Alignments for a candidate for hisG in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisG in Bacteroides thetaiotaomicron VPI-5482

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate 349728 BT0200 ATP phosphoribosyltransferase (NCBI ptt file)

Query= BRENDA::Q5HSJ4
         (299 letters)



>FitnessBrowser__Btheta:349728
          Length = 283

 Score =  254 bits (648), Expect = 2e-72
 Identities = 135/292 (46%), Positives = 202/292 (69%), Gaps = 11/292 (3%)

Query: 7   LRIAIQKSGRLSKESIELLSECGVKMHIHEQSLIAFSTNLPIDILRVRDDDIPGLIFDGV 66
           LRIA+Q  GRL +E++ LL E  +K+   +++L+  S+N PI++L +RDDDIP  +  GV
Sbjct: 2   LRIAVQAKGRLFEETMALLGESDIKISTTKRTLLVQSSNFPIEVLFLRDDDIPQTVATGV 61

Query: 67  VDLGIIGENVLEENELERQSLGENPSYKLLKKLDFGYCRLSLALPQENKFQNLKDFEGLR 126
            DLGI+GEN   E E + +         ++K+L F  CRLSLA+P++ ++  L  F G +
Sbjct: 62  ADLGIVGENEFMEKEEDAE---------IIKRLGFSKCRLSLAMPKDIEYPGLSWFNGKK 112

Query: 127 IATSYPQLLKRFMKENGINYKNCTLTGSVEVAPRANLADAICDLVSSGATLQANNLKEVK 186
           IATSYP +L+ F+K+NG+N +   +TGSVEV+P   LADAI D+VSSG+TL +N LKEV+
Sbjct: 113 IATSYPVILRNFLKKNGVNAEIHVITGSVEVSPGIGLADAIFDIVSSGSTLVSNRLKEVE 172

Query: 187 VIYESRACLIQKENALSKEKQALVDKIMLRVAGVMQARESKYIMLHAPKEKLDKIQALLP 246
           V+ +S A LI  +N +S EK+ ++++++ R+  V  A + KY++++APK+KL++I A+LP
Sbjct: 173 VVMKSEALLIGNKN-MSDEKKEVLEELLFRMNAVKTAEDKKYVLMNAPKDKLEEIIAVLP 231

Query: 247 GVERPTILPLAHDEKNVALHMVSKENLFWETMEALKEEGASSILVLPIEKML 298
           G++ PTI+PLA  E   ++H V  E  FWE +  LK  GA  ILVLPIEKM+
Sbjct: 232 GMKSPTIMPLA-QEGWCSVHTVLDEKRFWEIIGKLKGLGAEGILVLPIEKMI 282


Lambda     K      H
   0.317    0.135    0.371 

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: 243
Number of extensions: 12
Number of successful extensions: 4
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: 299
Length of database: 283
Length adjustment: 26
Effective length of query: 273
Effective length of database: 257
Effective search space:    70161
Effective search space used:    70161
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate 349728 BT0200 (ATP phosphoribosyltransferase (NCBI ptt file))
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.12046.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    5.1e-64  201.6   0.0    6.6e-64  201.2   0.0    1.1  1  lcl|FitnessBrowser__Btheta:349728  BT0200 ATP phosphoribosyltransfe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:349728  BT0200 ATP phosphoribosyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.2   0.0   6.6e-64   6.6e-64       1     182 [.       2     182 ..       2     183 .. 0.99

  Alignments for each domain:
  == domain 1  score: 201.2 bits;  conditional E-value: 6.6e-64
                          TIGR00070   1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlleEse 75 
                                        lriA++ KGrl+eet++ll ++++k+s+++ r+l++++++ ++evl+lr++dip++v++g+adlGi+G++ ++E+e
  lcl|FitnessBrowser__Btheta:349728   2 LRIAVQaKGRLFEETMALLGESDIKISTTK-RTLLVQSSNFPIEVLFLRDDDIPQTVATGVADLGIVGENEFMEKE 76 
                                        89****************************.********************************************* PP

                          TIGR00070  76 advvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGavElapllglad 151
                                        +d + +++lgf+kc+l+lA+p++ ++  l+ ++ gk+iAT+yp + r++l+k+gv++ei  ++G+vE++p +glad
  lcl|FitnessBrowser__Btheta:349728  77 EDAEIIKRLGFSKCRLSLAMPKDIEYPGLSWFN-GKKIATSYPVILRNFLKKNGVNAEIHVITGSVEVSPGIGLAD 151
                                        *********************************.9***************************************** PP

                          TIGR00070 152 aIvDivetGttLrengLkiieeilessarli 182
                                        aI+Div++G+tL +n+Lk++e++++s+a li
  lcl|FitnessBrowser__Btheta:349728 152 AIFDIVSSGSTLVSNRLKEVEVVMKSEALLI 182
                                        *****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (283 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: 10.19
//
[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