GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisG in Flavobacterium glycines Gm-149

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_066326080.1 BLR17_RS14025 ATP phosphoribosyltransferase

Query= BRENDA::Q5HSJ4
         (299 letters)



>NCBI__GCF_900100165.1:WP_066326080.1
          Length = 285

 Score =  233 bits (595), Expect = 3e-66
 Identities = 121/292 (41%), Positives = 198/292 (67%), Gaps = 11/292 (3%)

Query: 7   LRIAIQKSGRLSKESIELLSECGVKMHIHEQSLIAFSTNLPIDILRVRDDDIPGLIFDGV 66
           L+IAIQKSGRL+++SI++L + G+ ++     L A ++N P+++L +R+ DIP  + DGV
Sbjct: 4   LKIAIQKSGRLNEDSIQILKDAGISINNGIDQLKAEASNFPLEVLYLRNSDIPQYLIDGV 63

Query: 67  VDLGIIGENVLEENELERQSLGENPSYKLLKKLDFGYCRLSLALPQENKFQNLKDFEGLR 126
           VD+ I+G+N+L E         +    ++++KL F  C++S+A+P+  +++++KD +GLR
Sbjct: 64  VDIAIVGDNLLVE---------KGKDIEVIQKLGFSKCKVSVAVPKTFEYKSVKDLDGLR 114

Query: 127 IATSYPQLLKRFMKENGINYKNCTLTGSVEVAPRANLADAICDLVSSGATLQANNLKEVK 186
           IATSYP  +  F  + G++     ++GSVE+AP   LADAI D+VSSG+TL  NNLKEV+
Sbjct: 115 IATSYPNTVIEFFNKFGLSVDIHQISGSVEIAPNIGLADAIVDIVSSGSTLFKNNLKEVE 174

Query: 187 VIYESRACLIQKENALSKEKQALVDKIMLRVAGVMQARESKYIMLHAPKEKLDKIQALLP 246
           VI +S A L      ++ E Q ++D +  R+  V++AR+SKYI+++ P +K+D I  +LP
Sbjct: 175 VILKSEAVLAVSPK-VTPEAQKIIDTLKFRIESVLRARKSKYILMNVPNDKIDAIGKILP 233

Query: 247 GVERPTILPLAHDEKNVALHMVSKENLFWETMEALKEEGASSILVLPIEKML 298
            ++  T++PLA +  + ++H V  ++ FWE ++ LKE GA  ILV PIEKM+
Sbjct: 234 VLKSLTVMPLAQEGWS-SVHSVIDKDTFWEVIDQLKEAGAEGILVCPIEKMV 284


Lambda     K      H
   0.317    0.135    0.371 

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: 225
Number of extensions: 10
Number of successful extensions: 4
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: 299
Length of database: 285
Length adjustment: 26
Effective length of query: 273
Effective length of database: 259
Effective search space:    70707
Effective search space used:    70707
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: 48 (23.1 bits)

Align candidate WP_066326080.1 BLR17_RS14025 (ATP phosphoribosyltransferase)
to HMM TIGR00070 (hisG: ATP phosphoribosyltransferase (EC 2.4.2.17))

# 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/TIGR00070.hmm
# target sequence database:        /tmp/gapView.2182203.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00070  [M=183]
Accession:   TIGR00070
Description: hisG: ATP phosphoribosyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.8e-60  190.1   0.1    2.2e-60  189.7   0.1    1.1  1  NCBI__GCF_900100165.1:WP_066326080.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066326080.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.7   0.1   2.2e-60   2.2e-60       1     182 [.       4     184 ..       4     185 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.7 bits;  conditional E-value: 2.2e-60
                             TIGR00070   1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlle 72 
                                           l+iA++  Grl e+++++l++ag+++++   ++l a+a++ ++evl+lr++dip+y+ +g++d+ i+G +ll 
  NCBI__GCF_900100165.1:WP_066326080.1   4 LKIAIQkSGRLNEDSIQILKDAGISINNGI-DQLKAEASNFPLEVLYLRNSDIPQYLIDGVVDIAIVGDNLLV 75 
                                           89****99**********************.****************************************** PP

                             TIGR00070  73 EseadvvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGavElap 145
                                           E+++d++ + +lgf+kck+++Avp++ +++s++dl+ g riAT+ypn++ e+++k g++v+i +++G+vE+ap
  NCBI__GCF_900100165.1:WP_066326080.1  76 EKGKDIEVIQKLGFSKCKVSVAVPKTFEYKSVKDLD-GLRIATSYPNTVIEFFNKFGLSVDIHQISGSVEIAP 147
                                           ************************************.9*********************************** PP

                             TIGR00070 146 llgladaIvDivetGttLrengLkiieeilessarli 182
                                            +gladaIvDiv++G+tL +n+Lk++e+il+s+a+l 
  NCBI__GCF_900100165.1:WP_066326080.1 148 NIGLADAIVDIVSSGSTLFKNNLKEVEVILKSEAVLA 184
                                           **********************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (285 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.80
//
[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