Alignments for a candidate for trpD_2 in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Pseudomonas fluorescens FW300-N2E3

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate AO353_07215 AO353_07215 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_07215
          Length = 349

 Score =  289 bits (739), Expect = 8e-83
 Identities = 158/335 (47%), Positives = 211/335 (62%), Gaps = 4/335 (1%)

Query: 8   ALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREF 67
           AL R + H ++  DEM D+MR+IM G+ +DA + A +  +R+K E+I EI GA +VMRE 
Sbjct: 6   ALSRIVGHLDLSTDEMRDVMREIMTGQCTDAQIGAFMMAMRMKSESIDEIVGAVSVMREL 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  RR++G+RT+FN+LGPLTN
Sbjct: 126 LEAAGIYLNLTPVQVARCIDNVGIGFMFAQSHHGAMKHAAGPRRDLGLRTLFNMLGPLTN 185

Query: 188 PAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDGQV 247
           PAG  + ++GVF   L    A VLQ +G++  LVV  +DG+DE SL A T V EL++ Q+
Sbjct: 186 PAGVKHQVVGVFSQALCRPLAEVLQRMGSKHVLVVHSKDGLDEFSLAAPTFVAELKNDQI 245

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

Query: 304 VAGVADSIADGIVRARQVLADGSARACLDAYVAFT 338
            A  A S+ +G+  A   L  G AR  L+   AFT
Sbjct: 306 AADHAVSLKEGVALAHDALHTGLAREKLEELGAFT 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: 303
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 AO353_07215 AO353_07215 (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.9155.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
     1e-125  405.4   2.4   1.1e-125  405.2   2.4    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07215  AO353_07215 anthranilate phospho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_07215  AO353_07215 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.2   2.4  1.1e-125  1.1e-125       2     328 ..       8     337 ..       7     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 405.2 bits;  conditional E-value: 1.1e-125
                                     TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke 66 
                                                   ++++ + dLs++e++++m+eim+g+++daqi+A+++a+r+k+e+++ei+g++ ++re a+kve +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07215   8 SRIVGHLDLSTDEMRDVMREIMTGQCTDAQIGAFMMAMRMKSESIDEIVGAVSVMRELADKVELK 72 
                                                   67788889********************************************************* PP

                                     TIGR01245  67 eseelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelsp 131
                                                   + + +vD+vGTGGDg++ +N+STas++v+aaaG  vaKhGnr+vs+ksGsaD+Lea g+ l+l+p
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07215  73 TLDGVVDVVGTGGDGANIFNVSTASSFVVAAAGCTVAKHGNRAVSGKSGSADLLEAAGIYLNLTP 137
                                                   ***************************************************************** PP

                                     TIGR01245 132 ekvarsleevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlv 196
                                                    +var++++vgigF+fA  +h a+k++a+ R++Lg+rt+fN+LGPL+nPa +k+qv+Gv+s+ l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07215 138 VQVARCIDNVGIGFMFAQSHHGAMKHAAGPRRDLGLRTLFNMLGPLTNPAGVKHQVVGVFSQALC 202
                                                   ***************************************************************** PP

                                     TIGR01245 197 evlaevlknlgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkg 261
                                                   + laevl+++g+k++lvvh++dglDE+sl ++t vaelk+++i+ey ++ped+g+k ++l+ l++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07215 203 RPLAEVLQRMGSKHVLVVHSKDGLDEFSLAAPTFVAELKNDQISEYWVEPEDLGMKSQSLHGLAV 267
                                                   ***************************************************************** PP

                                     TIGR01245 262 gsaeenaellkevlegke...kkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalek 323
                                                   +s+++++el++++l  ++    +++++++vlNa+aaly+a++a +lkegv la++a+++g a ek
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07215 268 ESPAASLELIRDALGRRKtenGQKAAEMIVLNAGAALYAADHAVSLKEGVALAHDALHTGLAREK 332
                                                   **************7665332567889************************************** PP

                                     TIGR01245 324 leelv 328
                                                   leel 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_07215 333 LEELG 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: 00:00:00.01
# Mc/sec: 9.57
//
[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