GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Trichormus variabilis ATCC 29413

Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate WP_011321547.1 AVA_RS24820 anthranilate synthase

Query= curated2:Q57690
         (197 letters)



>NCBI__GCF_000204075.1:WP_011321547.1
          Length = 728

 Score =  131 bits (329), Expect = 3e-35
 Identities = 80/198 (40%), Positives = 112/198 (56%), Gaps = 12/198 (6%)

Query: 4   KKVLVIDNIDSFVWNLVQYVGTLGYKVKLVDNKITLDEIKKINPDRIIISPGPKTPKE-- 61
           K++L+ID  DSFV  L  Y+ T G  V  + +           PD +++SPGP  P +  
Sbjct: 526 KRILLIDYEDSFVHTLANYIRTTGATVTTLRHGFAESYFDTERPDLVVLSPGPGRPSDFR 585

Query: 62  AGNCIKIIQEVDIPILGVCLGHQCIVEAFGGEVGRAKRVMHGKASLINHDGEG--IFKDI 119
               +  +   +IPI GVCLG Q IVEAFGGE+G      HGK + I+       +F+ +
Sbjct: 586 VPQTVAALVGREIPIFGVCLGLQGIVEAFGGELGVLDYPQHGKPARISVTAPDSVLFQHL 645

Query: 120 PNPFYGGRYHSLIA--KEVPKELKITAKSLDDNYIMGVRHKKLPIEGVQFHPESILTESD 177
           P  F  GRYHSL A  + +P ELK+ A S +DN IM + H+ LPI  VQFHPESI+T + 
Sbjct: 646 PASFIVGRYHSLFAQPQTIPSELKVIAIS-EDNVIMAIEHQTLPIAAVQFHPESIMTLAG 704

Query: 178 NLKFPDLGLKLIKNFVES 195
                ++G  +IKN V++
Sbjct: 705 -----EVGQTIIKNVVQT 717


Lambda     K      H
   0.319    0.142    0.421 

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: 318
Number of extensions: 16
Number of successful extensions: 4
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: 197
Length of database: 728
Length adjustment: 30
Effective length of query: 167
Effective length of database: 698
Effective search space:   116566
Effective search space used:   116566
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: 49 (23.5 bits)

Align candidate WP_011321547.1 AVA_RS24820 (anthranilate synthase)
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.3926756.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.7e-41  127.1   0.0    5.9e-41  126.4   0.0    1.3  1  NCBI__GCF_000204075.1:WP_011321547.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000204075.1:WP_011321547.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   0.0   5.9e-41   5.9e-41       2     191 ..     528     716 ..     527     717 .. 0.88

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 5.9e-41
                             TIGR00566   2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGk 74 
                                           +llid  dsf + l +++   ga+v+    + +  +  ++  p+l +v+sPGP+ P +  +   + +  l G+
  NCBI__GCF_000204075.1:WP_011321547.1 528 ILLIDYEDSFVHTLANYIRTTGATVTT-LRHGFAESYFDTERPDL-VVLSPGPGRPSDFRVP--QTVAALVGR 596
                                           8*******************9999875.558999999********.************9988..667777776 PP

                             TIGR00566  75 .lPilGvClGhqalaqafGadvvraekvkhGkvseiehng..aavfaglfnPdalkatryhslvveaetldtl 144
                                            +Pi+GvClG q +  afG+++  ++  +hGk   i+     + +f+ l  P ++ ++ryhsl  +++t+++ 
  NCBI__GCF_000204075.1:WP_011321547.1 597 eIPIFGVCLGLQGIVEAFGGELGVLDYPQHGKPARISVTApdSVLFQHL--PASFIVGRYHSLFAQPQTIPSE 667
                                           48******************************99998765004444444..888******************* PP

                             TIGR00566 145 levtaleeeeieimairhrdlpleGvqfhPesils...elGkellanflk 191
                                           l+v a++e +  imai h+ lp+  vqfhPesi++   e G+++++n+++
  NCBI__GCF_000204075.1:WP_011321547.1 668 LKVIAISEDN-VIMAIEHQTLPIAAVQFHPESIMTlagEVGQTIIKNVVQ 716
                                           *******999.**********************98555788899999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (728 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: 39.68
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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