GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Sphingomonas indica Dd16

Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_085217038.1 B9N75_RS00565 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE

Query= metacyc::HISTCYCLOPRATPPHOS
         (203 letters)



>NCBI__GCF_900177405.1:WP_085217038.1
          Length = 216

 Score =  187 bits (476), Expect = 9e-53
 Identities = 98/194 (50%), Positives = 126/194 (64%), Gaps = 1/194 (0%)

Query: 10  LDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSG 69
           LDW+K DGL+P  VQ   S  VLM GYMN  AL+ T+ + +VTF+SR+K RLW KGETSG
Sbjct: 16  LDWKKMDGLLPATVQDRGSRRVLMTGYMNRAALEATIATREVTFWSRSKARLWKKGETSG 75

Query: 70  NFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGDTAHQWL-FLYQLEQLLAERKSA 128
           N L+   +  DCD D LLVLA P GP CH+GT+SCF    H    +L  L +++A R   
Sbjct: 76  NILSGADVYCDCDGDALLVLATPAGPVCHEGTASCFAAAPHAGPGWLADLARIIAARGRV 135

Query: 129 DPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLLQDQG 188
               SYTA+L A+G +RIAQKVGEEGVE ALA       E  +EA+DL+YH+ VLL+ + 
Sbjct: 136 AGSESYTARLLAAGPQRIAQKVGEEGVELALAGAAGTAAECVSEAADLLYHVAVLLEARN 195

Query: 189 LDLTTVIENLRKRH 202
           +    V+  L+ RH
Sbjct: 196 IGWDDVVHELQIRH 209


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: 135
Number of extensions: 5
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: 216
Length adjustment: 21
Effective length of query: 182
Effective length of database: 195
Effective search space:    35490
Effective search space used:    35490
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 WP_085217038.1 B9N75_RS00565 (bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE)
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/PF01502.22.hmm
# target sequence database:        /tmp/gapView.3179078.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       PRA-CH  [M=74]
Accession:   PF01502.22
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.2e-34  103.5   0.0    3.1e-34  103.0   0.0    1.2  1  NCBI__GCF_900177405.1:WP_085217038.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085217038.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   3.1e-34   3.1e-34       1      73 [.      39     111 ..      39     112 .. 0.99

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 3.1e-34
                                PRA-CH   1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtgersCF 73 
                                           m +ymn+ ale+t++t++++++Srs+ +lwkkGetsgn+++  ++++dcD+Dall+ ++++g++CH+g+ sCF
  NCBI__GCF_900177405.1:WP_085217038.1  39 MTGYMNRAALEATIATREVTFWSRSKARLWKKGETSGNILSGADVYCDCDGDALLVLATPAGPVCHEGTASCF 111
                                           99*********************************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (74 nodes)
Target sequences:                          1  (216 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: 10.35
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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