Alignments for a candidate for trpD_2 in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Pseudomonas fluorescens GW456-L13

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate PfGW456L13_1221 Anthranilate phosphoribosyltransferase (EC 2.4.2.18)

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1221
          Length = 349

 Score =  300 bits (768), Expect = 4e-86
 Identities = 162/335 (48%), Positives = 214/335 (63%), Gaps = 4/335 (1%)

Query: 8   ALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREF 67
           AL R ++H ++  DEM D+MR+IM G+ SDA + A +  +R+K E+I EI GA +VMRE 
Sbjct: 6   ALSRIVDHLDLSTDEMRDVMREIMTGQCSDAQIGAFMMAMRMKSESIDEIVGAVSVMREL 65

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

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

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

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

Query: 304 VAGVADSIADGIVRARQVLADGSARACLDAYVAFT 338
            A +A S+ +G+  A   L  G AR  L+   AFT
Sbjct: 306 AADLASSLKEGVALAHDALHTGLAREKLEELGAFT 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: 319
Number of extensions: 14
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 PfGW456L13_1221 (Anthranilate phosphoribosyltransferase (EC 2.4.2.18))
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.15486.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
     8e-127  409.0   2.0   9.1e-127  408.8   2.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1221  Anthranilate phosphoribosyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1221  Anthranilate phosphoribosyltransferase (EC 2.4.2.18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.8   2.0  9.1e-127  9.1e-127       1     328 [.       7     337 ..       7     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 408.8 bits;  conditional E-value: 9.1e-127
                                               TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglaka 55 
                                                             l++++d+ dLs++e++++m+eim+g++sdaqi+A+++a+r+k+e+++ei+g++ +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1221   7 LSRIVDHLDLSTDEMRDVMREIMTGQCSDAQIGAFMMAMRMKSESIDEIVGAVSV 61 
                                                             57899************************************************** PP

                                               TIGR01245  56 lrekakkvekeeseelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsv 110
                                                             +re a+kve ++ + +vD+vGTGGDg++ +N+STasa+v++aaG  vaKhGnr+v
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1221  62 MRELADKVELKTLDGVVDVVGTGGDGANIFNVSTASAFVVSAAGCTVAKHGNRAV 116
                                                             ******************************************************* PP

                                               TIGR01245 111 ssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpalkevapvRkeL 165
                                                             s+ksGsaD+Lea g+ l+l+p +var++++vgigF+fA ++h+a+k++a+ R++L
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1221 117 SGKSGSADLLEAAGIYLNLTPVQVARCIDNVGIGFMFAQTHHSAMKYAAGPRRDL 171
                                                             ******************************************************* PP

                                               TIGR01245 166 gvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedgl 220
                                                             g+rt+fN+LGPL+nPa +k+qv+Gv+ + l++ laevl++lg+k++lvvh++dgl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1221 172 GLRTLFNMLGPLTNPAGVKHQVVGVFTQALCRPLAEVLQRLGSKHVLVVHSKDGL 226
                                                             ******************************************************* PP

                                               TIGR01245 221 DEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevl 275
                                                             DE+sl ++t vaelkdg+++ey ++ped+g+k ++l+ l+++s+++++el++++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1221 227 DEFSLAAPTFVAELKDGQVTEYWVEPEDLGMKSQSLHGLAVESPAASLELIRDAL 281
                                                             ******************************************************* PP

                                               TIGR01245 276 egke...kkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleel 327
                                                               ++    +++++++vlNa+aaly+a+ a++lkegv la++a+++g a ekleel
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1221 282 GKRKtenGQKAAEMIVLNAGAALYAADLASSLKEGVALAHDALHTGLAREKLEEL 336
                                                             7776333567789****************************************98 PP

                                               TIGR01245 328 v 328
                                                              
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1221 337 G 337
                                                             6 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: 00:00:00.01
# Mc/sec: 7.33
//
[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