Alignments for a candidate for trpD_1 in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_1 in Desulfovibrio vulgaris Miyazaki F

Align Glutamine amidotransferase of anthranilate synthase (characterized, see rationale)
to candidate 8501008 DvMF_1745 glutamine amidotransferase of anthranilate synthase (RefSeq)

Query= uniprot:B8DM46_DESVM
         (192 letters)



>FitnessBrowser__Miya:8501008
          Length = 192

 Score =  400 bits (1029), Expect = e-117
 Identities = 192/192 (100%), Positives = 192/192 (100%)

Query: 1   MFLLIDNYDSFTFNLVQAFYGLGLHPVVVRNDDPAVPAMAEDPALEMVCISPGPSHPRNA 60
           MFLLIDNYDSFTFNLVQAFYGLGLHPVVVRNDDPAVPAMAEDPALEMVCISPGPSHPRNA
Sbjct: 1   MFLLIDNYDSFTFNLVQAFYGLGLHPVVVRNDDPAVPAMAEDPALEMVCISPGPSHPRNA 60

Query: 61  GFCLDFLSRLPHRVPVLGVCLGHQVLGLFAGATVDVGPRIMHGKTSDITHDGQGLFHGVP 120
           GFCLDFLSRLPHRVPVLGVCLGHQVLGLFAGATVDVGPRIMHGKTSDITHDGQGLFHGVP
Sbjct: 61  GFCLDFLSRLPHRVPVLGVCLGHQVLGLFAGATVDVGPRIMHGKTSDITHDGQGLFHGVP 120

Query: 121 SPMQVGRYHSLIVHAEERPDLLAVTARAPEGEVMALRYTDRPWVGVQFHPESVLTPDGVR 180
           SPMQVGRYHSLIVHAEERPDLLAVTARAPEGEVMALRYTDRPWVGVQFHPESVLTPDGVR
Sbjct: 121 SPMQVGRYHSLIVHAEERPDLLAVTARAPEGEVMALRYTDRPWVGVQFHPESVLTPDGVR 180

Query: 181 MLANFPAHVAGR 192
           MLANFPAHVAGR
Sbjct: 181 MLANFPAHVAGR 192


Lambda     K      H
   0.325    0.142    0.453 

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: 304
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: 192
Length of database: 192
Length adjustment: 20
Effective length of query: 172
Effective length of database: 172
Effective search space:    29584
Effective search space used:    29584
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 44 (21.6 bits)

Align candidate 8501008 DvMF_1745 (glutamine amidotransferase of anthranilate synthase (RefSeq))
to HMM TIGR00566 (glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase)

# 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/TIGR00566.hmm
# target sequence database:        /tmp/gapView.16618.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00566  [M=192]
Accession:   TIGR00566
Description: trpG_papA: glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase
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-61  193.1   0.0    2.5e-61  192.9   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501008  DvMF_1745 glutamine amidotransfe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501008  DvMF_1745 glutamine amidotransferase of anthranilate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.9   0.0   2.5e-61   2.5e-61       1     189 [.       1     185 [.       1     188 [. 0.98

  Alignments for each domain:
  == domain 1  score: 192.9 bits;  conditional E-value: 2.5e-61
                         TIGR00566   1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklPi 77 
                                       m llidnydsft+nlvq +  lg + vv rnd+  +  + +  +l  ++isPGP++P +a+   l+ + +l  ++P+
  lcl|FitnessBrowser__Miya:8501008   1 MFLLIDNYDSFTFNLVQAFYGLGLHPVVVRNDDPAVPAMAEDPALEMVCISPGPSHPRNAGFC-LDFLSRLPHRVPV 76 
                                       679********************9999999**999*99999999999***************9.************* PP

                         TIGR00566  78 lGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleeee 154
                                       lGvClGhq l++  Ga v    +++hGk+s+i+h+g+++f+g+ +P  ++++ryhsl+v+ae+ ++ll vta   e 
  lcl|FitnessBrowser__Miya:8501008  77 LGVCLGHQVLGLFAGATVDVGPRIMHGKTSDITHDGQGLFHGVPSP--MQVGRYHSLIVHAEERPDLLAVTARAPEG 151
                                       **********************************************..**************************999 PP

                         TIGR00566 155 ieimairhrdlpleGvqfhPesilselGkellanf 189
                                        e+ma+r  d p+ GvqfhPes+l+  G ++lanf
  lcl|FitnessBrowser__Miya:8501008 152 -EVMALRYTDRPWVGVQFHPESVLTPDGVRMLANF 185
                                       .*********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (192 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: 8.58
//
[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