GapMind for Amino acid biosynthesis

 

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

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate H281DRAFT_05651 H281DRAFT_05651 ATP phosphoribosyltransferase (homohexameric)

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



>FitnessBrowser__Burk376:H281DRAFT_05651
          Length = 232

 Score =  433 bits (1113), Expect = e-126
 Identities = 228/232 (98%), Positives = 230/232 (99%)

Query: 1   MSAMPQTSSSPAVSAPLTLALSKGRIFEETLPLLAAAGIEVAEDPETSRKLILPTTDANL 60
           MS+MPQTSSSPAVSAPLTLALSKGRIFEETLPLLAAAGIEVAEDPETSRKLILPTTDANL
Sbjct: 1   MSSMPQTSSSPAVSAPLTLALSKGRIFEETLPLLAAAGIEVAEDPETSRKLILPTTDANL 60

Query: 61  RVIIVRATDVPTYVEYGAADFGVAGKDVLLEHGGSGLYQPVDLDIARCRMSVAVAAGFDY 120
           RVIIVRATDVPTYVEYGAADFGVAGKDVLLEHGGSGLYQPVDLDIARCRMSVAVAAGFDY
Sbjct: 61  RVIIVRATDVPTYVEYGAADFGVAGKDVLLEHGGSGLYQPVDLDIARCRMSVAVAAGFDY 120

Query: 121 ANAVRQGARLRVATKYVETAREHFAAKGVHVDLIKLYGSMELAPLVGLADAIVDLVSSGN 180
           ANAVRQGARLRVATKYVETAREHFAAKGVHVDLIKLYGSMELAPLVGLADAIVDLVSSGN
Sbjct: 121 ANAVRQGARLRVATKYVETAREHFAAKGVHVDLIKLYGSMELAPLVGLADAIVDLVSSGN 180

Query: 181 TLRANNLVEVEEIMQISSRLVVNQAALKLKRAALRPILDAFERASKAGAATA 232
           TLRANNLVEVEEIMQISSRLVVNQAALKLKRAALRPILDAFERA+KAG A A
Sbjct: 181 TLRANNLVEVEEIMQISSRLVVNQAALKLKRAALRPILDAFERATKAGLAAA 232


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: 283
Number of extensions: 1
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: 232
Length of database: 232
Length adjustment: 23
Effective length of query: 209
Effective length of database: 209
Effective search space:    43681
Effective search space used:    43681
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 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.20808.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 8.31
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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