GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisG in Marinobacter adhaerens HP15

Align ATP phosphoribosyltransferase; ATP-PRT; ATP-PRTase; EC 2.4.2.17 (uncharacterized)
to candidate GFF2485 HP15_2429 ATP phosphoribosyltransferase

Query= curated2:Q6FEC9
         (228 letters)



>lcl|FitnessBrowser__Marino:GFF2485 HP15_2429 ATP
           phosphoribosyltransferase
          Length = 213

 Score =  263 bits (672), Expect = 2e-75
 Identities = 128/207 (61%), Positives = 165/207 (79%)

Query: 22  LTLALSKGRILKETLPLLEAAGINLLEDPEKSRKLIFPTTHQKVRILILRASDVPTYVEN 81
           +T+ALSKGRIL+ETLPLL  AGI L++D +KSRKL+FPTT   VR+LI+RA+DVPTYV+ 
Sbjct: 5   ITIALSKGRILEETLPLLAEAGIELIDDVKKSRKLVFPTTDPNVRVLIIRATDVPTYVQY 64

Query: 82  GAADFGVAGKDVLMEHGAQHVYELLDLKIANCKLMTAGKVGMQHPKGRLKIATKYVNLTR 141
           G AD GV GKDVLMEHG + +YE LDL I+ C+LMTAG      P GR+K+ATK+VNL R
Sbjct: 65  GGADLGVTGKDVLMEHGGEGLYEPLDLNISRCRLMTAGPKDQTPPSGRIKVATKFVNLAR 124

Query: 142 QYYASLGEQVDVIKLYGSMELAPLVGLGDYIVDVVDTGNTLRANGLEPLEEIMKVSSRLI 201
           +YY++ G Q D+IKLYG+MELAP++GL D IVD+VDTGNTL+ANGLE  E I  +SSRL+
Sbjct: 125 RYYSAQGRQADIIKLYGAMELAPILGLADEIVDIVDTGNTLKANGLEARELIEHISSRLV 184

Query: 202 VNKASFKRKQALLDPILAQVEEAVNQR 228
           VN+AS K K   ++PI+ ++  AV++R
Sbjct: 185 VNRASMKMKHERINPIIEKMSAAVDKR 211


Lambda     K      H
   0.318    0.137    0.382 

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: 195
Number of extensions: 3
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: 228
Length of database: 213
Length adjustment: 22
Effective length of query: 206
Effective length of database: 191
Effective search space:    39346
Effective search space used:    39346
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 GFF2485 HP15_2429 (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.26385.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    3.1e-59  186.0   0.0    3.6e-59  185.8   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF2485  HP15_2429 ATP phosphoribosyltran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2485  HP15_2429 ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.8   0.0   3.6e-59   3.6e-59       1     183 []       5     185 ..       5     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: 185.8 bits;  conditional E-value: 3.6e-59
                           TIGR00070   1 lriAlpKGrleeetlkllekaglklskke..erkliasaedeevevlllrakdiptyvekgaadlGitGkDlleE 73 
                                         ++iAl KGr++eetl ll++ag++l +    +rkl++ ++d++v+vl++ra+d+ptyv++g adlG+tGkD+l+E
  lcl|FitnessBrowser__Marino:GFF2485   5 ITIALSKGRILEETLPLLAEAGIELIDDVkkSRKLVFPTTDPNVRVLIIRATDVPTYVQYGGADLGVTGKDVLME 79 
                                         79*********************976544469******************************************* PP

                           TIGR00070  74 sead.vvelldlgfgkcklvlAvpeesdvesledlkegk.riATkypnltreylekkgvkveivkleGavElapl 146
                                         ++ + ++e ldl++++c+l+ A p++++  s      g+ ++ATk++nl+r+y++ +g +++i+kl+Ga+Elap+
  lcl|FitnessBrowser__Marino:GFF2485  80 HGGEgLYEPLDLNISRCRLMTAGPKDQTPPS------GRiKVATKFVNLARRYYSAQGRQADIIKLYGAMELAPI 148
                                         88777**********************6666......5559********************************** PP

                           TIGR00070 147 lgladaIvDivetGttLrengLkiieeilessarlia 183
                                         lglad IvDiv tG+tL++ngL+  e i ++s+rl++
  lcl|FitnessBrowser__Marino:GFF2485 149 LGLADEIVDIVDTGNTLKANGLEARELIEHISSRLVV 185
                                         *********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (213 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: 7.47
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see 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