GapMind for Amino acid biosynthesis

 

Aligments for a candidate for trpD_2 in Desulfovibrio vulgaris Miyazaki F

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate 8501007 DvMF_1744 anthranilate phosphoribosyltransferase (RefSeq)

Query= SwissProt::Q8PD71
         (345 letters)



>lcl|FitnessBrowser__Miya:8501007 DvMF_1744 anthranilate
           phosphoribosyltransferase (RefSeq)
          Length = 338

 Score =  210 bits (535), Expect = 4e-59
 Identities = 131/312 (41%), Positives = 177/312 (56%), Gaps = 9/312 (2%)

Query: 29  QIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREFSRRVEVTD-RRHMVDIVGTGG 87
           ++M GE++ A   + L GLR+K ET  E+  A  V    +R V VT      +DIVGTGG
Sbjct: 29  RLMDGEMTCAQAGSFLMGLRMKGETPQELTEA--VRAALARAVRVTGIDGPTIDIVGTGG 86

Query: 88  DGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSADALEALGAVIELQPEQVAASLA 147
           DG  +FN ST      A  G +V KHGNR+VSS  G+ADA+E LG  +EL PE V A +A
Sbjct: 87  DGRSSFNCSTATALTLAGMGHRVVKHGNRAVSSSCGAADAVEGLGLPLELDPEDVRALVA 146

Query: 148 QTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLTNPAGSPNILMGVFHPDLVGIQ 207
           Q    F++AP  HPA + V P+RRE+GVRT+FN+LGPL NPA   ++L+GV   +L+ + 
Sbjct: 147 QRNFAFLFAPRFHPAFRNVMPIRRELGVRTLFNLLGPLLNPARPSHMLLGVARAELLPLM 206

Query: 208 ARVLQELGAERALVVWGRDGMDELS-LGAGTLVGELRDGQVH----EYEVHPEDFGIAMS 262
           AR L   G  RA VV G  G DEL+ +G   ++    DGQ H    E  V P D+GIA  
Sbjct: 207 ARTLLLTGVRRAAVVHGAGGYDELTPMGPAHIMLLEGDGQGHGTLTEISVDPADYGIASC 266

Query: 263 ASRNLKVADAAESRAMLLQVLD-NVPGPALDIVALNAGAALYVAGVADSIADGIVRARQV 321
               L V D   +  +L ++L    P P  D++ LN G AL++     ++ D +  AR  
Sbjct: 267 TPEELAVPDRDTAVRVLRELLSGGGPAPMRDMLMLNVGMALHLLEPGLALPDAMAAARLA 326

Query: 322 LADGSARACLDA 333
           LA G+    L A
Sbjct: 327 LAAGAGGKVLHA 338


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: 333
Number of extensions: 18
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: 345
Length of database: 338
Length adjustment: 29
Effective length of query: 316
Effective length of database: 309
Effective search space:    97644
Effective search space used:    97644
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 8501007 DvMF_1744 (anthranilate phosphoribosyltransferase (RefSeq))
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.27716.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    4.5e-99  317.8   0.0      5e-99  317.7   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501007  DvMF_1744 anthranilate phosphori


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501007  DvMF_1744 anthranilate phosphoribosyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.7   0.0     5e-99     5e-99       1     324 [.       9     336 ..       9     338 .] 0.96

  Alignments for each domain:
  == domain 1  score: 317.7 bits;  conditional E-value: 5e-99
                         TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGT 77 
                                       le+l+++ dL+ e ae+ ++ +m+ge++ aq +++l+ lr+kget++e++++++a +++a++v+   +   +DivGT
  lcl|FitnessBrowser__Miya:8501007   9 LETLATGMDLAPELAEAGFSRLMDGEMTCAQAGSFLMGLRMKGETPQELTEAVRAALARAVRVTG-IDGPTIDIVGT 84 
                                       57899999*******************************************************99.699******** PP

                         TIGR01245  78 GGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpa 154
                                       GGDg +++N STa+al +a++G +v+KhGnr+vss++G+aD +e lg+ lel+pe v++ +++ +++FlfAP++hpa
  lcl|FitnessBrowser__Miya:8501007  85 GGDGRSSFNCSTATALTLAGMGHRVVKHGNRAVSSSCGAADAVEGLGLPLELDPEDVRALVAQRNFAFLFAPRFHPA 161
                                       ***************************************************************************** PP

                         TIGR01245 155 lkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkv 231
                                       +++v+p+R+eLgvrt+fNlLGPLlnPar+++ +lGv++++l+ ++a++l   gv+ra vvhg++g DE++++g++++
  lcl|FitnessBrowser__Miya:8501007 162 FRNVMPIRRELGVRTLFNLLGPLLNPARPSHMLLGVARAELLPLMARTLLLTGVRRAAVVHGAGGYDELTPMGPAHI 238
                                       ***************************************************************************** PP

                         TIGR01245 232 aelk.....dgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakd 303
                                       + l+     +g+ +e +++p+d+g++ ++ eel++ + +  +++l+e+l+g++  + rd+++lN+++al + +   +
  lcl|FitnessBrowser__Miya:8501007 239 MLLEgdgqgHGTLTEISVDPADYGIASCTPEELAVPDRDTAVRVLRELLSGGGPAPMRDMLMLNVGMALHLLEPGLA 315
                                       ***93333335799**********************************************************99999 PP

                         TIGR01245 304 lkegvelakeaiksgkalekl 324
                                       l +++ +a+ a+  g+  ++l
  lcl|FitnessBrowser__Miya:8501007 316 LPDAMAAARLALAAGAGGKVL 336
                                       999999999999999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (338 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: 7.80
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see 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