GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpD_2 in Pseudomonas simiae WCS417

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate GFF5019 PS417_25715 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__WCS417:GFF5019
          Length = 349

 Score =  286 bits (731), Expect = 7e-82
 Identities = 158/335 (47%), Positives = 210/335 (62%), Gaps = 4/335 (1%)

Query: 8   ALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREF 67
           AL R + H ++   EM D+MR+IM G+ +DA + A +  +R+K E+I EI GA +VMRE 
Sbjct: 6   ALSRIVGHLDLSTAEMSDVMREIMTGQCTDAQIGAFMMAMRMKSESIDEIVGAVSVMREL 65

Query: 68  SRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSADA 127
           + +VE+     +VD+VGTGGDG++ FN+ST + FV AA G  VAKHGNR+VS KSGSAD 
Sbjct: 66  ADKVELKTLDGVVDVVGTGGDGANIFNVSTASSFVVAAAGCTVAKHGNRAVSGKSGSADL 125

Query: 128 LEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLTN 187
           LEA G  + L P QVA  +   GIGFM+A  HH AMK  A  R+++G+RT+FN+LGPLTN
Sbjct: 126 LEAAGIYLNLTPVQVARCIDSVGIGFMFAQSHHGAMKHAAGPRKDLGLRTLFNMLGPLTN 185

Query: 188 PAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDGQV 247
           PAG  + ++GVF   L    A VLQ LG++  LVV  +DG+DE SL A T V EL++ QV
Sbjct: 186 PAGVKHQVVGVFSQALCRPLAEVLQRLGSKHVLVVHSKDGLDEFSLAAPTFVAELKNDQV 245

Query: 248 HEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVP----GPALDIVALNAGAALY 303
            EY V PED G+   +   L V   A S  ++   L          A +++ LNAGAALY
Sbjct: 246 TEYWVEPEDLGMKSQSLHGLAVESPAASLELIRDALGRRKTENGQKAAEMIVLNAGAALY 305

Query: 304 VAGVADSIADGIVRARQVLADGSARACLDAYVAFT 338
            A  A S+ +G+  A   L  G AR  L+   AFT
Sbjct: 306 AADHAYSLKEGVALAHDALHTGLAREKLEELGAFT 340


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: 304
Number of extensions: 15
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: 345
Length of database: 349
Length adjustment: 29
Effective length of query: 316
Effective length of database: 320
Effective search space:   101120
Effective search space used:   101120
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 GFF5019 PS417_25715 (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.10809.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.4e-125  403.0   2.5   6.1e-125  402.8   2.5    1.0  1  lcl|FitnessBrowser__WCS417:GFF5019  PS417_25715 anthranilate phospho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5019  PS417_25715 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.8   2.5  6.1e-125  6.1e-125       2     328 ..       8     337 ..       7     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 402.8 bits;  conditional E-value: 6.1e-125
                           TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivG 76 
                                         ++++ + dLs++e+ ++m+eim+g+++daqi+A+++a+r+k+e+++ei+g++ ++re a+kve ++ + +vD+vG
  lcl|FitnessBrowser__WCS417:GFF5019   8 SRIVGHLDLSTAEMSDVMREIMTGQCTDAQIGAFMMAMRMKSESIDEIVGAVSVMRELADKVELKTLDGVVDVVG 82 
                                         67788889******************************************************************* PP

                           TIGR01245  77 TGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPky 151
                                         TGGDg++ +N+STas++v+aaaG  vaKhGnr+vs+ksGsaD+Lea g+ l+l+p +var++++vgigF+fA  +
  lcl|FitnessBrowser__WCS417:GFF5019  83 TGGDGANIFNVSTASSFVVAAAGCTVAKHGNRAVSGKSGSADLLEAAGIYLNLTPVQVARCIDSVGIGFMFAQSH 157
                                         *************************************************************************** PP

                           TIGR01245 152 hpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEislt 226
                                         h a+k++a+ Rk+Lg+rt+fN+LGPL+nPa +k+qv+Gv+s+ l++ laevl++lg+k++lvvh++dglDE+sl 
  lcl|FitnessBrowser__WCS417:GFF5019 158 HGAMKHAAGPRKDLGLRTLFNMLGPLTNPAGVKHQVVGVFSQALCRPLAEVLQRLGSKHVLVVHSKDGLDEFSLA 232
                                         *************************************************************************** PP

                           TIGR01245 227 getkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegke...kkakrdivvlNaaaalyva 298
                                         ++t vaelk+++++ey ++ped+g+k ++l+ l+++s+++++el++++l  ++    +++++++vlNa+aaly+a
  lcl|FitnessBrowser__WCS417:GFF5019 233 APTFVAELKNDQVTEYWVEPEDLGMKSQSLHGLAVESPAASLELIRDALGRRKtenGQKAAEMIVLNAGAALYAA 307
                                         *************************************************7665332567889************* PP

                           TIGR01245 299 gkakdlkegvelakeaiksgkalekleelv 328
                                         ++a +lkegv la++a+++g a ekleel 
  lcl|FitnessBrowser__WCS417:GFF5019 308 DHAYSLKEGVALAHDALHTGLAREKLEELG 337
                                         ***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (349 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: 11.56
//
[ok]

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

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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