GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Echvi_2512 Echvi_2512 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::Q9WYH8
         (338 letters)



>FitnessBrowser__Cola:Echvi_2512
          Length = 339

 Score =  280 bits (716), Expect = 4e-80
 Identities = 145/329 (44%), Positives = 209/329 (63%), Gaps = 2/329 (0%)

Query: 1   MIVVLKPGSTEEDIRKVVKLAESYNLKCHISKGQERTVIGIIGDDRYVVADKFESLDCVE 60
           MI+ +K   TE    +++K       K      Q+ T +  IG   + +  KF   + ++
Sbjct: 1   MIIQVKQDITEVQKERLIKEINQIGYKITEVITQKGTYLVGIGSAEFDIR-KFGHHEGIQ 59

Query: 61  SVVRVLKPYKLVSREFHPEDTVIDLGD-VKIGNGYFTIIAGPCSVEGREMLMETAHFLSE 119
            +  V   YKLVSR++    T IDLGD V I  G   ++AGPCS+E  E +++    L  
Sbjct: 60  DIHIVSDAYKLVSRKWKVNPTSIDLGDGVYIKEGDMAVMAGPCSIESEEQIVKVIDHLKA 119

Query: 120 LGVKVLRGGAYKPRTSPYSFQGLGEKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYAD 179
             +K++RGG YKPR+SPY+F+GLG +GL+   E A K G+ ++TE +    + ++ +Y D
Sbjct: 120 NNIKIMRGGVYKPRSSPYAFRGLGIEGLKLWHELASKAGIKIITEVMQVSQIEEMMDYVD 179

Query: 180 IIQIGARNAQNFRLLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGI 239
           + Q+GARN QNF LL + G  +KPV++KRG   TIEE L SAEY+ + GN K+ILCERGI
Sbjct: 180 VFQVGARNTQNFNLLDELGKVDKPVMIKRGISGTIEELLQSAEYVFSGGNEKLILCERGI 239

Query: 240 RTFEKATRNTLDISAVPIIRKESHLPILVDPSHSGGRRDLVIPLSRAAIAVGAHGIIVEV 299
           RT+EKATRNTLD++AVP+++ +SHLP++VDPSH  G R  V  ++ A +  GA GII E 
Sbjct: 240 RTYEKATRNTLDLNAVPVLKDKSHLPVVVDPSHGIGIRKFVHQMALAGVMAGADGIIYET 299

Query: 300 HPEPEKALSDGKQSLDFELFKELVQEMKK 328
           H  PEKA SDG+Q+LDF    +L  +++K
Sbjct: 300 HEIPEKAYSDGQQTLDFAQSSQLASQIRK 328


Lambda     K      H
   0.318    0.138    0.388 

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: 326
Number of extensions: 12
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: 338
Length of database: 339
Length adjustment: 28
Effective length of query: 310
Effective length of database: 311
Effective search space:    96410
Effective search space used:    96410
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate Echvi_2512 Echvi_2512 (phospho-2-dehydro-3-deoxyheptonate aldolase)
to HMM TIGR01361 (aroF: 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR01361.hmm
# target sequence database:        /tmp/gapView.2902.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01361  [M=260]
Accession:   TIGR01361
Description: DAHP_synth_Bsub: 3-deoxy-7-phosphoheptulonate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
     8e-106  339.1   0.1     1e-105  338.8   0.1    1.1  1  lcl|FitnessBrowser__Cola:Echvi_2512  Echvi_2512 phospho-2-dehydro-3-d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2512  Echvi_2512 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.8   0.1    1e-105    1e-105       2     258 ..      70     327 ..      69     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 338.8 bits;  conditional E-value: 1e-105
                            TIGR01361   2 laskkvkkeetvvdved.vkiGegeliviaGPCsveseeqivetakavkeaGakllrGgafkPrtsPysfqGlg 74 
                                          l+s+k+k + t +d+ d v i eg+++v+aGPCs+eseeqiv++  ++k++ +k++rGg++kPr sPy+f+Glg
  lcl|FitnessBrowser__Cola:Echvi_2512  70 LVSRKWKVNPTSIDLGDgVYIKEGDMAVMAGPCSIESEEQIVKVIDHLKANNIKIMRGGVYKPRSSPYAFRGLG 143
                                          7899*****999999755******************************************************** PP

                            TIGR01361  75 eeglkllkrakdetgllvvtevlderdveivaeyvDilqiGarnmqnfelLkevgkskkPvlLkrglaatieew 148
                                           eglkl ++ ++++g++++tev++++++e + +yvD++q+Garn+qnf+lL+e+gk +kPv++krg++ tiee+
  lcl|FitnessBrowser__Cola:Echvi_2512 144 IEGLKLWHELASKAGIKIITEVMQVSQIEEMMDYVDVFQVGARNTQNFNLLDELGKVDKPVMIKRGISGTIEEL 217
                                          ************************************************************************** PP

                            TIGR01361 149 leaaeYilsegnenvilcerGirtfekatrftldlsavallkklthlPvivDpshaaGrrdlvlplakaavavG 222
                                          l++aeY+ s gne++ilcerGirt+ekatr+tldl+av++lk+++hlPv+vDpsh+ G r++v+ +a a+v +G
  lcl|FitnessBrowser__Cola:Echvi_2512 218 LQSAEYVFSGGNEKLILCERGIRTYEKATRNTLDLNAVPVLKDKSHLPVVVDPSHGIGIRKFVHQMALAGVMAG 291
                                          ************************************************************************** PP

                            TIGR01361 223 adgllievhpdPekalsDseqqltpeefkelvkelk 258
                                          adg++ e h+ Peka sD++q l++++ ++l ++++
  lcl|FitnessBrowser__Cola:Echvi_2512 292 ADGIIYETHEIPEKAYSDGQQTLDFAQSSQLASQIR 327
                                          *************************99999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (260 nodes)
Target sequences:                          1  (339 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: 9.39
//
[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:

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