Alignments for a candidate for hisG in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisG in Shewanella loihica PV-4

Align ATP phosphoribosyltransferase (characterized)
to candidate 5209744 Shew_2197 ATP phosphoribosyltransferase (RefSeq)

Query= CharProtDB::CH_024688
         (299 letters)



>FitnessBrowser__PV4:5209744
          Length = 299

 Score =  405 bits (1042), Expect = e-118
 Identities = 202/298 (67%), Positives = 244/298 (81%)

Query: 1   MTDNTRLRIAMQKSGRLSDDSRELLARCGIKINLHTQRLIAMAENMPIDILRVRDDDIPG 60
           M+++ RLRIA+QKSGRLS +S++LL  CGIK N++ QRLIA ++NMPID+LRVRDDDIPG
Sbjct: 1   MSESNRLRIAIQKSGRLSKESQKLLKSCGIKFNVNEQRLIAHSDNMPIDLLRVRDDDIPG 60

Query: 61  LVMDGVVDLGIIGENVLEEELLNRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAWDGPL 120
           LVMDGVVDLGIIGENVLEEE + R+   +      LR+LDFG CRLSLA P +  +    
Sbjct: 61  LVMDGVVDLGIIGENVLEEEQIERQTLDKPSECIKLRQLDFGACRLSLAVPTEFRYQDAS 120

Query: 121 SLNGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEAN 180
           SL G RIATSYP+LL+RY+ +KGIS++ C+L GSVEVAPRAGLAD ICDLVSTGATLEAN
Sbjct: 121 SLEGLRIATSYPNLLRRYMQEKGISYRDCMLKGSVEVAPRAGLADGICDLVSTGATLEAN 180

Query: 181 GLREVEVIYRSKACLIQRDGEMEESKQQLIDKLLTRIQGVIQARESKYIMMHAPTERLDE 240
           GL E EVIYRS AC+IQ   E  E+KQ LIDK+L+R+ GV++A+ESKYI++HAPTE LD+
Sbjct: 181 GLYETEVIYRSMACIIQSTQEQSEAKQALIDKILSRVNGVVRAKESKYILLHAPTETLDQ 240

Query: 241 VIALLPGAERPTILPLAGDQQRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMM 298
           ++ALLPGAE PT+LPL  D  RVA+H VSSE LFW+TME L  LGASSILV+PIEKMM
Sbjct: 241 IVALLPGAENPTVLPLNDDTNRVAIHAVSSEDLFWDTMEALTQLGASSILVMPIEKMM 298


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: 333
Number of extensions: 9
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: 299
Length of database: 299
Length adjustment: 27
Effective length of query: 272
Effective length of database: 272
Effective search space:    73984
Effective search space used:    73984
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 5209744 Shew_2197 (ATP phosphoribosyltransferase (RefSeq))
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.4112.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
    3.4e-59  185.9   0.0    4.6e-59  185.5   0.0    1.2  1  lcl|FitnessBrowser__PV4:5209744  Shew_2197 ATP phosphoribosyltran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209744  Shew_2197 ATP phosphoribosyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.5   0.0   4.6e-59   4.6e-59       1     183 []       7     197 ..       7     197 .. 0.96

  Alignments for each domain:
  == domain 1  score: 185.5 bits;  conditional E-value: 4.6e-59
                        TIGR00070   1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlleEsead 77 
                                      lriA++  Grl++e+ kll+++g+k++ +e ++lia++++ ++++l +r++dip  v +g++dlGi+G+++leE++ +
  lcl|FitnessBrowser__PV4:5209744   7 LRIAIQkSGRLSKESQKLLKSCGIKFNVNE-QRLIAHSDNMPIDLLRVRDDDIPGLVMDGVVDLGIIGENVLEEEQIE 83 
                                      89****99********************99.99*****************************************5555 PP

                        TIGR00070  78 .........vvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGavElapl 146
                                                ++l +l+fg+c+l+lAvp e +++++++l+ g riAT+ypnl r+y+++kg++++ + l+G+vE+ap+
  lcl|FitnessBrowser__PV4:5209744  84 rqtldkpseCIKLRQLDFGACRLSLAVPTEFRYQDASSLE-GLRIATSYPNLLRRYMQEKGISYRDCMLKGSVEVAPR 160
                                      556778888**************************99999.9************************************ PP

                        TIGR00070 147 lgladaIvDivetGttLrengLkiieeilessarlia 183
                                      +glad I+D+v+tG+tL++ngL ++e+i++s a++i+
  lcl|FitnessBrowser__PV4:5209744 161 AGLADGICDLVSTGATLEANGLYETEVIYRSMACIIQ 197
                                      **********************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (299 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: 9.09
//
[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