GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisG in Sphingomonas koreensis DSMZ 15582

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate Ga0059261_1280 Ga0059261_1280 ATP phosphoribosyltransferase

Query= reanno::Korea:Ga0059261_1280
         (219 letters)



>FitnessBrowser__Korea:Ga0059261_1280
          Length = 219

 Score =  424 bits (1091), Expect = e-124
 Identities = 219/219 (100%), Positives = 219/219 (100%)

Query: 1   MSEPIILAVPKGRILEEALPLLAHAGIIPEPAFADEGSRALRFKTNRPDIDLIRVRAFDV 60
           MSEPIILAVPKGRILEEALPLLAHAGIIPEPAFADEGSRALRFKTNRPDIDLIRVRAFDV
Sbjct: 1   MSEPIILAVPKGRILEEALPLLAHAGIIPEPAFADEGSRALRFKTNRPDIDLIRVRAFDV 60

Query: 61  ATFVAHGAAQLGIVGSDVLAEFAYSELYAPVDLGIGYCRLSVAEPAALAATDDPRGWSHV 120
           ATFVAHGAAQLGIVGSDVLAEFAYSELYAPVDLGIGYCRLSVAEPAALAATDDPRGWSHV
Sbjct: 61  ATFVAHGAAQLGIVGSDVLAEFAYSELYAPVDLGIGYCRLSVAEPAALAATDDPRGWSHV 120

Query: 121 RVATKYPSLTRRHFEARGVQAECIKLNGAMELAPLLDLAPRIVDLVSSGRTLKENGLVEV 180
           RVATKYPSLTRRHFEARGVQAECIKLNGAMELAPLLDLAPRIVDLVSSGRTLKENGLVEV
Sbjct: 121 RVATKYPSLTRRHFEARGVQAECIKLNGAMELAPLLDLAPRIVDLVSSGRTLKENGLVEV 180

Query: 181 ETIMEVSSRLVANRAAFKTRPEIVPLIDAFRRAVEAKAA 219
           ETIMEVSSRLVANRAAFKTRPEIVPLIDAFRRAVEAKAA
Sbjct: 181 ETIMEVSSRLVANRAAFKTRPEIVPLIDAFRRAVEAKAA 219


Lambda     K      H
   0.321    0.137    0.390 

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: 325
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: 219
Length of database: 219
Length adjustment: 22
Effective length of query: 197
Effective length of database: 197
Effective search space:    38809
Effective search space used:    38809
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate Ga0059261_1280 Ga0059261_1280 (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.12864.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      9e-60  187.7   0.0      1e-59  187.6   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1280  Ga0059261_1280 ATP phosphoribosy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1280  Ga0059261_1280 ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.6   0.0     1e-59     1e-59       2     183 .]       6     192 ..       5     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 187.6 bits;  conditional E-value: 1e-59
                                 TIGR00070   2 riAlpKGrleeetlkllekaglk....lskkeerkliasaedeevevlllrakdiptyvekgaadlGit 66 
                                                +A+pKGr++ee+l ll++ag+     + ++ +r+l +++++++++++ +ra d++t+v++gaa+lGi+
  lcl|FitnessBrowser__Korea:Ga0059261_1280   6 ILAVPKGRILEEALPLLAHAGIIpepaFADEGSRALRFKTNRPDIDLIRVRAFDVATFVAHGAAQLGIV 74 
                                               58******************996444356666************************************* PP

                                 TIGR00070  67 GkDlleE.seadvvelldlgfgkcklvlAvpees.dvesledlkegkriATkypnltreylekkgvkve 133
                                               G+D+l+E  +++++  +dlg+g c+l++A p +  + +++   + + r+ATkyp+ltr+++e +gv++e
  lcl|FitnessBrowser__Korea:Ga0059261_1280  75 GSDVLAEfAYSELYAPVDLGIGYCRLSVAEPAALaATDDPRGWS-HVRVATKYPSLTRRHFEARGVQAE 142
                                               *******88999*********************95556666666.78********************** PP

                                 TIGR00070 134 ivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183
                                               ++kl+Ga+Elapll+la  IvD+v++G+tL+engL+++e+i+e+s+rl+a
  lcl|FitnessBrowser__Korea:Ga0059261_1280 143 CIKLNGAMELAPLLDLAPRIVDLVSSGRTLKENGLVEVETIMEVSSRLVA 192
                                               ************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (219 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: 5.68
//
[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