GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_1 in Marinobacter adhaerens HP15

Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate GFF3347 HP15_3289 para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II

Query= SwissProt::P00901
         (198 letters)



>FitnessBrowser__Marino:GFF3347
          Length = 193

 Score =  316 bits (810), Expect = 2e-91
 Identities = 145/191 (75%), Positives = 172/191 (90%)

Query: 2   LLMMIDNYDSFTYNVVQYLGELGAEVKVIRNDEMTIAQIEALNPERIVVSPGPCTPSEAG 61
           +L+MIDNYDSFTYNVVQYL ELGA+V+V RNDE+TI QIEALNPER+V+SPGPCTP+EAG
Sbjct: 1   MLLMIDNYDSFTYNVVQYLAELGADVQVHRNDEITIEQIEALNPERLVISPGPCTPNEAG 60

Query: 62  VSIEAILHFAGKLPILGVCLGHQSIGQAFGGDVVRARQVMHGKTSPVHHRDLGVFTGLNN 121
           +S+ AI HFAGK+PILG+CLGHQ+IGQ +GGDV+RA +VMHGK SPV H+D GVF GL+N
Sbjct: 61  ISMAAIRHFAGKVPILGICLGHQAIGQVYGGDVIRAGRVMHGKVSPVFHKDTGVFRGLSN 120

Query: 122 PLTVTRYHSLVVKRETLPDCLEVTAWTAHEDGSVDEIMGLRHKTLNIEGVQFHPESILTE 181
           PL  TRYHSLV+ + TLPDCLEVTAWT ++DGS++EIMG+RHKTL IEGVQFHPESI+TE
Sbjct: 121 PLQATRYHSLVIDKATLPDCLEVTAWTRNDDGSIEEIMGVRHKTLPIEGVQFHPESIMTE 180

Query: 182 QGHELFANFLK 192
           QGHEL  NFL+
Sbjct: 181 QGHELLRNFLR 191


Lambda     K      H
   0.320    0.138    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: 206
Number of extensions: 2
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: 198
Length of database: 193
Length adjustment: 20
Effective length of query: 178
Effective length of database: 173
Effective search space:    30794
Effective search space used:    30794
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 (21.8 bits)
S2: 44 (21.6 bits)

Align candidate GFF3347 HP15_3289 (para-aminobenzoate/anthranilate synthase glutamine amidotransferase 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.21272.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    1.9e-92  294.4   0.0    2.1e-92  294.2   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF3347  HP15_3289 para-aminobenzoate/ant


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF3347  HP15_3289 para-aminobenzoate/anthranilate synthase glutamine amidotransferase com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.2   0.0   2.1e-92   2.1e-92       1     191 [.       1     191 [.       1     192 [. 0.98

  Alignments for each domain:
  == domain 1  score: 294.2 bits;  conditional E-value: 2.1e-92
                           TIGR00566   1 mvllidnydsftynlvqlleelgaevvvkrndsltlqeieallpllsivisPGPctPdeaaissleliehlaGkl 75 
                                         m+l+idnydsftyn+vq+l+elga+v v+rnd++t+++ieal p+  +visPGPctP+ea+is +++i+h+aGk+
  lcl|FitnessBrowser__Marino:GFF3347   1 MLLMIDNYDSFTYNVVQYLAELGADVQVHRNDEITIEQIEALNPER-LVISPGPCTPNEAGIS-MAAIRHFAGKV 73 
                                         79********************************************.****************.899******** PP

                           TIGR00566  76 PilGvClGhqalaqafGadvvraekvkhGkvseiehngaavfaglfnPdalkatryhslvveaetldtllevtal 150
                                         PilG+ClGhqa++q+ G+dv+ra +v+hGkvs + h++++vf+gl+nP  l+atryhslv++ +tl+++levta+
  lcl|FitnessBrowser__Marino:GFF3347  74 PILGICLGHQAIGQVYGGDVIRAGRVMHGKVSPVFHKDTGVFRGLSNP--LQATRYHSLVIDKATLPDCLEVTAW 146
                                         ************************************************..************************* PP

                           TIGR00566 151 eeee....ieimairhrdlpleGvqfhPesilselGkellanflk 191
                                         + ++    +eim++rh+ lp+eGvqfhPesi++e+G+ell+nfl+
  lcl|FitnessBrowser__Marino:GFF3347 147 TRNDdgsiEEIMGVRHKTLPIEGVQFHPESIMTEQGHELLRNFLR 191
                                         998878888**********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (192 nodes)
Target sequences:                          1  (193 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: 6.76
//
[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:

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