Alignments for a candidate for hisE in Caminibacter mediatlanticus TB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisE in Caminibacter mediatlanticus TB-2

Align putative bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (EC 3.5.4.19; EC 3.6.1.31) (characterized)
to candidate WP_007474690.1 CMTB2_RS05665 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE

Query= metacyc::HISTCYCLOPRATPPHOS
         (203 letters)



>NCBI__GCF_000170735.1:WP_007474690.1
          Length = 220

 Score =  154 bits (390), Expect = 9e-43
 Identities = 80/204 (39%), Positives = 119/204 (58%), Gaps = 12/204 (5%)

Query: 10  LDWEKTDGLMPVIVQHAVSGEVLMLGYMNPEALDKTLESGKVTFFSRTKQRLWTKGETSG 69
           +D+EK  GL+PVIVQ   + EVLML YMN EAL+ T ++G   FFSR++ ++W KGE+SG
Sbjct: 2   VDFEKNGGLVPVIVQDIDTNEVLMLAYMNKEALELTKKTGLAHFFSRSRNKIWQKGESSG 61

Query: 70  NFLNVVSIAPDCDNDTLLVLANPIGPTCHKGTSSCF------------GDTAHQWLFLYQ 117
           N   V  I  DCDNDT+L+     G  CH G  SCF             +   ++ F+ +
Sbjct: 62  NIQEVKDILVDCDNDTILLKVKQKGVACHTGRKSCFFTKLDTNEVILDKEKEIEYNFIDK 121

Query: 118 LEQLLAERKSADPETSYTAKLYASGTKRIAQKVGEEGVETALAATVHDRFELTNEASDLM 177
           L   L +RK+ADP+TSY + LY  G   + +K+ EE  E   A   +++ E+  EA+DL 
Sbjct: 122 LYHTLLDRKNADPKTSYVSSLYNKGENSLLKKIAEEAAEFCFAVKDNNKNEIIYEAADLA 181

Query: 178 YHLLVLLQDQGLDLTTVIENLRKR 201
           +H L+ L  + +    ++E L++R
Sbjct: 182 FHTLIALAYKNIHPEAILEELKRR 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: 123
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: 220
Length adjustment: 21
Effective length of query: 182
Effective length of database: 199
Effective search space:    36218
Effective search space used:    36218
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_007474690.1 CMTB2_RS05665 (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.567125.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.7e-41  124.4   0.3    2.6e-40  122.5   0.2    1.9  2  NCBI__GCF_000170735.1:WP_007474690.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000170735.1:WP_007474690.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.5   0.2   2.6e-40   2.6e-40       1      74 []      25      98 ..      25      98 .. 0.99
   2 ?   -1.0   0.0     0.089     0.089      28      36 ..     141     149 ..     135     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 122.5 bits;  conditional E-value: 2.6e-40
                                PRA-CH  1 mlaymneealektletgkavyySrsrqklwkkGetsgnvqkvkeirldcDeDalllkveqkgaaCHtgersCFy 74
                                          mlaymn+eale t +tg a+++Srsr+k+w+kGe+sgn+q+vk+i +dcD+D++llkv+qkg aCHtg++sCF+
  NCBI__GCF_000170735.1:WP_007474690.1 25 MLAYMNKEALELTKKTGLAHFFSRSRNKIWQKGESSGNIQEVKDILVDCDNDTILLKVKQKGVACHTGRKSCFF 98
                                          9************************************************************************6 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.089
                                PRA-CH  28 klwkkGets 36 
                                           +l++kGe+s
  NCBI__GCF_000170735.1:WP_007474690.1 141 SLYNKGENS 149
                                           688999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (74 nodes)
Target sequences:                          1  (220 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: 9.79
//
[ok]

This GapMind analysis is from Jul 25 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:

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