GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisE in Enterococcus termitis LMG 8895

Align Phosphoribosyl-AMP cyclohydrolase; PRA-CH; EC 3.5.4.19 (uncharacterized)
to candidate WP_069661635.1 BCR25_RS00410 phosphoribosyl-AMP cyclohydrolase

Query= curated2:P62393
         (101 letters)



>NCBI__GCF_001730305.1:WP_069661635.1
          Length = 101

 Score =  152 bits (383), Expect = 1e-42
 Identities = 67/101 (66%), Positives = 85/101 (84%)

Query: 1   MKPNFSKGLLPAVVIEEDTKEVLMLAYMNEEAYEKTIETKRTWFYSRSRRSLWNKGETSG 60
           MKP+FSKGLLPA++IEE +KEVLMLAYMN E+Y+KT+ET  TWFYSRSR+ LWNKGETSG
Sbjct: 1   MKPDFSKGLLPAIIIEETSKEVLMLAYMNAESYQKTLETGMTWFYSRSRQKLWNKGETSG 60

Query: 61  NVQHVQSLYLDCDQDSIVVVVKQVGPACHTGEKTCFHYKII 101
           N Q V+ +  DCD+D++++ V+Q GPACHTG  +CF+  II
Sbjct: 61  NQQKVKGIVTDCDRDTLLITVEQTGPACHTGAHSCFYNVII 101


Lambda     K      H
   0.318    0.132    0.400 

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: 76
Number of extensions: 2
Number of successful extensions: 1
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: 101
Length of database: 101
Length adjustment: 11
Effective length of query: 90
Effective length of database: 90
Effective search space:     8100
Effective search space used:     8100
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: 39 (20.8 bits)
S2: 39 (19.6 bits)

Align candidate WP_069661635.1 BCR25_RS00410 (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.3811500.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    9.9e-42  127.0   0.6    1.2e-41  126.8   0.6    1.1  1  NCBI__GCF_001730305.1:WP_069661635.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069661635.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8   0.6   1.2e-41   1.2e-41       1      74 []      24      97 ..      24      97 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 1.2e-41
                                PRA-CH  1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtgersCFy 74
                                          mlaymn+e+++ktletg +++ySrsrqklw+kGetsgn qkvk i +dcD+D+ll++veq+g+aCHtg++sCFy
  NCBI__GCF_001730305.1:WP_069661635.1 24 MLAYMNAESYQKTLETGMTWFYSRSRQKLWNKGETSGNQQKVKGIVTDCDRDTLLITVEQTGPACHTGAHSCFY 97
                                          9************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (74 nodes)
Target sequences:                          1  (101 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: 6.10
//
[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