GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisE in Cupriavidus basilensis 4G11

Align Phosphoribosyl-AMP cyclohydrolase; PRA-CH; EC 3.5.4.19 (characterized)
to candidate RR42_RS18880 RR42_RS18880 phosphoribosyl-AMP cyclohydrolase

Query= SwissProt::O26347
         (138 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS18880 RR42_RS18880
           phosphoribosyl-AMP cyclohydrolase
          Length = 135

 Score =  111 bits (278), Expect = 4e-30
 Identities = 58/118 (49%), Positives = 78/118 (66%), Gaps = 7/118 (5%)

Query: 23  LIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSGHVQRVKDV 82
           L+  + Q+  + +VLM A+MNREAL+RT E G A +WS SR +LW KGE SGHVQ+V ++
Sbjct: 16  LVPVIVQEVGSNDVLMFAFMNREALQRTAEIGEAVFWSRSRKRLWHKGEESGHVQKVHEM 75

Query: 83  LVDCDGDAVVLKVEQEGG-ACHTGYRSCFYRSIDGD----ELKVREDAVKVFDPEEIY 135
            +DCD D V+LKV Q  G ACHTG  SCF++  +GD    + +  E  +K  DP  IY
Sbjct: 76  RLDCDEDVVLLKVTQNDGIACHTGRHSCFFQKFEGDAESGDWQTVEPVLK--DPSTIY 131


Lambda     K      H
   0.318    0.137    0.410 

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: 84
Number of extensions: 8
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: 138
Length of database: 135
Length adjustment: 15
Effective length of query: 123
Effective length of database: 120
Effective search space:    14760
Effective search space used:    14760
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: 42 (20.8 bits)

Align candidate RR42_RS18880 RR42_RS18880 (phosphoribosyl-AMP cyclohydrolase)
to HMM PF01502 (PRA-CH)

# 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/PF01502.18.hmm
# target sequence database:        /tmp/gapView.8355.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       PRA-CH  [M=74]
Accession:   PF01502.18
Description: Phosphoribosyl-AMP cyclohydrolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.4e-40  121.0   0.3    1.7e-39  119.9   0.4    1.5  2  lcl|FitnessBrowser__Cup4G11:RR42_RS18880  RR42_RS18880 phosphoribosyl-AMP 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS18880  RR42_RS18880 phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.9   0.4   1.7e-39   1.7e-39       1      74 []      31     105 ..      31     105 .. 0.97
   2 ?   -2.7   0.0       0.3       0.3      35      46 ..     113     124 ..     110     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 1.7e-39
                                               EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEES.S-SSTTS CS
                                    PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqk.gaaCHtg 68 
                                               m+a+mn+eal++t e g+av++Srsrk+lW+KGe+Sg+vqkv+e+rlDcD+D++llkv+q+ g aCHtg
  lcl|FitnessBrowser__Cup4G11:RR42_RS18880  31 MFAFMNREALQRTAEIGEAVFWSRSRKRLWHKGEESGHVQKVHEMRLDCDEDVVLLKVTQNdGIACHTG 99 
                                               9**********************************************************99568***** PP

                                               BSSS-- CS
                                    PRA-CH  69 kesCFy 74 
                                               ++sCF+
  lcl|FitnessBrowser__Cup4G11:RR42_RS18880 100 RHSCFF 105
                                               *****6 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.3
                                               TTS--EEEEEEE CS
                                    PRA-CH  35 tSgnvqkvkeir 46 
                                               +Sg+ q+v+ + 
  lcl|FitnessBrowser__Cup4G11:RR42_RS18880 113 ESGDWQTVEPVL 124
                                               799999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (74 nodes)
Target sequences:                          1  (135 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: 4.68
//
[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