Alignments for a candidate for dapA in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapA in Desulfovibrio vulgaris Hildenborough

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; Protein MosA; EC 4.3.3.7 (characterized)
to candidate 207334 DVU1868 dihydrodipicolinate synthase

Query= SwissProt::Q07607
         (292 letters)



>MicrobesOnline__882:207334
          Length = 292

 Score =  297 bits (761), Expect = 2e-85
 Identities = 151/290 (52%), Positives = 197/290 (67%)

Query: 2   FEGSITALVTPFADDRIDEVALHDLVEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVVEI 61
           F G+ TA+VTPF + R+DE    +L+EWQIE+G  GLVPCGTTGES TLS  EH  V+ I
Sbjct: 3   FTGAFTAIVTPFRNGRVDEERFRELIEWQIEQGINGLVPCGTTGESATLSHDEHRDVIRI 62

Query: 62  TIKTANGRVPVIAGAGSNSTAEAIAFVRHAQNAGADGVLIVSPYYNKPTQEGIYQHFKAI 121
            ++   GR+PV+AGAGSN+T EAI   R A+ AGADG L+++PYYNKPTQEG+Y HFKAI
Sbjct: 63  CVEQVKGRIPVLAGAGSNNTREAIDLTRFAKEAGADGALLITPYYNKPTQEGLYLHFKAI 122

Query: 122 DAASTIPIIVYNIPGRSAIEIHVETLARIFEDCPNVKGVKDATGNLLRPSLERMACGEDF 181
            +  ++P IVYN+P R+   I  ETLAR+  D P V GVK+ATGNL++ S     CG DF
Sbjct: 123 ASEVSMPFIVYNVPSRTGTNICPETLARLNRDIPEVVGVKEATGNLIQVSEILEYCGTDF 182

Query: 182 NLLTGEDGTALGYMAHGGHGCISVTANVAPALCADFQQACLNGDFAAALKLQDRLMPLHR 241
            +L+G+D T L  ++ GG G ISVT+NV PA  +D  +A   GD A A +L   L P++R
Sbjct: 183 QVLSGDDFTVLPLLSVGGCGVISVTSNVVPAKMSDMCRAFKAGDLATARRLHFELSPINR 242

Query: 242 ALFLETNPAGAKYALQRLGRMRGDLRLPLVTISPSFQEEIDDAMRHAGIL 291
           A+FLETNP   K AL  +GR+  ++RLPL  +    Q  + D +  AGIL
Sbjct: 243 AMFLETNPIPVKTALALMGRIDLEMRLPLCPLQQVNQSRLRDILAAAGIL 292


Lambda     K      H
   0.319    0.136    0.402 

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: 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: 292
Length of database: 292
Length adjustment: 26
Effective length of query: 266
Effective length of database: 266
Effective search space:    70756
Effective search space used:    70756
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: 48 (23.1 bits)

Align candidate 207334 DVU1868 (dihydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

# 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/TIGR00674.hmm
# target sequence database:        /tmp/gapView.30069.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00674  [M=286]
Accession:   TIGR00674
Description: dapA: 4-hydroxy-tetrahydrodipicolinate synthase
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-116  373.9   0.0   2.1e-116  373.7   0.0    1.0  1  lcl|MicrobesOnline__882:207334  DVU1868 dihydrodipicolinate synt


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207334  DVU1868 dihydrodipicolinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.7   0.0  2.1e-116  2.1e-116       2     284 ..       6     287 ..       5     289 .. 0.99

  Alignments for each domain:
  == domain 1  score: 373.7 bits;  conditional E-value: 2.1e-116
                       TIGR00674   2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsnate 80 
                                       tA++TPf++   vd + + +lie qie+g++++v++GtTGEsatLs++E+ +vi++ ve vk+r+pv+aG+gsn+t+
  lcl|MicrobesOnline__882:207334   6 AFTAIVTPFRNGR-VDEERFRELIEWQIEQGINGLVPCGTTGESATLSHDEHRDVIRICVEQVKGRIPVLAGAGSNNTR 83 
                                     579******9988.***************************************************************** PP

                       TIGR00674  81 eaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeve.ivaiK 158
                                     eai+lt++a+++g+dg+l++tPyYnkPtqeGly hfkaia+ev++P i+YnvPsRtg+++ pet++rL ++ + +v++K
  lcl|MicrobesOnline__882:207334  84 EAIDLTRFAKEAGADGALLITPYYNKPTQEGLYLHFKAIASEVSMPFIVYNVPSRTGTNICPETLARLNRDIPeVVGVK 162
                                     *********************************************************************99888***** PP

                       TIGR00674 159 easgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteeareihqkllklf 237
                                     ea+g+l +vsei ++ + df+vlsGdD ++l++l++G++GviSV+snv+p ++++m++a+ +gd + ar +h +l ++ 
  lcl|MicrobesOnline__882:207334 163 EATGNLIQVSEILEYCGTDFQVLSGDDFTVLPLLSVGGCGVISVTSNVVPAKMSDMCRAFKAGDLATARRLHFELSPIN 241
                                     ******************************************************************************* PP

                       TIGR00674 238 kalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlk 284
                                     +a+f+etNPipvKtalal+g i   e+RlPL++l++ ++++l+++l+
  lcl|MicrobesOnline__882:207334 242 RAMFLETNPIPVKTALALMGRIDL-EMRLPLCPLQQVNQSRLRDILA 287
                                     ************************.*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (292 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: 00:00:00.01
# Mc/sec: 6.33
//
[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