GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisG in Pseudomonas stutzeri RCH2

Align ATP phosphoribosyltransferase; ATP-PRT; ATP-PRTase; EC 2.4.2.17 (uncharacterized)
to candidate GFF3236 Psest_3299 ATP phosphoribosyltransferase

Query= curated2:Q6FEC9
         (228 letters)



>lcl|FitnessBrowser__psRCH2:GFF3236 Psest_3299 ATP
           phosphoribosyltransferase
          Length = 210

 Score =  281 bits (718), Expect = 9e-81
 Identities = 146/206 (70%), Positives = 171/206 (83%), Gaps = 4/206 (1%)

Query: 22  LTLALSKGRILKETLPLLEAAGINLLEDPEKSRKLIFPTTHQKVRILILRASDVPTYVEN 81
           LT+ALSKGRIL +TLPLL AAGI   E+P+KSRKLI PTT   VR+LI+RA+DVPTYVE+
Sbjct: 2   LTIALSKGRILDDTLPLLAAAGIVPTENPDKSRKLIIPTTQDDVRLLIVRATDVPTYVEH 61

Query: 82  GAADFGVAGKDVLMEHGAQHVYELLDLKIANCKLMTAGKVGMQHPKGRLKIATKYVNLTR 141
           GAAD GVAGKDVLME+G Q +YE LDL+IANCKLMTAGKVG   PKGRL++ATK+VN+ +
Sbjct: 62  GAADLGVAGKDVLMEYGGQGLYEPLDLRIANCKLMTAGKVGAPEPKGRLRVATKFVNVAK 121

Query: 142 QYYASLGEQVDVIKLYGSMELAPLVGLGDYIVDVVDTGNTLRANGLEPLEEIMKVSSRLI 201
           +YYA  G QVD+IKLYGSMELAPLVGL D I+DVVDTGNTLRANGLEP E I  +SSRL+
Sbjct: 122 RYYAEQGRQVDIIKLYGSMELAPLVGLADKIIDVVDTGNTLRANGLEPQELIAHISSRLV 181

Query: 202 VNKASFK----RKQALLDPILAQVEE 223
           VNKAS K    R QAL+D + A V++
Sbjct: 182 VNKASMKMQHARIQALIDILHAAVQQ 207


Lambda     K      H
   0.318    0.137    0.382 

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: 224
Number of extensions: 5
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: 228
Length of database: 210
Length adjustment: 22
Effective length of query: 206
Effective length of database: 188
Effective search space:    38728
Effective search space used:    38728
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: 45 (21.9 bits)

Align candidate GFF3236 Psest_3299 (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.27188.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    5.7e-58  181.9   0.0    6.7e-58  181.6   0.0    1.1  1  lcl|FitnessBrowser__psRCH2:GFF3236  Psest_3299 ATP phosphoribosyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3236  Psest_3299 ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.6   0.0   6.7e-58   6.7e-58       1     183 []       2     182 ..       2     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 181.6 bits;  conditional E-value: 6.7e-58
                           TIGR00070   1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitGkDlleE 73 
                                         l+iAl KGr++++tl ll++ag+  +++   +rkli+ +++++v++l++ra+d+ptyve+gaadlG+ GkD+l+E
  lcl|FitnessBrowser__psRCH2:GFF3236   2 LTIALSKGRILDDTLPLLAAAGIVPTENPdkSRKLIIPTTQDDVRLLIVRATDVPTYVEHGAADLGVAGKDVLME 76 
                                         79********************9987766699******************************************* PP

                           TIGR00070  74 sead.vvelldlgfgkcklvlAvpeesdvesledlkegk.riATkypnltreylekkgvkveivkleGavElapl 146
                                          + + ++e ldl++ +ckl+ A +   +  +      g+ r+ATk++n++++y++++g +v+i+kl+G++Elapl
  lcl|FitnessBrowser__psRCH2:GFF3236  77 YGGQgLYEPLDLRIANCKLMTAGKVGAPEPK------GRlRVATKFVNVAKRYYAEQGRQVDIIKLYGSMELAPL 145
                                         65555*********************96655......556*********************************** PP

                           TIGR00070 147 lgladaIvDivetGttLrengLkiieeilessarlia 183
                                         +glad I+D+v tG+tLr+ngL+  e i ++s+rl++
  lcl|FitnessBrowser__psRCH2:GFF3236 146 VGLADKIIDVVDTGNTLRANGLEPQELIAHISSRLVV 182
                                         **********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (210 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: 5.49
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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