Alignments for a candidate for trpD_2 in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Cupriavidus basilensis 4G11

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate RR42_RS18305 RR42_RS18305 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__Cup4G11:RR42_RS18305
          Length = 342

 Score =  485 bits (1249), Expect = e-142
 Identities = 245/340 (72%), Positives = 281/340 (82%)

Query: 1   MPITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGA 60
           M ITPQ+AL R IEHREIFHDEM+ LMRQIM+G++S  M +AILTGLRVKKETIGEI+ A
Sbjct: 1   MSITPQEALTRCIEHREIFHDEMLHLMRQIMQGQMSPVMAAAILTGLRVKKETIGEISAA 60

Query: 61  ATVMREFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSS 120
           A VMREF+ +V V DR + VDIVGTGGDGSHTFNIST +MFVA+A GA++AKHGNR VSS
Sbjct: 61  AQVMREFANKVPVKDRENFVDIVGTGGDGSHTFNISTASMFVASAAGARIAKHGNRGVSS 120

Query: 121 KSGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFN 180
           KSGSAD LEALG  I L PEQV   + QTGIGFM+AP HHPAMK VAP+R+EMGVRTIFN
Sbjct: 121 KSGSADVLEALGVNIMLTPEQVGQCIEQTGIGFMFAPTHHPAMKNVAPIRKEMGVRTIFN 180

Query: 181 ILGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVG 240
           ILGPLTNPA +PNILMGVFHPDLVGIQ RV+Q LGA  ALVV+G+DGMDE+SLGA TLVG
Sbjct: 181 ILGPLTNPADAPNILMGVFHPDLVGIQVRVMQRLGARHALVVYGKDGMDEVSLGAATLVG 240

Query: 241 ELRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGA 300
           EL+DG+V EYEVHPEDFG+ M ++R LKVADA ES+ MLL+ L +VPG   +IV LNAG 
Sbjct: 241 ELKDGEVREYEVHPEDFGLQMISNRGLKVADATESKEMLLEALTDVPGTPREIVTLNAGT 300

Query: 301 ALYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340
           ALY A VA SI DGI RAR+ +A G+AR  LD +V  TQQ
Sbjct: 301 ALYAANVASSIEDGIQRAREAIASGAAREKLDQFVRATQQ 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: 424
Number of extensions: 10
Number of successful extensions: 1
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: 342
Length adjustment: 29
Effective length of query: 316
Effective length of database: 313
Effective search space:    98908
Effective search space used:    98908
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 RR42_RS18305 RR42_RS18305 (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.1254.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-131  422.9   1.7   5.4e-131  422.7   1.7    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS18305  RR42_RS18305 anthranilate phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS18305  RR42_RS18305 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.7   1.7  5.4e-131  5.4e-131       2     329 ..      10     336 ..       9     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 422.7 bits;  conditional E-value: 5.4e-131
                                 TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeesee 70 
                                                ++++++++ ++e+ +lm++im+g++s++  aAil+ lrvk et+ ei+++a+++re a+kv+++++e+
  lcl|FitnessBrowser__Cup4G11:RR42_RS18305  10 TRCIEHREIFHDEMLHLMRQIMQGQMSPVMAAAILTGLRVKKETIGEISAAAQVMREFANKVPVKDREN 78 
                                               6899***************************************************************** PP

                                 TIGR01245  71 lvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsle 139
                                               +vDivGTGGDg++t+NiSTas++va+aaG+++aKhGnr vssksGsaDvLealgvn+ l+pe+v +++e
  lcl|FitnessBrowser__Cup4G11:RR42_RS18305  79 FVDIVGTGGDGSHTFNISTASMFVASAAGARIAKHGNRGVSSKSGSADVLEALGVNIMLTPEQVGQCIE 147
                                               ********************************************************************* PP

                                 TIGR01245 140 evgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgv 208
                                               ++gigF+fAP++hpa+k+vap+Rke+gvrt+fN+LGPL+nPa a++ ++Gv+++dlv + ++v+++lg+
  lcl|FitnessBrowser__Cup4G11:RR42_RS18305 148 QTGIGFMFAPTHHPAMKNVAPIRKEMGVRTIFNILGPLTNPADAPNILMGVFHPDLVGIQVRVMQRLGA 216
                                               ********************************************************************* PP

                                 TIGR01245 209 kralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevleg 277
                                               ++alvv g+dg+DE+sl + t v elkdge++ey+++pedfgl++ + + lk+++a e+ e+l e+l+ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS18305 217 RHALVVYGKDGMDEVSLGAATLVGELKDGEVREYEVHPEDFGLQMISNRGLKVADATESKEMLLEALTD 285
                                               ********************************************************************9 PP

                                 TIGR01245 278 kekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                                  +  r+iv lNa++aly+a++a+++++g+++a+eai sg+a ekl+++v+
  lcl|FitnessBrowser__Cup4G11:RR42_RS18305 286 VP-GTPREIVTLNAGTALYAANVASSIEDGIQRAREAIASGAAREKLDQFVR 336
                                               98.6779*****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (342 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: 7.66
//
[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