Alignments for a candidate for hisG in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisG in Shewanella oneidensis MR-1

Align ATP phosphoribosyltransferase (characterized)
to candidate 201231 SO2074 ATP phosphoribosyltransferase (NCBI ptt file)

Query= CharProtDB::CH_024688
         (299 letters)



>FitnessBrowser__MR1:201231
          Length = 324

 Score =  406 bits (1043), Expect = e-118
 Identities = 202/298 (67%), Positives = 245/298 (82%)

Query: 1   MTDNTRLRIAMQKSGRLSDDSRELLARCGIKINLHTQRLIAMAENMPIDILRVRDDDIPG 60
           MT++ RLRIA+QKSGRLS DS++LL  CG+K +++ QRLIA A+NMPID+LRVRDDDIPG
Sbjct: 26  MTESNRLRIAIQKSGRLSTDSQQLLKSCGVKFSINEQRLIAHADNMPIDLLRVRDDDIPG 85

Query: 61  LVMDGVVDLGIIGENVLEEELLNRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAWDGPL 120
           LVMDGVVDLGIIGENVLEEE + R+   +   Y  LR+LDFG CRLSLA P + ++    
Sbjct: 86  LVMDGVVDLGIIGENVLEEEQIERQTLNKPAEYVKLRQLDFGACRLSLAVPTEFSYADAS 145

Query: 121 SLNGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEAN 180
           SL G RIATSYP+LL+R++ QK I+++ C+L GSVEVAPRAGLAD ICDLVSTGATLEAN
Sbjct: 146 SLEGLRIATSYPNLLRRFMQQKSINYRDCMLKGSVEVAPRAGLADGICDLVSTGATLEAN 205

Query: 181 GLREVEVIYRSKACLIQRDGEMEESKQQLIDKLLTRIQGVIQARESKYIMMHAPTERLDE 240
           GL E EVIYRS AC+IQ       SKQ LID++L+R+ GVI+ARESKYI++HAPTE LD+
Sbjct: 206 GLYETEVIYRSMACIIQSTQTQAPSKQALIDRILSRVNGVIRARESKYILLHAPTETLDQ 265

Query: 241 VIALLPGAERPTILPLAGDQQRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMM 298
           ++ALLPGAE PT+LPL  D  RVA+H VS+E LFW+TME+L ALGASSILV+PIEKMM
Sbjct: 266 IVALLPGAENPTVLPLNDDTNRVAIHAVSTEDLFWDTMEQLTALGASSILVMPIEKMM 323


Lambda     K      H
   0.320    0.137    0.389 

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: 334
Number of extensions: 7
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: 299
Length of database: 324
Length adjustment: 27
Effective length of query: 272
Effective length of database: 297
Effective search space:    80784
Effective search space used:    80784
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate 201231 SO2074 (ATP phosphoribosyltransferase (NCBI ptt file))
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.21888.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    2.2e-58  183.2   0.0    2.9e-58  182.8   0.0    1.2  1  lcl|FitnessBrowser__MR1:201231  SO2074 ATP phosphoribosyltransfe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201231  SO2074 ATP phosphoribosyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8   0.0   2.9e-58   2.9e-58       1     183 []      32     222 ..      32     222 .. 0.96

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 2.9e-58
                       TIGR00070   1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlleEsead. 77 
                                     lriA++  Grl+ ++ +ll+++g+k+s +e ++lia+a++ ++++l +r++dip  v +g++dlGi+G+++leE++ + 
  lcl|FitnessBrowser__MR1:201231  32 LRIAIQkSGRLSTDSQQLLKSCGVKFSINE-QRLIAHADNMPIDLLRVRDDDIPGLVMDGVVDLGIIGENVLEEEQIEr 109
                                     89****99********************99.99*****************************************55555 PP

                       TIGR00070  78 ........vvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGavElapllg 148
                                             +v+l +l+fg+c+l+lAvp e ++ ++++l+ g riAT+ypnl r+++++k ++++ + l+G+vE+ap++g
  lcl|FitnessBrowser__MR1:201231 110 qtlnkpaeYVKLRQLDFGACRLSLAVPTEFSYADASSLE-GLRIATSYPNLLRRFMQQKSINYRDCMLKGSVEVAPRAG 187
                                     56777778**************************99999.9************************************** PP

                       TIGR00070 149 ladaIvDivetGttLrengLkiieeilessarlia 183
                                     lad I+D+v+tG+tL++ngL ++e+i++s a++i+
  lcl|FitnessBrowser__MR1:201231 188 LADGICDLVSTGATLEANGLYETEVIYRSMACIIQ 222
                                     ********************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (324 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: 8.69
//
[ok]

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