Alignments for a candidate for hisG in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisG in Acidovorax sp. GW101-3H11

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate Ac3H11_4722 ATP phosphoribosyltransferase (EC 2.4.2.17)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_4722
          Length = 214

 Score =  314 bits (804), Expect = 1e-90
 Identities = 160/208 (76%), Positives = 179/208 (86%)

Query: 17  LTLALSKGRIFEETLPLLAAAGIEVAEDPETSRKLILPTTDANLRVIIVRATDVPTYVEY 76
           +TLALSKGRIF+ETLPLLAAAGIEV EDPE SRKLILPT   N+RV++VRATDVPTYVEY
Sbjct: 3   ITLALSKGRIFDETLPLLAAAGIEVLEDPEKSRKLILPTNQPNVRVVLVRATDVPTYVEY 62

Query: 77  GAADFGVAGKDVLLEHGGSGLYQPVDLDIARCRMSVAVAAGFDYANAVRQGARLRVATKY 136
           G AD GV GKD L+EHGG GLYQP+DL IA+CR+SVAV   FDY  AV+QGARL+VATKY
Sbjct: 63  GGADIGVTGKDTLIEHGGQGLYQPLDLQIAKCRVSVAVRNDFDYERAVKQGARLKVATKY 122

Query: 137 VETAREHFAAKGVHVDLIKLYGSMELAPLVGLADAIVDLVSSGNTLRANNLVEVEEIMQI 196
              AR+ FA KGVHVD++KLYGSMELAPL GLADAIVDLVS+GNTL+AN+LVEVE IM I
Sbjct: 123 TSIARDFFATKGVHVDMVKLYGSMELAPLTGLADAIVDLVSTGNTLKANHLVEVERIMDI 182

Query: 197 SSRLVVNQAALKLKRAALRPILDAFERA 224
           SS LVVNQAALKLK+A LR I+DAF  A
Sbjct: 183 SSYLVVNQAALKLKQAPLRRIIDAFAGA 210


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: 189
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: 214
Length adjustment: 22
Effective length of query: 210
Effective length of database: 192
Effective search space:    40320
Effective search space used:    40320
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 Ac3H11_4722 (ATP phosphoribosyltransferase (EC 2.4.2.17))
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.479.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
    6.8e-64  201.2   0.1    7.9e-64  201.0   0.1    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4722  ATP phosphoribosyltransferase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4722  ATP phosphoribosyltransferase (EC 2.4.2.17)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.0   0.1   7.9e-64   7.9e-64       1     183 []       3     188 ..       3     188 .. 0.95

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 7.9e-64
                                        TIGR00070   1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekga 60 
                                                      +++Al KGr+++etl ll++ag+++ +    +rkli  +++++v+v+l+ra+d+ptyve+g 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4722   3 ITLALSKGRIFDETLPLLAAAGIEVLEDPekSRKLILPTNQPNVRVVLVRATDVPTYVEYGG 64 
                                                      799*********************87765589****************************** PP

                                        TIGR00070  61 adlGitGkDlleEsead.vvelldlgfgkcklvlAvpeesdvesledlkegk..riATkypn 119
                                                      ad+G+tGkD+l E++ + +++ ldl++ kc++++Av+++ d+e+  ++k+g+  ++ATky++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4722  65 ADIGVTGKDTLIEHGGQgLYQPLDLQIAKCRVSVAVRNDFDYER--AVKQGArlKVATKYTS 124
                                                      *************88777************************99..45544446******** PP

                                        TIGR00070 120 ltreylekkgvkveivkleGavElapllgladaIvDivetGttLrengLkiieeilessarl 181
                                                      ++r+++++kgv+v++vkl+G++Elapl+gladaIvD+v+tG+tL++n+L+++e+i+++s++l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4722 125 IARDFFATKGVHVDMVKLYGSMELAPLTGLADAIVDLVSTGNTLKANHLVEVERIMDISSYL 186
                                                      *************************************************************9 PP

                                        TIGR00070 182 ia 183
                                                      ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4722 187 VV 188
                                                      85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (214 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: 6.45
//
[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:

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
the source code
instructions for running GapMind on your computer
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