Alignments for a candidate for hisE in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisE in Dyella japonica UNC79MFTsu3.2

Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate N515DRAFT_2931 N515DRAFT_2931 phosphoribosyl-ATP pyrophosphatase /phosphoribosyl-AMP cyclohydrolase

Query= metacyc::HISTCYCLOPRATPPHOS
         (203 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2931
          Length = 209

 Score =  219 bits (558), Expect = 3e-62
 Identities = 115/197 (58%), Positives = 140/197 (71%), Gaps = 3/197 (1%)

Query: 10  LDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSG 69
           LDW K DGL+P IVQH ++GEVLMLGYMN EAL  +L S +VTFFSR+KQRLWTKGE+SG
Sbjct: 11  LDWSKGDGLLPAIVQHWLTGEVLMLGYMNAEALAHSLSSAQVTFFSRSKQRLWTKGESSG 70

Query: 70  NFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCFG---DTAHQWLFLYQLEQLLAERK 126
           + L + S   DCD DTLL+ A P GPTCH GTSSCFG   D A    FL  L++L+ +R 
Sbjct: 71  HVLALKSARIDCDGDTLLLQAEPQGPTCHLGTSSCFGERADVAPPLGFLATLDRLVEQRA 130

Query: 127 SADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLMYHLLVLLQD 186
           +  P  SYT +L+  G +RIAQKVGEEGVETALAA V D   L  EA+DL++HL+V L+ 
Sbjct: 131 AERPAGSYTTRLFEDGIRRIAQKVGEEGVETALAAVVQDDEALLGEAADLVFHLMVALRA 190

Query: 187 QGLDLTTVIENLRKRHQ 203
           +GL  + V   L  RHQ
Sbjct: 191 RGLSTSDVCRVLEARHQ 207


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: 144
Number of extensions: 3
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: 209
Length adjustment: 21
Effective length of query: 182
Effective length of database: 188
Effective search space:    34216
Effective search space used:    34216
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 N515DRAFT_2931 N515DRAFT_2931 (phosphoribosyl-ATP pyrophosphatase /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.21933.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    2.7e-36  109.6   0.0    4.4e-36  108.9   0.0    1.3  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2931  N515DRAFT_2931 phosphoribosyl-AT


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2931  N515DRAFT_2931 phosphoribosyl-ATP pyrophosphatase /phosphoribosyl-AMP cy
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.9   0.0   4.4e-36   4.4e-36       1      73 [.      34     106 ..      34     107 .. 0.99

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 4.4e-36
                                       PRA-CH   1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCH 66 
                                                  ml+ymn+eal+++l++ +++++Srs+q+lw+kGe+sg+v+ +k+ r+dcD+D+lll++e++g++CH
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2931  34 MLGYMNAEALAHSLSSAQVTFFSRSKQRLWTKGESSGHVLALKSARIDCDGDTLLLQAEPQGPTCH 99 
                                                  9***************************************************************** PP

                                       PRA-CH  67 tgersCF 73 
                                                   g++sCF
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2931 100 LGTSSCF 106
                                                  ******* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (74 nodes)
Target sequences:                          1  (209 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: 6.28
//
[ok]

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

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis