Alignments for a candidate for trpD_2 in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Dechlorosoma suillum PS

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate Dsui_0169 Dsui_0169 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__PS:Dsui_0169
          Length = 340

 Score =  428 bits (1100), Expect = e-124
 Identities = 216/339 (63%), Positives = 266/339 (78%)

Query: 3   ITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAAT 62
           ++PQ+AL R IEHREIFHDEM++LMRQIM GE+S  M++AI T LRVKKETIGEIA AA 
Sbjct: 1   MSPQEALTRCIEHREIFHDEMLELMRQIMSGEMSPVMIAAITTALRVKKETIGEIAAAAQ 60

Query: 63  VMREFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKS 122
           VMREF+ +V V D   +VDIVGTGGDG+HTFN+ST +MFV AA GAKVAKHG RSVSSKS
Sbjct: 61  VMREFATKVPVRDPSAVVDIVGTGGDGAHTFNVSTSSMFVCAAAGAKVAKHGGRSVSSKS 120

Query: 123 GSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNIL 182
           GSAD LEALG  + L PE++A  +   GIGFM+AP HH AMK  APVRRE+GVRTIFNIL
Sbjct: 121 GSADVLEALGVNLNLPPERIAECIDTVGIGFMFAPNHHGAMKHAAPVRRELGVRTIFNIL 180

Query: 183 GPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGEL 242
           GPLTNPAG+   ++GVFH DLVGI  RVLQ LG++RA  V+G DG+DE+S    TL+GEL
Sbjct: 181 GPLTNPAGAERQVLGVFHADLVGILIRVLQRLGSQRAFTVFGVDGLDEISNSGRTLIGEL 240

Query: 243 RDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAAL 302
           +DG++HEYE+HPEDF + +   R ++V +  ES+ M+L  L+   GPA DIVALNAGA+L
Sbjct: 241 KDGRIHEYEIHPEDFNLPVHDPRVIRVGNVEESKTMVLAALEGRHGPARDIVALNAGASL 300

Query: 303 YVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQA 341
           YVAG+ADS+A G+ +A   +A G+ARA LD +V FT+ A
Sbjct: 301 YVAGLADSMAQGVEKALDAIACGAARAKLDEFVRFTEVA 339


Lambda     K      H
   0.320    0.134    0.377 

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: 404
Number of extensions: 12
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: 345
Length of database: 340
Length adjustment: 29
Effective length of query: 316
Effective length of database: 311
Effective search space:    98276
Effective search space used:    98276
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: 49 (23.5 bits)

Align candidate Dsui_0169 Dsui_0169 (anthranilate phosphoribosyltransferase)
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))

# 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/TIGR01245.hmm
# target sequence database:        /tmp/gapView.8209.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01245  [M=330]
Accession:   TIGR01245
Description: trpD: anthranilate phosphoribosyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   8.4e-132  425.4   0.3   9.5e-132  425.2   0.3    1.0  1  lcl|FitnessBrowser__PS:Dsui_0169  Dsui_0169 anthranilate phosphori


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0169  Dsui_0169 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.2   0.3  9.5e-132  9.5e-132       2     329 ..       8     334 ..       7     335 .. 0.99

  Alignments for each domain:
  == domain 1  score: 425.2 bits;  conditional E-value: 9.5e-132
                         TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGTG 78 
                                        ++++++++ ++e+ +lm++imsge+s++ iaAi +alrvk et+ eia++a+++re a+kv++++ + +vDivGTG
  lcl|FitnessBrowser__PS:Dsui_0169   8 TRCIEHREIFHDEMLELMRQIMSGEMSPVMIAAITTALRVKKETIGEIAAAAQVMREFATKVPVRDPSAVVDIVGTG 84 
                                       6899************************************************************************* PP

                         TIGR01245  79 GDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpal 155
                                       GDg++t+N+ST s++v aaaG+kvaKhG rsvssksGsaDvLealgvnl+l pe++a+++++vgigF+fAP++h a+
  lcl|FitnessBrowser__PS:Dsui_0169  85 GDGAHTFNVSTSSMFVCAAAGAKVAKHGGRSVSSKSGSADVLEALGVNLNLPPERIAECIDTVGIGFMFAPNHHGAM 161
                                       ***************************************************************************** PP

                         TIGR01245 156 kevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkva 232
                                       k++apvR+eLgvrt+fN+LGPL+nPa a++qvlGv+++dlv +l++vl++lg++ra+ v g dglDEis  g+t + 
  lcl|FitnessBrowser__PS:Dsui_0169 162 KHAAPVRRELGVRTIFNILGPLTNPAGAERQVLGVFHADLVGILIRVLQRLGSQRAFTVFGVDGLDEISNSGRTLIG 238
                                       ***************************************************************************** PP

                         TIGR01245 233 elkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegve 309
                                       elkdg+i+ey+++pedf l+ ++ + +++g+ ee+ +++ ++leg++ +++rdiv+lNa+a lyvag a+++++gve
  lcl|FitnessBrowser__PS:Dsui_0169 239 ELKDGRIHEYEIHPEDFNLPVHDPRVIRVGNVEESKTMVLAALEGRH-GPARDIVALNAGASLYVAGLADSMAQGVE 314
                                       **********************************************9.999************************** PP

                         TIGR01245 310 lakeaiksgkalekleelva 329
                                        a++ai  g+a +kl+e+v+
  lcl|FitnessBrowser__PS:Dsui_0169 315 KALDAIACGAARAKLDEFVR 334
                                       *****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (340 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: 00:00:00.01
# Mc/sec: 9.30
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis