GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Sinorhizobium meliloti 1021

Align Anthranilate synthase component II (characterized, see rationale)
to candidate SMc02725 SMc02725 anthranilate synthase

Query= uniprot:Q8AAD4_BACTN
         (188 letters)



>FitnessBrowser__Smeli:SMc02725
          Length = 729

 Score =  128 bits (321), Expect = 3e-34
 Identities = 70/178 (39%), Positives = 99/178 (55%)

Query: 1   MKILLLDNYDSFTYNLLHAVKELGATDVEVVRNDQINLDEVERFDKIILSPGPGIPEEAG 60
           + ILL+D+ DSF + L +  ++ GA+   V       + +  + D ++LSPGPG P++  
Sbjct: 529 VSILLVDHEDSFVHTLANYFRQTGASVTTVRTPVAEEIFDRVKPDLVVLSPGPGTPKDFD 588

Query: 61  LLLPIIKRYAPTKSILGVCLGHQAIGEAFGARLENLKEVYHGVQTPISILQKDVLFEGLG 120
               I K  A    I GVCLG QA+ EA+G  L  L    HG  + I +L+  ++F GLG
Sbjct: 589 CKATIKKARARDLPIFGVCLGLQALAEAYGGDLRQLAIPMHGKPSRIRVLEPGIVFSGLG 648

Query: 121 KEIPVGRYHSWVVSREGFPECLEITAESQEGQIMALRHKTYDVHGIQFHPESVLTPQG 178
           KE+ VGRYHS        P    ITAES++G IM + H    V  +QFHPES++T  G
Sbjct: 649 KEVTVGRYHSIFADPSNLPREFVITAESEDGTIMGIEHSKEPVAAVQFHPESIMTLGG 706


Lambda     K      H
   0.319    0.141    0.411 

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: 308
Number of extensions: 10
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: 188
Length of database: 729
Length adjustment: 29
Effective length of query: 159
Effective length of database: 700
Effective search space:   111300
Effective search space used:   111300
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 SMc02725 SMc02725 (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.23622.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    3.2e-44  137.1   0.0    4.8e-44  136.5   0.0    1.3  1  lcl|FitnessBrowser__Smeli:SMc02725  SMc02725 anthranilate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02725  SMc02725 anthranilate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.5   0.0   4.8e-44   4.8e-44       2     190 ..     531     717 ..     530     719 .. 0.88

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 4.8e-44
                           TIGR00566   2 vllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGklP 76 
                                         +ll+d  dsf + l +++ + ga+v+  r  ++  +  ++++p+l +v+sPGP+tP++   + + + +  a  lP
  lcl|FitnessBrowser__Smeli:SMc02725 531 ILLVDHEDSFVHTLANYFRQTGASVTTVRT-PVAEEIFDRVKPDL-VVLSPGPGTPKDFDCK-ATIKKARARDLP 602
                                         9*********************99875554.5566677*******.************9888.56666667779* PP

                           TIGR00566  77 ilGvClGhqalaqafGadvvraekvkhGkvseiehngaa.vfaglfnPdalkatryhslvveaetldtllevtal 150
                                         i+GvClG qala a G+d+ +++  +hGk s i+  + + vf gl +   ++++ryhs+  ++ +l+  + +ta 
  lcl|FitnessBrowser__Smeli:SMc02725 603 IFGVCLGLQALAEAYGGDLRQLAIPMHGKPSRIRVLEPGiVFSGLGKE--VTVGRYHSIFADPSNLPREFVITAE 675
                                         **********************************98877369999998..9********************9999 PP

                           TIGR00566 151 eeeeieimairhrdlpleGvqfhPesils...elGkellanfl 190
                                         +e    im+i h + p+  vqfhPesi++   + G ++++n++
  lcl|FitnessBrowser__Smeli:SMc02725 676 SEDG-TIMGIEHSKEPVAAVQFHPESIMTlggDAGMRMIENVV 717
                                         8888.9**********************844456677888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (729 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: 24.75
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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