GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisG in Azohydromonas australica DSM 1124

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_029000578.1 H537_RS0128475 ATP phosphoribosyltransferase

Query= reanno::BFirm:BPHYT_RS17715
         (232 letters)



>NCBI__GCF_000430725.1:WP_029000578.1
          Length = 225

 Score =  317 bits (813), Expect = 9e-92
 Identities = 167/212 (78%), Positives = 183/212 (86%), Gaps = 4/212 (1%)

Query: 17  LTLALSKGRIFEETLPLLAAAGIEVAEDPETSRKLILPTTDANLRVIIVRATDVPTYVEY 76
           +TLALSKGRIFEETLPLL AAGIEV EDPE SRKLILPT    +RV++VRATDVPTYV+Y
Sbjct: 5   ITLALSKGRIFEETLPLLRAAGIEVGEDPEKSRKLILPTNRPEVRVVLVRATDVPTYVQY 64

Query: 77  GAADFGVAGKDVLLEHGG----SGLYQPVDLDIARCRMSVAVAAGFDYANAVRQGARLRV 132
           G AD GVAG DVLLEH G    +GLYQP+DL IA CRMSVAV A FDY  AVRQG+R+RV
Sbjct: 65  GGADLGVAGLDVLLEHAGGETATGLYQPLDLRIASCRMSVAVRADFDYEAAVRQGSRIRV 124

Query: 133 ATKYVETAREHFAAKGVHVDLIKLYGSMELAPLVGLADAIVDLVSSGNTLRANNLVEVEE 192
           ATKY   AR+HFA KGVHVDLIKLYGSMELAPL GLADAIVDLVS+G+TLRANNLVEVE+
Sbjct: 125 ATKYTHIARQHFADKGVHVDLIKLYGSMELAPLTGLADAIVDLVSTGSTLRANNLVEVEQ 184

Query: 193 IMQISSRLVVNQAALKLKRAALRPILDAFERA 224
           IM ISSRLVVNQAALKLKRAAL+P++DAF  A
Sbjct: 185 IMPISSRLVVNQAALKLKRAALKPLIDAFAGA 216


Lambda     K      H
   0.318    0.132    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: 211
Number of extensions: 4
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: 232
Length of database: 225
Length adjustment: 23
Effective length of query: 209
Effective length of database: 202
Effective search space:    42218
Effective search space used:    42218
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: 46 (22.3 bits)

Align candidate WP_029000578.1 H537_RS0128475 (ATP phosphoribosyltransferase)
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.2375134.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.3e-62  196.2   0.0    2.7e-62  196.0   0.0    1.0  1  NCBI__GCF_000430725.1:WP_029000578.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000430725.1:WP_029000578.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.0   0.0   2.7e-62   2.7e-62       1     183 []       5     194 ..       5     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 196.0 bits;  conditional E-value: 2.7e-62
                             TIGR00070   1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitGkDll 71 
                                           +++Al KGr++eetl ll++ag+++ +    +rkli  ++++ev+v+l+ra+d+ptyv++g adlG+ G D+l
  NCBI__GCF_000430725.1:WP_029000578.1   5 ITLALSKGRIFEETLPLLRAAGIEVGEDPekSRKLILPTNRPEVRVVLVRATDVPTYVQYGGADLGVAGLDVL 77 
                                           799*********************98876689***************************************** PP

                             TIGR00070  72 eE...sead....vvelldlgfgkcklvlAvpeesdvesledlkegk..riATkypnltreylekkgvkveiv 135
                                            E      +    +++ ldl++  c++++Av+ + d+e+  ++++g+  r+ATky++++r+++++kgv+v+++
  NCBI__GCF_000430725.1:WP_029000578.1  78 LEhagG--EtatgLYQPLDLRIASCRMSVAVRADFDYEA--AVRQGSriRVATKYTHIARQHFADKGVHVDLI 146
                                           **6541..14567************************99..55554447************************ PP

                             TIGR00070 136 kleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183
                                           kl+G++Elapl+gladaIvD+v+tG+tLr+n+L+++e+i+ +s+rl++
  NCBI__GCF_000430725.1:WP_029000578.1 147 KLYGSMELAPLTGLADAIVDLVSTGSTLRANNLVEVEQIMPISSRLVV 194
                                           *********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (225 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: 14.60
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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