Alignments for a candidate for trpD_2 in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Pseudomonas stutzeri RCH2

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate GFF3581 Psest_3648 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__psRCH2:GFF3581
          Length = 348

 Score =  307 bits (786), Expect = 3e-88
 Identities = 168/337 (49%), Positives = 216/337 (64%), Gaps = 5/337 (1%)

Query: 6   QQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMR 65
           ++AL R +   ++  +EM  +MRQIM G+ +DA V A L G+R+K ETI EI GA  VMR
Sbjct: 4   KEALNRIVGQLDLSTEEMQAVMRQIMTGQCTDAQVGAFLMGMRMKSETIDEIVGAVQVMR 63

Query: 66  EFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSA 125
           E +  V   D   +VD  GTGGDG + FN+ST A FV AA G KVAKHGNR+VS KSGSA
Sbjct: 64  ELAAPVRF-DTDKLVDTCGTGGDGMNIFNVSTAASFVVAAAGGKVAKHGNRAVSGKSGSA 122

Query: 126 DALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPL 185
           D LEA G  ++L PEQVA S+   G+GFM+AP HH AMK  A  RRE+G+RT+FNILGP+
Sbjct: 123 DLLEAAGVFLDLTPEQVARSVDTVGVGFMFAPAHHGAMKHAAGPRRELGLRTLFNILGPM 182

Query: 186 TNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDG 245
            NPAG  + ++GVF   L    A VL  LG++  LVV  +DG+DE+SL A T V EL+DG
Sbjct: 183 ANPAGVRHQVLGVFSKALCRPMAEVLARLGSKHVLVVHAQDGLDEISLAAPTHVAELKDG 242

Query: 246 QVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPG----PALDIVALNAGAA 301
           ++ EY + PEDFGI   +   L V DA  S A++   L          A D++ LNAGAA
Sbjct: 243 EIREYSIQPEDFGIKSQSLIGLNVEDAQGSLALIRDALGRRQSENGQKAADMIVLNAGAA 302

Query: 302 LYVAGVADSIADGIVRARQVLADGSARACLDAYVAFT 338
           LY A +A S+  G+  A   L+ G AR  L+  V+FT
Sbjct: 303 LYAADLASSLKQGVEMAHDALSTGLARDKLEELVSFT 339


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: 329
Number of extensions: 17
Number of successful extensions: 3
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: 348
Length adjustment: 29
Effective length of query: 316
Effective length of database: 319
Effective search space:   100804
Effective search space used:   100804
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 GFF3581 Psest_3648 (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.13340.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.1e-130  421.7   2.8   1.2e-130  421.6   2.8    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3581  Psest_3648 anthranilate phosphor


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3581  Psest_3648 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.6   2.8  1.2e-130  1.2e-130       2     329 ..       8     337 ..       7     338 .. 0.97

  Alignments for each domain:
  == domain 1  score: 421.6 bits;  conditional E-value: 1.2e-130
                           TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivG 76 
                                         ++++ + dLs+ee++++m++im+g+++daq++A+l+ +r+k+et++ei+g+++++re a  v+ + +++lvD++G
  lcl|FitnessBrowser__psRCH2:GFF3581   8 NRIVGQLDLSTEEMQAVMRQIMTGQCTDAQVGAFLMGMRMKSETIDEIVGAVQVMRELAAPVRFD-TDKLVDTCG 81 
                                         7888999*******************************************************995.9******** PP

                           TIGR01245  77 TGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPky 151
                                         TGGDg++ +N+STa+++v+aaaG kvaKhGnr+vs+ksGsaD+Lea gv l+l+pe+vars+++vg+gF+fAP++
  lcl|FitnessBrowser__psRCH2:GFF3581  82 TGGDGMNIFNVSTAASFVVAAAGGKVAKHGNRAVSGKSGSADLLEAAGVFLDLTPEQVARSVDTVGVGFMFAPAH 156
                                         *************************************************************************** PP

                           TIGR01245 152 hpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEislt 226
                                         h a+k++a+ R+eLg+rt+fN+LGP++nPa +++qvlGv+sk l++ +aevl +lg+k++lvvh++dglDEisl 
  lcl|FitnessBrowser__psRCH2:GFF3581 157 HGAMKHAAGPRRELGLRTLFNILGPMANPAGVRHQVLGVFSKALCRPMAEVLARLGSKHVLVVHAQDGLDEISLA 231
                                         *************************************************************************** PP

                           TIGR01245 227 getkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegke...kkakrdivvlNaaaalyva 298
                                         ++t+vaelkdgei+ey+++pedfg+k ++l  l++++a+ +++l++++l  ++    ++++d++vlNa+aaly+a
  lcl|FitnessBrowser__psRCH2:GFF3581 232 APTHVAELKDGEIREYSIQPEDFGIKSQSLIGLNVEDAQGSLALIRDALGRRQsenGQKAADMIVLNAGAALYAA 306
                                         *************************************************655422267889************** PP

                           TIGR01245 299 gkakdlkegvelakeaiksgkalekleelva 329
                                         + a++lk+gve+a++a+++g a +kleelv+
  lcl|FitnessBrowser__psRCH2:GFF3581 307 DLASSLKQGVEMAHDALSTGLARDKLEELVS 337
                                         ****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (348 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: 11.45
//
[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