GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisG in Salinicoccus carnicancri Crm

Align ATP phosphoribosyltransferase; ATP-PRT; ATP-PRTase; EC 2.4.2.17 (uncharacterized)
to candidate WP_017550011.1 C792_RS0113590 ATP phosphoribosyltransferase

Query= curated2:B9DQ89
         (205 letters)



>NCBI__GCF_000330705.1:WP_017550011.1
          Length = 200

 Score =  196 bits (498), Expect = 2e-55
 Identities = 100/200 (50%), Positives = 135/200 (67%), Gaps = 1/200 (0%)

Query: 1   MLTVALSKGRLLKDFIKFLERNNNHVWADAIIHRERKLQITADSIKFILVKGSDVPTYVE 60
           M+TVAL+KGRL KDFI+++E N  + +  A+    R L    D +KFI  KG DVPTYVE
Sbjct: 1   MITVALTKGRLFKDFIEYMEENGLNDYIGALTGETRSLYTVVDDVKFIFAKGPDVPTYVE 60

Query: 61  EGIADIGITGSDILKERPNRNINNYIDLPFGECHFSVAAKPNVTNIQRVATTYVKTTRDY 120
            G+AD+GI GSDI+ E    NI N   LPFG+CHFSVAA P       +AT Y     ++
Sbjct: 61  SGVADLGIVGSDIIAE-DEFNILNVSQLPFGDCHFSVAALPGQEAFGTIATKYTNVAFEH 119

Query: 121 FNQKGTDISIIQLSGSVELAAVVDMVDAIVDIVQTGTTLKSNGLEEREQIGEINARLITN 180
           F  +  D+S++ L+GSVELA ++ + DAIVDIVQTG TL+ NGL E E+I +I+ARLI N
Sbjct: 120 FKNRKMDVSLVHLNGSVELAPLLGLSDAIVDIVQTGGTLRDNGLIEYEKIMDIHARLIAN 179

Query: 181 KHSFFSKSKAIENFIQQLGV 200
           K +F++K   I  F++++GV
Sbjct: 180 KRTFYTKEDGIYAFLKEIGV 199


Lambda     K      H
   0.319    0.135    0.374 

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: 138
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: 205
Length of database: 200
Length adjustment: 21
Effective length of query: 184
Effective length of database: 179
Effective search space:    32936
Effective search space used:    32936
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 (21.7 bits)
S2: 45 (21.9 bits)

Align candidate WP_017550011.1 C792_RS0113590 (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.2116067.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.6e-56  176.5   0.0    3.1e-56  176.2   0.0    1.1  1  NCBI__GCF_000330705.1:WP_017550011.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017550011.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.2   0.0   3.1e-56   3.1e-56       1     183 []       2     178 ..       2     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 176.2 bits;  conditional E-value: 3.1e-56
                             TIGR00070   1 lriAlpKGrleeetlkllekaglk..lskke....erkliasaedeevevlllrakdiptyvekgaadlGitG 67 
                                           +++Al+KGrl+++ ++++e++gl+  +   +    +r+l+  +  ++v++++++  d+ptyve+g+adlGi+G
  NCBI__GCF_000330705.1:WP_017550011.1   2 ITVALTKGRLFKDFIEYMEENGLNdyI--GAltgeTRSLY--TVVDDVKFIFAKGPDVPTYVESGVADLGIVG 70 
                                           79*********************9553..33333245555..55568************************** PP

                             TIGR00070  68 kDlleEseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGa 140
                                           +D+++E+e ++ ++ +l fg c++++A+   ++            iATky+n++ e++++++++v++v+l+G+
  NCBI__GCF_000330705.1:WP_017550011.1  71 SDIIAEDEFNILNVSQLPFGDCHFSVAALPGQEAFG--------TIATKYTNVAFEHFKNRKMDVSLVHLNGS 135
                                           ****************************99995544........6**************************** PP

                             TIGR00070 141 vElapllgladaIvDivetGttLrengLkiieeilessarlia 183
                                           vElapllgl+daIvDiv+tG tLr ngL ++e+i++++arlia
  NCBI__GCF_000330705.1:WP_017550011.1 136 VELAPLLGLSDAIVDIVQTGGTLRDNGLIEYEKIMDIHARLIA 178
                                           *****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (200 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: 9.52
//
[ok]

This GapMind analysis is from Jul 26 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