GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cmutase in Paraburkholderia bryophila 376MFSha3.1

Align Secreted chorismate mutase; CM; EC 5.4.99.5 (characterized)
to candidate H281DRAFT_03996 H281DRAFT_03996 chorismate mutase (EC 5.4.99.5)

Query= SwissProt::A0QU81
         (181 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03996 H281DRAFT_03996
           chorismate mutase (EC 5.4.99.5)
          Length = 198

 Score = 87.8 bits (216), Expect = 1e-22
 Identities = 64/184 (34%), Positives = 97/184 (52%), Gaps = 9/184 (4%)

Query: 3   ASVALAALAGV----GTPHATADDASPLVPLVDAAAQRLQTADPVAASKFRSGGAIDDPD 58
           A  ALA LA +    G+  A  DD + L  L+  A+QRL  A+PVA  K+ +  AI D  
Sbjct: 9   APCALALLASLLAAPGSALADGDDTA-LTNLIALASQRLALAEPVARWKWANHQAITDTP 67

Query: 59  REQQVIAAVTGDATRHNIDPGYVHDVFRNQIDATSSVEHTRFAQWK-LDPAAAPSSAPDL 117
           REQ ++A V   A   N+DP +    F++QIDA+  V++  FA W+   P   P  APDL
Sbjct: 68  REQALLADVEKRAAAANVDPAFARAFFQDQIDASKDVQNALFASWRATQPPQEP--APDL 125

Query: 118 SES-RQKIDTLNRTMVDEIARQWPVLHSPVCRPDLDRALDAVATARGFDPVYRHALEYAT 176
           + S R ++D L +++V  +AR  P+  +P C   + ++L +  +   +D     AL  A 
Sbjct: 126 ATSTRPQLDRLTQSLVAGLARVQPLRAAPDCPSRVAQSLASWKSMTRYDSARSTALNRAL 185

Query: 177 HSYC 180
              C
Sbjct: 186 AHVC 189


Lambda     K      H
   0.318    0.130    0.387 

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: 90
Number of extensions: 4
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: 181
Length of database: 198
Length adjustment: 20
Effective length of query: 161
Effective length of database: 178
Effective search space:    28658
Effective search space used:    28658
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: 44 (21.6 bits)

Align candidate H281DRAFT_03996 H281DRAFT_03996 (chorismate mutase (EC 5.4.99.5))
to HMM TIGR01806 (putative chorismate mutase (EC 5.4.99.5))

# 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/TIGR01806.hmm
# target sequence database:        /tmp/gapView.31890.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01806  [M=114]
Accession:   TIGR01806
Description: CM_mono2: putative chorismate mutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    4.9e-34  103.1   0.9    7.8e-34  102.5   0.9    1.3  1  lcl|FitnessBrowser__Burk376:H281DRAFT_03996  H281DRAFT_03996 chorismate mutas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_03996  H281DRAFT_03996 chorismate mutase (EC 5.4.99.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.9   7.8e-34   7.8e-34       4     112 ..      33     142 ..      31     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 7.8e-34
                                    TIGR01806   4 aaldqlvdlaneRleladaValyKaesnlpieDsereeqvLdslraqaksagldedsverlfqaqi 69 
                                                  +al +l+ la++Rl+la++Va +K+ ++++i+D++re+++L+++ + a +a +d+  ++ +fq+qi
  lcl|FitnessBrowser__Burk376:H281DRAFT_03996  33 TALTNLIALASQRLALAEPVARWKWANHQAITDTPREQALLADVEKRAAAANVDPAFARAFFQDQI 98 
                                                  57999************************************************************* PP

                                    TIGR01806  70 nAnkaiqyrllsdWkskaeppvevrdLe.dlRakidqlntelLe 112
                                                  +A+k +q++l++ W+ ++ p  +++dL   +R+++d l++ l+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_03996  99 DASKDVQNALFASWRATQPPQEPAPDLAtSTRPQLDRLTQSLVA 142
                                                  ***************************99**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (114 nodes)
Target sequences:                          1  (198 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 4.45
//
[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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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