Aligments for a candidate for dapA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Aligments for a candidate for dapA in Synechococcus elongatus PCC 7942

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate Synpcc7942_1847 Synpcc7942_1847 dihydrodipicolinate synthase

Query= BRENDA::Q81WN7
         (292 letters)



>FitnessBrowser__SynE:Synpcc7942_1847
          Length = 299

 Score =  270 bits (691), Expect = 2e-77
 Identities = 134/288 (46%), Positives = 196/288 (68%), Gaps = 1/288 (0%)

Query: 4   FGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYR 63
           FG + TAM+TPF+  G + +     L  +L++ G+  +V+ GTTGESPTLT EE++ L+R
Sbjct: 7   FGRVITAMITPFNAEGQVAYDIAQSLAVHLVEQGSDGLVICGTTGESPTLTWEEELQLFR 66

Query: 64  HVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHFKA 123
            V   V  R  VIAGTGSN T  +I  T+ A  +G++  + V PYYNKP QEG+Y HF+A
Sbjct: 67  AVKEAVGDRAAVIAGTGSNCTREAIAATQSAATLGLNGSLQVVPYYNKPPQEGLYAHFRA 126

Query: 124 IAESTP-LPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADD 182
           IAE+ P LP+MLYN+PGR+   +  +TV RL+ + N+VAIK A G+V  ++ + +   D 
Sbjct: 127 IAEACPDLPLMLYNIPGRTGQSLQPETVARLASLPNVVAIKAASGNVEEVSALRQLLPDS 186

Query: 183 FAVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVT 242
           FA+YSGDD LTLP +AVGA+G+VSVASH++G ++Q +I AF+AG   +AQ+LH  L  + 
Sbjct: 187 FAIYSGDDSLTLPMLAVGAQGVVSVASHLVGPQLQALIQAFEAGNVARAQQLHHQLYPLF 246

Query: 243 DSLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQSI 290
            +LF+  +P PV+ A++++G  +G  RLPL+P + E R  L S +  +
Sbjct: 247 KALFLTTNPIPVRAAMELLGWSIGLPRLPLVPASAEIRQALASCLTEL 294


Lambda     K      H
   0.316    0.132    0.362 

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: 201
Number of extensions: 6
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: 292
Length of database: 299
Length adjustment: 26
Effective length of query: 266
Effective length of database: 273
Effective search space:    72618
Effective search space used:    72618
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate Synpcc7942_1847 Synpcc7942_1847 (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.16357.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.7e-111  355.1   0.0   1.1e-110  355.0   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1847  Synpcc7942_1847 dihydrodipicolin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1847  Synpcc7942_1847 dihydrodipicolinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.0   0.0  1.1e-110  1.1e-110       2     285 ..      10     293 ..       9     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 355.0 bits;  conditional E-value: 1.1e-110
                                 TIGR00674   2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 
                                               v+tA+iTPf+++g+v ++  ++l  +++e+g+d++v++GtTGEs+tL++eE+ ++++ + e v +r  v
  lcl|FitnessBrowser__SynE:Synpcc7942_1847  10 VITAMITPFNAEGQVAYDIAQSLAVHLVEQGSDGLVICGTTGESPTLTWEEELQLFRAVKEAVGDRAAV 78 
                                               89******************************************************************* PP

                                 TIGR00674  71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeev.elPiilYnvPsRtgv 138
                                               iaGtgsn+t+eai  t+ a+ lg +g l+v+PyYnkP qeGly+hf aiae++ +lP++lYn+P+Rtg+
  lcl|FitnessBrowser__SynE:Synpcc7942_1847  79 IAGTGSNCTREAIAATQSAATLGLNGSLQVVPYYNKPPQEGLYAHFRAIAEACpDLPLMLYNIPGRTGQ 147
                                               ***************************************************999*************** PP

                                 TIGR00674 139 slepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnva 207
                                               sl+petv+rLa+ +++vaiK asg++e+vs +++  +++f+++sGdD+ltl++la+Ga+Gv+SVas+++
  lcl|FitnessBrowser__SynE:Synpcc7942_1847 148 SLQPETVARLASLPNVVAIKAASGNVEEVSALRQLLPDSFAIYSGDDSLTLPMLAVGAQGVVSVASHLV 216
                                               ********************************************************************* PP

                                 TIGR00674 208 pkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekk 276
                                               + +l+ +++a+ +g++++a+++h++l +lfkalf++tNPipv++a++llg+  +   RlPL+++s e +
  lcl|FitnessBrowser__SynE:Synpcc7942_1847 217 GPQLQALIQAFEAGNVARAQQLHHQLYPLFKALFLTTNPIPVRAAMELLGWSIG-LPRLPLVPASAEIR 284
                                               ******************************************************.9************* PP

                                 TIGR00674 277 eklkevlke 285
                                               + l++ l+e
  lcl|FitnessBrowser__SynE:Synpcc7942_1847 285 QALASCLTE 293
                                               ***999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (299 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: 8.50
//
[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