GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Synechococcus elongatus PCC 7942

Align dihydrodipicolinate synthase subunit (EC 4.3.3.7) (characterized)
to candidate Synpcc7942_1847 Synpcc7942_1847 dihydrodipicolinate synthase

Query= metacyc::MONOMER-6565
         (289 letters)



>FitnessBrowser__SynE:Synpcc7942_1847
          Length = 299

 Score =  287 bits (734), Expect = 2e-82
 Identities = 144/289 (49%), Positives = 201/289 (69%), Gaps = 3/289 (1%)

Query: 3   FGNIATAMVTPFDKNENIDFQKLSKLIDYLLNNGTDSLVVAGTTGESPTLSEEEKVALIQ 62
           FG + TAM+TPF+    + +     L  +L+  G+D LV+ GTTGESPTL+ EE++ L +
Sbjct: 7   FGRVITAMITPFNAEGQVAYDIAQSLAVHLVEQGSDGLVICGTTGESPTLTWEEELQLFR 66

Query: 63  YSVKEAAG-RAPIIAGTGSNNTKASIKLTKKAEEAGADAVMLVTPYYNKPSQEGMYRHFR 121
            +VKEA G RA +IAGTGSN T+ +I  T+ A   G +  + V PYYNKP QEG+Y HFR
Sbjct: 67  -AVKEAVGDRAAVIAGTGSNCTREAIAATQSAATLGLNGSLQVVPYYNKPPQEGLYAHFR 125

Query: 122 AIAEET-SLPVMLYNVPGRTAASLAPETTIRLAEIPNIIAIKEASGDLDAITKIVAETPE 180
           AIAE    LP+MLYN+PGRT  SL PET  RLA +PN++AIK ASG+++ ++ +    P+
Sbjct: 126 AIAEACPDLPLMLYNIPGRTGQSLQPETVARLASLPNVVAIKAASGNVEEVSALRQLLPD 185

Query: 181 DFAVYSGDDSLTLPALSVGARGIVSVASHIIGPEMQEMIKHYTEGNTAQAALIHQKLLPL 240
            FA+YSGDDSLTLP L+VGA+G+VSVASH++GP++Q +I+ +  GN A+A  +H +L PL
Sbjct: 186 SFAIYSGDDSLTLPMLAVGAQGVVSVASHLVGPQLQALIQAFEAGNVARAQQLHHQLYPL 245

Query: 241 MKGLFAAPNPSPLKTALQLKGLDVGSVRLPLIPLNEDERLRLSSLMNGL 289
            K LF   NP P++ A++L G  +G  RLPL+P + + R  L+S +  L
Sbjct: 246 FKALFLTTNPIPVRAAMELLGWSIGLPRLPLVPASAEIRQALASCLTEL 294


Lambda     K      H
   0.313    0.131    0.357 

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: 244
Number of extensions: 3
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: 289
Length of database: 299
Length adjustment: 26
Effective length of query: 263
Effective length of database: 273
Effective search space:    71799
Effective search space used:    71799
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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.8022.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: 7.23
//
[ok]

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

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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:

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:

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:

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:

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