GapMind for Amino acid biosynthesis

 

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

Align ATP phosphoribosyltransferase; ATP-PRT; ATP-PRTase; EC 2.4.2.17 (uncharacterized)
to candidate H281DRAFT_05651 H281DRAFT_05651 ATP phosphoribosyltransferase (homohexameric)

Query= curated2:Q7WDY5
         (223 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05651 H281DRAFT_05651 ATP
           phosphoribosyltransferase (homohexameric)
          Length = 232

 Score =  317 bits (811), Expect = 2e-91
 Identities = 166/220 (75%), Positives = 193/220 (87%), Gaps = 4/220 (1%)

Query: 2   SPA-AAPLTLALSKGRIFEETMPLLAEAGIEVPENPESSRKLILPTSDPGLRLIIVRASD 60
           SPA +APLTLALSKGRIFEET+PLLA AGIEV E+PE+SRKLILPT+D  LR+IIVRA+D
Sbjct: 10  SPAVSAPLTLALSKGRIFEETLPLLAAAGIEVAEDPETSRKLILPTTDANLRVIIVRATD 69

Query: 61  VPTYVQYGAADLGIAGKDVLIEHAAQQSGRLYQPIDLNIAKCRLCVAVRQDFDYQAAVHQ 120
           VPTYV+YGAAD G+AGKDVL+EH    SG LYQP+DL+IA+CR+ VAV   FDY  AV Q
Sbjct: 70  VPTYVEYGAADFGVAGKDVLLEHGG--SG-LYQPVDLDIARCRMSVAVAAGFDYANAVRQ 126

Query: 121 GARLRVATKYVQSAREHFAAKGVHVDIIKLYGSMELAPLVGLADAIVDLVSTGGTLRANG 180
           GARLRVATKYV++AREHFAAKGVHVD+IKLYGSMELAPLVGLADAIVDLVS+G TLRAN 
Sbjct: 127 GARLRVATKYVETAREHFAAKGVHVDLIKLYGSMELAPLVGLADAIVDLVSSGNTLRANN 186

Query: 181 LAAVEDVMPISSRLIVNQAALKTRGARLQPLIDAFRRASE 220
           L  VE++M ISSRL+VNQAALK + A L+P++DAF RA++
Sbjct: 187 LVEVEEIMQISSRLVVNQAALKLKRAALRPILDAFERATK 226


Lambda     K      H
   0.320    0.135    0.377 

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: 220
Number of extensions: 3
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: 223
Length of database: 232
Length adjustment: 22
Effective length of query: 201
Effective length of database: 210
Effective search space:    42210
Effective search space used:    42210
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: 46 (22.3 bits)

Align candidate H281DRAFT_05651 H281DRAFT_05651 (ATP phosphoribosyltransferase (homohexameric))
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.14772.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    1.6e-63  200.0   0.1    1.9e-63  199.7   0.1    1.1  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05651  H281DRAFT_05651 ATP phosphoribos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05651  H281DRAFT_05651 ATP phosphoribosyltransferase (homohexameric)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.7   0.1   1.9e-63   1.9e-63       1     183 []      17     202 ..      17     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 199.7 bits;  conditional E-value: 1.9e-63
                                    TIGR00070   1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlG 64 
                                                  l++Al KGr++eetl ll++ag+++ +    +rkli  ++d++++v+++ra+d+ptyve+gaad+G
  lcl|FitnessBrowser__Burk376:H281DRAFT_05651  17 LTLALSKGRIFEETLPLLAAAGIEVAEDPetSRKLILPTTDANLRVIIVRATDVPTYVEYGAADFG 82 
                                                  79**********************98877789********************************** PP

                                    TIGR00070  65 itGkDlleEsead.vvelldlgfgkcklvlAvpeesdvesledlkegk..riATkypnltreylek 127
                                                  + GkD+l E++ + +++ +dl++ +c++++Av    d+ +  ++++g+  r+ATky++++re+++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05651  83 VAGKDVLLEHGGSgLYQPVDLDIARCRMSVAVAAGFDYAN--AVRQGArlRVATKYVETAREHFAA 146
                                                  *********87777**********************9988..44444346**************** PP

                                    TIGR00070 128 kgvkveivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183
                                                  kgv+v+++kl+G++Elapl+gladaIvD+v++G+tLr+n+L+++eei+++s+rl++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05651 147 KGVHVDLIKLYGSMELAPLVGLADAIVDLVSSGNTLRANNLVEVEEIMQISSRLVV 202
                                                  *****************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (232 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: 6.63
//
[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