Alignments for a candidate for hisG in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisG in Desulfovibrio vulgaris Miyazaki F

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate 8501229 DvMF_1963 ATP phosphoribosyltransferase (RefSeq)

Query= reanno::Miya:8501229
         (293 letters)



>FitnessBrowser__Miya:8501229
          Length = 293

 Score =  581 bits (1497), Expect = e-171
 Identities = 293/293 (100%), Positives = 293/293 (100%)

Query: 1   MSGNNMLKIGIPKGSLEEATVNLFARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRY 60
           MSGNNMLKIGIPKGSLEEATVNLFARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRY
Sbjct: 1   MSGNNMLKIGIPKGSLEEATVNLFARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRY 60

Query: 61  LEDGVLDVGLTGKDWLLETGADVVTVSDLVYSKVSNRPARWVLAVAGDSPYVRPEDLAGC 120
           LEDGVLDVGLTGKDWLLETGADVVTVSDLVYSKVSNRPARWVLAVAGDSPYVRPEDLAGC
Sbjct: 61  LEDGVLDVGLTGKDWLLETGADVVTVSDLVYSKVSNRPARWVLAVAGDSPYVRPEDLAGC 120

Query: 121 TIATELLGVTRRYFEDAGIPVKVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRII 180
           TIATELLGVTRRYFEDAGIPVKVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRII
Sbjct: 121 TIATELLGVTRRYFEDAGIPVKVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRII 180

Query: 181 AEVLLTNTVLIAGKAAWADPWKRAKIEQIDLLLQGALRADSLVGLKMNVPAHNLDAVLDQ 240
           AEVLLTNTVLIAGKAAWADPWKRAKIEQIDLLLQGALRADSLVGLKMNVPAHNLDAVLDQ
Sbjct: 181 AEVLLTNTVLIAGKAAWADPWKRAKIEQIDLLLQGALRADSLVGLKMNVPAHNLDAVLDQ 240

Query: 241 LPSLNSPTVAGLRDSTWYAVEIVVENDLVRDLIPRLRAAGAEGIIEYSLNKVI 293
           LPSLNSPTVAGLRDSTWYAVEIVVENDLVRDLIPRLRAAGAEGIIEYSLNKVI
Sbjct: 241 LPSLNSPTVAGLRDSTWYAVEIVVENDLVRDLIPRLRAAGAEGIIEYSLNKVI 293


Lambda     K      H
   0.318    0.136    0.401 

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: 501
Number of extensions: 25
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: 293
Length of database: 293
Length adjustment: 26
Effective length of query: 267
Effective length of database: 267
Effective search space:    71289
Effective search space used:    71289
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: 48 (23.1 bits)

Align candidate 8501229 DvMF_1963 (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.24326.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    3.5e-54  169.5   0.0    4.4e-54  169.2   0.0    1.1  1  lcl|FitnessBrowser__Miya:8501229  DvMF_1963 ATP phosphoribosyltran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501229  DvMF_1963 ATP phosphoribosyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   0.0   4.4e-54   4.4e-54       1     183 []       7     192 ..       7     192 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 4.4e-54
                         TIGR00070   1 lriAlpKGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkDlleEsead 77 
                                       l+i++pKG+lee t++l++++g+k++k++ r+++ +++d+e+++ l+r ++ip+y+e+g++d+G+tGkD+l E +ad
  lcl|FitnessBrowser__Miya:8501229   7 LKIGIPKGSLEEATVNLFARSGWKIRKHH-RNYFPEINDPELTARLCRVQEIPRYLEDGVLDVGLTGKDWLLETGAD 82 
                                       89***************************.*********************************************** PP

                         TIGR00070  78 vvelldlgfgkc.....klvlAvpeesdvesledlkegkriATkypnltreylekkgvkveivkleGavElapllgl 149
                                       vv++ dl ++k      ++vlAv  +s++ ++edl+ g  iAT+   +tr+y+e+ g++v++  ++Ga+E++++ gl
  lcl|FitnessBrowser__Miya:8501229  83 VVTVSDLVYSKVsnrpaRWVLAVAGDSPYVRPEDLA-GCTIATELLGVTRRYFEDAGIPVKVQYSWGATEAKVVEGL 158
                                       *******9988777777*******************.9*************************************** PP

                         TIGR00070 150 adaIvDivetGttLrengLkiieeilessarlia 183
                                       adaIv ++etGtt++++gL+ii+e+l ++++lia
  lcl|FitnessBrowser__Miya:8501229 159 ADAIVEVTETGTTIKAHGLRIIAEVLLTNTVLIA 192
                                       ********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (293 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: 12.22
//
[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