GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Desulfovibrio vulgaris Hildenborough

Align Phosphoribosyl-AMP cyclohydrolase; PRA-CH; EC 3.5.4.19 (characterized)
to candidate 209043 DVU0113 phosphoribosyl-AMP cyclohydrolase

Query= SwissProt::O26347
         (138 letters)



>MicrobesOnline__882:209043
          Length = 126

 Score =  135 bits (341), Expect = 2e-37
 Identities = 65/114 (57%), Positives = 85/114 (74%), Gaps = 3/114 (2%)

Query: 23  LIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSGHVQRVKDV 82
           L+ A+AQD +TGEVLM+A+MN EA   TL+TG AHY+S SRG+LW KG +SGH Q ++ V
Sbjct: 14  LVPAIAQDADTGEVLMMAWMNAEAFEMTLKTGEAHYFSRSRGRLWHKGGTSGHTQHIRAV 73

Query: 83  LVDCDGDAVVLKVEQEGG-ACHTGYRSCFYRSIDGDELKVREDAVKVFDPEEIY 135
            +DCD D ++L VEQ GG ACH GYRSCFYR +   E+ +   + KVFDP+E+Y
Sbjct: 74  RLDCDSDTILLLVEQRGGAACHEGYRSCFYREMKDGEVSI--CSPKVFDPKEVY 125


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: 93
Number of extensions: 6
Number of successful extensions: 3
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: 126
Length adjustment: 15
Effective length of query: 123
Effective length of database: 111
Effective search space:    13653
Effective search space used:    13653
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: 41 (20.4 bits)

Align candidate 209043 DVU0113 (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/PF01502.22.hmm
# target sequence database:        /tmp/gapView.6223.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.3e-39  120.3   0.4    1.7e-39  119.9   0.4    1.2  1  lcl|MicrobesOnline__882:209043  DVU0113 phosphoribosyl-AMP cyclo


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209043  DVU0113 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 []      29     103 ..      29     103 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 1.7e-39
                          PRA-CH   1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkg.aaCHtgersCFy 74 
                                     m+a+mn+ea+e tl+tg+a+y+Srsr +lw+kG tsg++q+++ +rldcD+D++ll veq+g aaCH+g+rsCFy
  lcl|MicrobesOnline__882:209043  29 MMAWMNAEAFEMTLKTGEAHYFSRSRGRLWHKGGTSGHTQHIRAVRLDCDSDTILLLVEQRGgAACHEGYRSCFY 103
                                     9************************************************************649**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (74 nodes)
Target sequences:                          1  (126 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: 4.53
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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