GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Xenophilus azovorans DSM 13620

Align anthranilate synthase (subunit 2/2) (EC 4.1.3.27) (characterized)
to candidate WP_038204236.1 Q392_RS07760 aminodeoxychorismate/anthranilate synthase component II

Query= BRENDA::P20576
         (201 letters)



>NCBI__GCF_000745855.1:WP_038204236.1
          Length = 195

 Score =  232 bits (592), Expect = 3e-66
 Identities = 124/197 (62%), Positives = 146/197 (74%), Gaps = 12/197 (6%)

Query: 2   LLMIDNYDSFTYNLVQYFGELKAEVKVVRNDELSVEQIEA---LAPERIVLSPGPCTPNE 58
           LLMIDNYDSFTYNLVQYFGEL A+V+ VRNDE++VE I         R+V+SPGPC+P E
Sbjct: 4   LLMIDNYDSFTYNLVQYFGELGAQVETVRNDEITVEGIGERIDAGVTRLVISPGPCSPAE 63

Query: 59  AGVSLAVIERFAGKLPLLGVCLGHQSIGQAFGGEVVRARQVMHGKTSPIHHKDLGVFAGL 118
           AGVS+  I  FAG+LP+LGVCLGHQSIG AFG ++VRA+Q+MHGK S I     GVFAGL
Sbjct: 64  AGVSVPAIRAFAGRLPILGVCLGHQSIGAAFGAKIVRAQQLMHGKVSEITTTREGVFAGL 123

Query: 119 ANPLTVTRYHSLVVKRESLPECLEVTAWTQHADGSLDEIMGVRH----KTLNVEGVQFHP 174
               TV RYHSL ++R+S PE L +TAWT   DG   EIMGVRH      + +EGVQFHP
Sbjct: 124 PERFTVNRYHSLAIERDSRPEELALTAWTD--DG---EIMGVRHTGFAHEVRLEGVQFHP 178

Query: 175 ESILTEQGHELLANFLR 191
           ESILTE GH +L NFL+
Sbjct: 179 ESILTEHGHAMLRNFLQ 195


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: 187
Number of extensions: 10
Number of successful extensions: 3
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: 195
Length adjustment: 20
Effective length of query: 181
Effective length of database: 175
Effective search space:    31675
Effective search space used:    31675
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: 45 (21.9 bits)

Align candidate WP_038204236.1 Q392_RS07760 (aminodeoxychorismate/anthranilate synthase component II)
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.747256.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.6e-74  235.2   0.0    2.9e-74  235.1   0.0    1.0  1  NCBI__GCF_000745855.1:WP_038204236.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038204236.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.1   0.0   2.9e-74   2.9e-74       2     191 ..       4     195 .]       3     195 .] 0.94

  Alignments for each domain:
  == domain 1  score: 235.1 bits;  conditional E-value: 2.9e-74
                             TIGR00566   2 vllidnydsftynlvqlleelgaevvvkrndsltlqei.eallplls.ivisPGPctPdeaaissleliehla 72 
                                           +l+idnydsftynlvq++ elga+v   rnd++t++ i e++ + ++ +visPGPc+P+ea++s + +i+ +a
  NCBI__GCF_000745855.1:WP_038204236.1   4 LLMIDNYDSFTYNLVQYFGELGAQVETVRNDEITVEGIgERIDAGVTrLVISPGPCSPAEAGVS-VPAIRAFA 75 
                                           89***********************************95677776556****************.******** PP

                             TIGR00566  73 GklPilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtll 145
                                           G+lPilGvClGhq+++ afGa++vra++++hGkvsei+   ++vfagl +   +++ ryhsl +e ++ ++ l
  NCBI__GCF_000745855.1:WP_038204236.1  76 GRLPILGVCLGHQSIGAAFGAKIVRAQQLMHGKVSEITTTREGVFAGLPER--FTVNRYHSLAIERDSRPEEL 146
                                           ************************************************655..******************** PP

                             TIGR00566 146 evtaleeeeieimairh....rdlpleGvqfhPesilselGkellanflk 191
                                            +ta+++   eim++rh    +++ leGvqfhPesil+e+G+++l+nfl+
  NCBI__GCF_000745855.1:WP_038204236.1 147 ALTAWTDDG-EIMGVRHtgfaHEVRLEGVQFHPESILTEHGHAMLRNFLQ 195
                                           *******99.******9333346789**********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (195 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: 11.14
//
[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