Alignments for a candidate for hisG in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisG in Klebsiella michiganensis M5al

Align ATP phosphoribosyltransferase (characterized)
to candidate BWI76_RS18920 BWI76_RS18920 ATP phosphoribosyltransferase

Query= CharProtDB::CH_024688
         (299 letters)



>FitnessBrowser__Koxy:BWI76_RS18920
          Length = 299

 Score =  555 bits (1430), Expect = e-163
 Identities = 279/299 (93%), Positives = 293/299 (97%)

Query: 1   MTDNTRLRIAMQKSGRLSDDSRELLARCGIKINLHTQRLIAMAENMPIDILRVRDDDIPG 60
           M DN+RLRIA+QKSGRLS+DSRELL+RCGIK+NLHTQRLIA+AENMPIDILRVRDDDIPG
Sbjct: 1   MLDNSRLRIAIQKSGRLSEDSRELLSRCGIKVNLHTQRLIALAENMPIDILRVRDDDIPG 60

Query: 61  LVMDGVVDLGIIGENVLEEELLNRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAWDGPL 120
           L+MDGVVDLGIIGENVLEEELL+RRAQGEDPRYFTLRRLDFGGCRLSLATP DE WDGP 
Sbjct: 61  LIMDGVVDLGIIGENVLEEELLSRRAQGEDPRYFTLRRLDFGGCRLSLATPADEPWDGPA 120

Query: 121 SLNGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEAN 180
            LNGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEAN
Sbjct: 121 MLNGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEAN 180

Query: 181 GLREVEVIYRSKACLIQRDGEMEESKQQLIDKLLTRIQGVIQARESKYIMMHAPTERLDE 240
           GLREVEV++RSKACLIQRDGEM +SKQQLID+LLTRIQGVIQARESKYIMMHAPTERL+E
Sbjct: 181 GLREVEVMFRSKACLIQRDGEMADSKQQLIDRLLTRIQGVIQARESKYIMMHAPTERLEE 240

Query: 241 VIALLPGAERPTILPLAGDQQRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMME 299
           VIALLPGAERPTILPLAGD+QRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMME
Sbjct: 241 VIALLPGAERPTILPLAGDKQRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMME 299


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: 426
Number of extensions: 8
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 BWI76_RS18920 BWI76_RS18920 (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.17904.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
    1.1e-61  194.0   0.0    1.5e-61  193.5   0.0    1.2  1  lcl|FitnessBrowser__Koxy:BWI76_RS18920  BWI76_RS18920 ATP phosphoribosyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS18920  BWI76_RS18920 ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.5   0.0   1.5e-61   1.5e-61       1     183 []       7     197 ..       7     197 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.5 bits;  conditional E-value: 1.5e-61
                               TIGR00070   1 lriAlp.KGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDl 70 
                                             lriA++  Grl+e++ +ll+++g+k++ ++ ++lia ae+ ++++l +r++dip  + +g++dlGi+G+++
  lcl|FitnessBrowser__Koxy:BWI76_RS18920   7 LRIAIQkSGRLSEDSRELLSRCGIKVNLHT-QRLIALAENMPIDILRVRDDDIPGLIMDGVVDLGIIGENV 76 
                                             89****99*********************9.99************************************** PP

                               TIGR00070  71 leE......sead.....vvelldlgfgkcklvlAvpeesdvesledlkegkriATkypnltreylekkgv 130
                                             leE         +     +++l +l+fg c+l+lA+p +++++ ++ l+ gkriAT+yp+l ++yl++kg+
  lcl|FitnessBrowser__Koxy:BWI76_RS18920  77 LEEellsrrA--QgedprYFTLRRLDFGGCRLSLATPADEPWDGPAMLN-GKRIATSYPHLLKRYLDQKGI 144
                                             ***8876440..256677*******************************.9******************** PP

                               TIGR00070 131 kveivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183
                                             +++ + l+G+vE+ap++gladaI+D+v+tG+tL++ngL+++e++++s+a+li+
  lcl|FitnessBrowser__Koxy:BWI76_RS18920 145 SFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEANGLREVEVMFRSKACLIQ 197
                                             ***************************************************95 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.02
//
[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