GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisG in Pseudomonas putida KT2440

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate PP_0965 PP_0965 ATP phosphoribosyltransferase

Query= reanno::Putida:PP_0965
         (211 letters)



>FitnessBrowser__Putida:PP_0965
          Length = 211

 Score =  407 bits (1045), Expect = e-118
 Identities = 211/211 (100%), Positives = 211/211 (100%)

Query: 1   MLTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQDDVRLLIVRATDVPTYVE 60
           MLTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQDDVRLLIVRATDVPTYVE
Sbjct: 1   MLTIALSKGRILDDTLPLLAEAGIVPTENPDKSRKLIIPTTQDDVRLLIVRATDVPTYVE 60

Query: 61  HGAADLGVAGKDVLMEYGGQGLYEPLDLQIAQCKLMTAGVVGAAEPKGRLRVATKFVNVA 120
           HGAADLGVAGKDVLMEYGGQGLYEPLDLQIAQCKLMTAGVVGAAEPKGRLRVATKFVNVA
Sbjct: 61  HGAADLGVAGKDVLMEYGGQGLYEPLDLQIAQCKLMTAGVVGAAEPKGRLRVATKFVNVA 120

Query: 121 KRYYAEQGRQVDIIKLYGSMELAPLINLADKIIDVVDTGNTLRANGLEPQELIATISSRL 180
           KRYYAEQGRQVDIIKLYGSMELAPLINLADKIIDVVDTGNTLRANGLEPQELIATISSRL
Sbjct: 121 KRYYAEQGRQVDIIKLYGSMELAPLINLADKIIDVVDTGNTLRANGLEPQELIATISSRL 180

Query: 181 VVNKASMKMQHARIQSLIDTLRAAVESRHRG 211
           VVNKASMKMQHARIQSLIDTLRAAVESRHRG
Sbjct: 181 VVNKASMKMQHARIQSLIDTLRAAVESRHRG 211


Lambda     K      H
   0.318    0.136    0.373 

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: 291
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: 211
Length of database: 211
Length adjustment: 21
Effective length of query: 190
Effective length of database: 190
Effective search space:    36100
Effective search space used:    36100
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 PP_0965 PP_0965 (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.13289.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    3.5e-57  179.3   0.1    4.2e-57  179.1   0.1    1.1  1  lcl|FitnessBrowser__Putida:PP_0965  PP_0965 ATP phosphoribosyltransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0965  PP_0965 ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.1   0.1   4.2e-57   4.2e-57       1     183 []       2     182 ..       2     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 4.2e-57
                           TIGR00070   1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitGkDlleE 73 
                                         l+iAl KGr++++tl ll++ag+  +++   +rkli+ +++++v++l++ra+d+ptyve+gaadlG+ GkD+l+E
  lcl|FitnessBrowser__Putida:PP_0965   2 LTIALSKGRILDDTLPLLAEAGIVPTENPdkSRKLIIPTTQDDVRLLIVRATDVPTYVEHGAADLGVAGKDVLME 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__Putida:PP_0965  77 YGGQgLYEPLDLQIAQCKLMTAGVVGAAEPK------GRlRVATKFVNVAKRYYAEQGRQVDIIKLYGSMELAPL 145
                                         65555*****************999984333......556*********************************** PP

                           TIGR00070 147 lgladaIvDivetGttLrengLkiieeilessarlia 183
                                         ++lad I+D+v tG+tLr+ngL+  e i ++s+rl++
  lcl|FitnessBrowser__Putida:PP_0965 146 INLADKIIDVVDTGNTLRANGLEPQELIATISSRLVV 182
                                         **********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (211 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.60
//
[ok]

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

Links

Downloads

Related tools

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