GapMind for Amino acid biosynthesis

 

Aligments for a candidate for trpD_1 in Escherichia coli BW25113

Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate 17423 b3360 para-aminobenzoate synthase component II (NCBI)

Query= SwissProt::P20576
         (201 letters)



>lcl|FitnessBrowser__Keio:17423 b3360 para-aminobenzoate synthase
           component II (NCBI)
          Length = 187

 Score =  268 bits (685), Expect = 5e-77
 Identities = 129/192 (67%), Positives = 160/192 (83%), Gaps = 5/192 (2%)

Query: 1   MLLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEALAPERIVLSPGPCTPNEAG 60
           M+L+IDNYDSFT+NL QYF EL A+V V RND L++  I+AL P++IV+SPGPCTP+EAG
Sbjct: 1   MILLIDNYDSFTWNLYQYFCELGADVLVKRNDALTLADIDALKPQKIVISPGPCTPDEAG 60

Query: 61  VSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGLAN 120
           +SL VI  +AG+LP+LGVCLGHQ++ QAFGG+VVRA +VMHGKTSPI H   GVF GLAN
Sbjct: 61  ISLDVIRHYAGRLPILGVCLGHQAMAQAFGGKVVRAAKVMHGKTSPITHNGEGVFRGLAN 120

Query: 121 PLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRHKTLNVEGVQFHPESILTE 180
           PLTVTRYHSLVV+ +SLP C +VTAW++       EIMG+RH+  ++EGVQFHPESIL+E
Sbjct: 121 PLTVTRYHSLVVEPDSLPACFDVTAWSE-----TREIMGIRHRQWDLEGVQFHPESILSE 175

Query: 181 QGHELLANFLRQ 192
           QGH+LLANFL +
Sbjct: 176 QGHQLLANFLHR 187


Lambda     K      H
   0.319    0.137    0.403 

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: 172
Number of extensions: 4
Number of successful extensions: 2
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: 201
Length of database: 187
Length adjustment: 20
Effective length of query: 181
Effective length of database: 167
Effective search space:    30227
Effective search space used:    30227
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 (21.7 bits)
S2: 44 (21.6 bits)

Align candidate 17423 b3360 (para-aminobenzoate synthase component II (NCBI))
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.29136.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.3e-103  329.1   0.0   4.8e-103  328.9   0.0    1.0  1  lcl|FitnessBrowser__Keio:17423  b3360 para-aminobenzoate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17423  b3360 para-aminobenzoate synthase component II (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.9   0.0  4.8e-103  4.8e-103       1     192 []       1     187 []       1     187 [] 0.99

  Alignments for each domain:
  == domain 1  score: 328.9 bits;  conditional E-value: 4.8e-103
                       TIGR00566   1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklPilG 79 
                                     m+llidnydsft+nl+q+++elga+v+vkrnd+ltl++i+al+p++ ivisPGPctPdea+is l++i+h+aG+lPilG
  lcl|FitnessBrowser__Keio:17423   1 MILLIDNYDSFTWNLYQYFCELGADVLVKRNDALTLADIDALKPQK-IVISPGPCTPDEAGIS-LDVIRHYAGRLPILG 77 
                                     79********************************************.****************.*************** PP

                       TIGR00566  80 vClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtaleeeeieim 158
                                     vClGhqa+aqafG++vvra+kv+hGk+s i+hng++vf+gl+nP  l++tryhslvve+++l+++++vta++e++ eim
  lcl|FitnessBrowser__Keio:17423  78 VCLGHQAMAQAFGGKVVRAAKVMHGKTSPITHNGEGVFRGLANP--LTVTRYHSLVVEPDSLPACFDVTAWSETR-EIM 153
                                     ********************************************..****************************9.*** PP

                       TIGR00566 159 airhrdlpleGvqfhPesilselGkellanflkr 192
                                     +irhr+++leGvqfhPesilse+G++llanfl+r
  lcl|FitnessBrowser__Keio:17423 154 GIRHRQWDLEGVQFHPESILSEQGHQLLANFLHR 187
                                     ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (187 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: 4.89
//
[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 paper from 2022 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