Alignments for a candidate for hisG in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisG in Escherichia coli BW25113

Align ATP phosphoribosyltransferase (characterized)
to candidate 16127 b2019 ATP phosphoribosyltransferase (NCBI)

Query= CharProtDB::CH_024688
         (299 letters)



>FitnessBrowser__Keio:16127
          Length = 299

 Score =  585 bits (1507), Expect = e-172
 Identities = 299/299 (100%), Positives = 299/299 (100%)

Query: 1   MTDNTRLRIAMQKSGRLSDDSRELLARCGIKINLHTQRLIAMAENMPIDILRVRDDDIPG 60
           MTDNTRLRIAMQKSGRLSDDSRELLARCGIKINLHTQRLIAMAENMPIDILRVRDDDIPG
Sbjct: 1   MTDNTRLRIAMQKSGRLSDDSRELLARCGIKINLHTQRLIAMAENMPIDILRVRDDDIPG 60

Query: 61  LVMDGVVDLGIIGENVLEEELLNRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAWDGPL 120
           LVMDGVVDLGIIGENVLEEELLNRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAWDGPL
Sbjct: 61  LVMDGVVDLGIIGENVLEEELLNRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAWDGPL 120

Query: 121 SLNGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEAN 180
           SLNGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEAN
Sbjct: 121 SLNGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEAN 180

Query: 181 GLREVEVIYRSKACLIQRDGEMEESKQQLIDKLLTRIQGVIQARESKYIMMHAPTERLDE 240
           GLREVEVIYRSKACLIQRDGEMEESKQQLIDKLLTRIQGVIQARESKYIMMHAPTERLDE
Sbjct: 181 GLREVEVIYRSKACLIQRDGEMEESKQQLIDKLLTRIQGVIQARESKYIMMHAPTERLDE 240

Query: 241 VIALLPGAERPTILPLAGDQQRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMME 299
           VIALLPGAERPTILPLAGDQQRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMME
Sbjct: 241 VIALLPGAERPTILPLAGDQQRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMME 299


Lambda     K      H
   0.320    0.137    0.389 

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: 454
Number of extensions: 6
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: 299
Length of database: 299
Length adjustment: 27
Effective length of query: 272
Effective length of database: 272
Effective search space:    73984
Effective search space used:    73984
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 16127 b2019 (ATP phosphoribosyltransferase (NCBI))
to HMM TIGR00070 (hisG: ATP phosphoribosyltransferase (EC 2.4.2.17))

# 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/TIGR00070.hmm
# target sequence database:        /tmp/gapView.24001.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00070  [M=183]
Accession:   TIGR00070
Description: hisG: ATP phosphoribosyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.7e-61  193.4   0.0    2.4e-61  192.9   0.0    1.2  1  lcl|FitnessBrowser__Keio:16127  b2019 ATP phosphoribosyltransfer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16127  b2019 ATP phosphoribosyltransferase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.9   0.0   2.4e-61   2.4e-61       1     183 []       7     197 ..       7     197 .. 0.96

  Alignments for each domain:
  == domain 1  score: 192.9 bits;  conditional E-value: 2.4e-61
                       TIGR00070   1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlleE..... 73 
                                     lriA++  Grl++++ +ll+++g+k++ ++ ++lia ae+ ++++l +r++dip  v +g++dlGi+G+++leE     
  lcl|FitnessBrowser__Keio:16127   7 LRIAMQkSGRLSDDSRELLARCGIKINLHT-QRLIAMAENMPIDILRVRDDDIPGLVMDGVVDLGIIGENVLEEellnr 84 
                                     89****99*********************9.99*****************************************77764 PP

                       TIGR00070  74 .sead.....vvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGavElapl 146
                                         +     +++l +l+fg c+l+lA+p +++++ + +l+ gkriAT+yp+l ++yl++kg++++ + l+G+vE+ap+
  lcl|FitnessBrowser__Keio:16127  85 rA--QgedprYFTLRRLDFGGCRLSLATPVDEAWDGPLSLN-GKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPR 160
                                     40..266677*******************************.9************************************ PP

                       TIGR00070 147 lgladaIvDivetGttLrengLkiieeilessarlia 183
                                     +gladaI+D+v+tG+tL++ngL+++e+i++s+a+li+
  lcl|FitnessBrowser__Keio:16127 161 AGLADAICDLVSTGATLEANGLREVEVIYRSKACLIQ 197
                                     ***********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 7.92
//
[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