Alignments for a candidate for trpD_2 in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Pseudomonas putida KT2440

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate PP_0421 PP_0421 Anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__Putida:PP_0421
          Length = 349

 Score =  282 bits (722), Expect = 8e-81
 Identities = 159/337 (47%), Positives = 209/337 (62%), Gaps = 4/337 (1%)

Query: 6   QQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMR 65
           + AL R +   ++  +EM ++MRQIM G+ S+A + A L G+R+K E+I EI GA +VMR
Sbjct: 4   KSALSRIVGQLDLTTEEMREVMRQIMTGQCSEAQIGAFLMGMRMKSESIDEIVGAVSVMR 63

Query: 66  EFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSA 125
           E + +VE+     +VDIVGTGGDG++ FN+ST + FV AA G  VAKHGNR+VS KSGSA
Sbjct: 64  ELAEKVELQSLDGVVDIVGTGGDGANIFNVSTASSFVLAAAGCPVAKHGNRAVSGKSGSA 123

Query: 126 DALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPL 185
           D LEA G  + L P QVA  +   GIGFM+A  HH AMK  A  RRE+G+RT+FN+LGPL
Sbjct: 124 DLLEAAGIYLNLTPTQVARCIDSLGIGFMFAQSHHSAMKHAAGPRRELGLRTLFNMLGPL 183

Query: 186 TNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDG 245
           TNPAG  + ++GVF   L    A VLQ LG++  LVV  +DG+DE SL A T V EL++ 
Sbjct: 184 TNPAGVKHQVVGVFAQTLCRPLAEVLQRLGSKHVLVVHSKDGLDEFSLAAPTFVAELKND 243

Query: 246 QVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVP----GPALDIVALNAGAA 301
           ++ EY V PED G+   +   L V     S  ++   L          A +++ LNAGAA
Sbjct: 244 EITEYWVEPEDLGMKSQSLHGLAVESPQASLELIRDALGRRKTENGQKAAEMIVLNAGAA 303

Query: 302 LYVAGVADSIADGIVRARQVLADGSARACLDAYVAFT 338
           LY A  A S+  G+  A  VL  G A   L    AFT
Sbjct: 304 LYAADHAMSLKAGVELAHDVLHTGLAWEKLQELGAFT 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: 313
Number of extensions: 16
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 PP_0421 PP_0421 (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.29869.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.5e-128  413.5   0.8     4e-128  413.3   0.8    1.0  1  lcl|FitnessBrowser__Putida:PP_0421  PP_0421 Anthranilate phosphoribo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0421  PP_0421 Anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.3   0.8    4e-128    4e-128       2     328 ..       8     337 ..       7     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 413.3 bits;  conditional E-value: 4e-128
                           TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivG 76 
                                         ++++ + dL++ee++++m++im+g++s+aqi+A+l+ +r+k+e+++ei+g++ ++re a+kve ++ + +vDivG
  lcl|FitnessBrowser__Putida:PP_0421   8 SRIVGQLDLTTEEMREVMRQIMTGQCSEAQIGAFLMGMRMKSESIDEIVGAVSVMRELAEKVELQSLDGVVDIVG 82 
                                         6788899******************************************************************** PP

                           TIGR01245  77 TGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPky 151
                                         TGGDg++ +N+STas++v+aaaG +vaKhGnr+vs+ksGsaD+Lea g+ l+l+p++var+++++gigF+fA  +
  lcl|FitnessBrowser__Putida:PP_0421  83 TGGDGANIFNVSTASSFVLAAAGCPVAKHGNRAVSGKSGSADLLEAAGIYLNLTPTQVARCIDSLGIGFMFAQSH 157
                                         *************************************************************************** PP

                           TIGR01245 152 hpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEislt 226
                                         h+a+k++a+ R+eLg+rt+fN+LGPL+nPa +k+qv+Gv+ + l++ laevl++lg+k++lvvh++dglDE+sl 
  lcl|FitnessBrowser__Putida:PP_0421 158 HSAMKHAAGPRRELGLRTLFNMLGPLTNPAGVKHQVVGVFAQTLCRPLAEVLQRLGSKHVLVVHSKDGLDEFSLA 232
                                         *************************************************************************** PP

                           TIGR01245 227 getkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegke...kkakrdivvlNaaaalyva 298
                                         ++t vaelk++ei+ey ++ped+g+k ++l+ l+++s+++++el++++l  ++    +++++++vlNa+aaly+a
  lcl|FitnessBrowser__Putida:PP_0421 233 APTFVAELKNDEITEYWVEPEDLGMKSQSLHGLAVESPQASLELIRDALGRRKtenGQKAAEMIVLNAGAALYAA 307
                                         *************************************************7665332567889************* PP

                           TIGR01245 299 gkakdlkegvelakeaiksgkalekleelv 328
                                         ++a +lk+gvela++++++g a+ekl+el 
  lcl|FitnessBrowser__Putida:PP_0421 308 DHAMSLKAGVELAHDVLHTGLAWEKLQELG 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.04
//
[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