GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Lentibacillus jeotgali Grbi

Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_010529312.1 ON01_RS01875 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE

Query= metacyc::HISTCYCLOPRATPPHOS
         (203 letters)



>NCBI__GCF_000224785.1:WP_010529312.1
          Length = 214

 Score =  165 bits (417), Expect = 6e-46
 Identities = 88/204 (43%), Positives = 126/204 (61%), Gaps = 6/204 (2%)

Query: 4   EQQRRELDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWT 63
           ++Q  +L +++  GL+P I+Q A + EVL L YMN E+L++TLE+G+  F+SR +Q LW 
Sbjct: 3   DEQLNKLTFDQ-QGLIPAIIQDAETAEVLTLAYMNKESLNRTLETGETWFYSRKRQELWH 61

Query: 64  KGETSGNFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFGDTAHQ-----WLFLYQL 118
           KG TSGN  +V +I  DCD DTLLVL  P+GP CH G  SCF  T  +      + L +L
Sbjct: 62  KGATSGNKQHVKTIRYDCDADTLLVLVEPLGPVCHTGEKSCFYSTLQKIESPDQMGLNEL 121

Query: 119 EQLLAERKSADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMY 178
             L+ +R+    E SYT  L+  G  +I +KVGEE  E  + A  +D  E+T E +DL Y
Sbjct: 122 AALIRQRRKEANEGSYTTYLFEEGIDKILKKVGEETSEVIIGAKNNDHSEMTWEIADLTY 181

Query: 179 HLLVLLQDQGLDLTTVIENLRKRH 202
           H LVL+   G+ ++ + + L KRH
Sbjct: 182 HTLVLMDLMGVSISDIKQELAKRH 205


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: 136
Number of extensions: 7
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: 214
Length adjustment: 21
Effective length of query: 182
Effective length of database: 193
Effective search space:    35126
Effective search space used:    35126
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_010529312.1 ON01_RS01875 (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.3411270.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-39  119.5   0.1    3.5e-39  118.9   0.1    1.3  1  NCBI__GCF_000224785.1:WP_010529312.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010529312.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.1   3.5e-39   3.5e-39       2      74 .]      32     104 ..      31     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 3.5e-39
                                PRA-CH   2 laymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtgersCFy 74 
                                           laymn+e+l++tletg++++ySr+rq+lw+kG+tsgn q+vk+ir+dcD+D+ll+ ve+ g++CHtge+sCFy
  NCBI__GCF_000224785.1:WP_010529312.1  32 LAYMNKESLNRTLETGETWFYSRKRQELWHKGATSGNKQHVKTIRYDCDADTLLVLVEPLGPVCHTGEKSCFY 104
                                           79**********************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (74 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.27
//
[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