GapMind for Amino acid biosynthesis

 

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

Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate 350905 BT1377 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (NCBI ptt file)

Query= metacyc::HISTCYCLOPRATPPHOS
         (203 letters)



>FitnessBrowser__Btheta:350905
          Length = 203

 Score =  207 bits (528), Expect = 8e-59
 Identities = 103/195 (52%), Positives = 137/195 (70%), Gaps = 1/195 (0%)

Query: 9   ELDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETS 68
           ELD++K +GL+P I+Q   + +VLMLG+MN EA DKT+E+GKVTFFSRTK RLWTKGE S
Sbjct: 2   ELDFDKMNGLVPAIIQDNETRKVLMLGFMNKEAYDKTVETGKVTFFSRTKNRLWTKGEES 61

Query: 69  GNFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGDTAHQ-WLFLYQLEQLLAERKS 127
           GNFL+VVSI  DCDNDTLL+ A+P GP CH GT +C+G+   +  +FL  L+  + +R  
Sbjct: 62  GNFLHVVSIKADCDNDTLLIQADPAGPVCHTGTDTCWGEKNEEPVMFLKALQDFIDKRHE 121

Query: 128 ADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLLQDQ 187
             P+ SYT  L+ SG  +IAQKVGEE VET + AT      L  E +DL+YH++VLL  +
Sbjct: 122 EMPQGSYTTSLFESGINKIAQKVGEEAVETVIEATNGTNERLIYEGADLIYHMIVLLTSK 181

Query: 188 GLDLTTVIENLRKRH 202
           G  +  +   L++RH
Sbjct: 182 GYRIEDLARELQERH 196


Lambda     K      H
   0.317    0.132    0.384 

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: 130
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: 203
Length of database: 203
Length adjustment: 21
Effective length of query: 182
Effective length of database: 182
Effective search space:    33124
Effective search space used:    33124
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: 45 (21.9 bits)

Align candidate 350905 BT1377 (phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (NCBI ptt file))
to HMM TIGR03188 (hisE: phosphoribosyl-ATP diphosphatase (EC 3.6.1.31))

# 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/TIGR03188.hmm
# target sequence database:        /tmp/gapView.25342.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03188  [M=84]
Accession:   TIGR03188
Description: histidine_hisI: phosphoribosyl-ATP diphosphatase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    1.7e-34  104.2   0.1    2.7e-34  103.5   0.1    1.3  1  lcl|FitnessBrowser__Btheta:350905  BT1377 phosphoribosyl-AMP cycloh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350905  BT1377 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.5   0.1   2.7e-34   2.7e-34       1      84 []     109     192 ..     109     192 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 2.7e-34
                          TIGR03188   1 leeLeevieerkeedpeeSytakllekgedkilkKvgEEavEviiaaknedkeelveEaaDllYhllVllaekgvs 76 
                                        l++L++ i++r+ee p++Syt++l+e+g++ki++KvgEEavE++i+a+n+++e+l++E aDl+Yh++Vll++kg +
  lcl|FitnessBrowser__Btheta:350905 109 LKALQDFIDKRHEEMPQGSYTTSLFESGINKIAQKVGEEAVETVIEATNGTNERLIYEGADLIYHMIVLLTSKGYR 184
                                        689************************************************************************* PP

                          TIGR03188  77 ledvlaeL 84 
                                        +ed+++eL
  lcl|FitnessBrowser__Btheta:350905 185 IEDLAREL 192
                                        ****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (84 nodes)
Target sequences:                          1  (203 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 5.15
//
[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