137  72 VDFTFPDLTLENAEFCKANGKMLVIGTTGMSDAEKQQLALAAES--TAVVFAPNMSVGVNVVLNLLRTAAATLGd 144
                                         ***************************************99999..************************99972 PP

                           TIGR00036 151 dvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgehtvlF 225
                                         d+D+EiiE+HHrhKkDaPSGTAl+++e++a+a g+dlke+av++reg+tGer+++eiG+ ++R+gdvvg+htvlF
  lcl|FitnessBrowser__Marino:GFF3137 145 DYDVEIIEAHHRHKKDAPSGTALRMGEVVADALGRDLKECAVYGREGFTGERTRKEIGFETIRAGDVVGDHTVLF 219
                                         57************************************************************************* PP

                           TIGR00036 226 asdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                         a++Ger+e+tHkassR++fakG++ra+ wl+dk +++yd++dvld
  lcl|FitnessBrowser__Marino:GFF3137 220 ATEGERIEVTHKASSRMTFAKGAMRAALWLKDKPAGLYDMQDVLD 264
                                         *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (266 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: 7.62
//
[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