Alignments for a candidate for trpD_2 in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Dyella japonica UNC79MFTsu3.2

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate N515DRAFT_2112 N515DRAFT_2112 anthranilate phosphoribosyltransferase (EC 2.4.2.18)

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2112
          Length = 351

 Score =  491 bits (1264), Expect = e-143
 Identities = 254/342 (74%), Positives = 289/342 (84%), Gaps = 1/342 (0%)

Query: 3   ITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAAT 62
           ITPQ+ALQRTIEHREIFHDEM++LMRQIMRGEVS  M +AI+TGLRVKKETIGEI GAA 
Sbjct: 10  ITPQEALQRTIEHREIFHDEMIELMRQIMRGEVSPLMTAAIITGLRVKKETIGEITGAAR 69

Query: 63  VMREFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKS 122
           VMRE + +VE     H VDIVGTGGDG+ +FNIST +MFVAAA GA+VAKHG RSVSSKS
Sbjct: 70  VMRELAEKVEAAPHAHFVDIVGTGGDGASSFNISTASMFVAAAAGARVAKHGGRSVSSKS 129

Query: 123 GSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNIL 182
           GSAD LEALGA I+L P +VA  + +T IGFM+AP HHPAMKVVAPVR+EMGVRT+FNIL
Sbjct: 130 GSADVLEALGASIDLAPARVAQCMDETDIGFMFAPNHHPAMKVVAPVRKEMGVRTLFNIL 189

Query: 183 GPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGEL 242
           GPLTNPAG+PNILMGVFHPDLVGIQ RVLQ+LGA  ALVVWGRDGMDE+SLGA TLVGEL
Sbjct: 190 GPLTNPAGAPNILMGVFHPDLVGIQVRVLQQLGARHALVVWGRDGMDEISLGASTLVGEL 249

Query: 243 RDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAAL 302
           RDG+V EYEV PEDFG+AM++SRNL+V +AAESRAMLL+ L+   G   DIV LNAGAAL
Sbjct: 250 RDGEVREYEVEPEDFGLAMASSRNLRVENAAESRAMLLEALEGRRGVPHDIVCLNAGAAL 309

Query: 303 YVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ-ATA 343
           Y A VA SIA GI  AR  +A G+ARA +DA+VA T++ ATA
Sbjct: 310 YAADVAPSIAAGIELARATIASGAARAKMDAFVATTRRLATA 351


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: 439
Number of extensions: 12
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: 351
Length adjustment: 29
Effective length of query: 316
Effective length of database: 322
Effective search space:   101752
Effective search space used:   101752
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 N515DRAFT_2112 N515DRAFT_2112 (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.16635.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   6.1e-129  416.0   1.6   6.9e-129  415.8   1.6    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2112  N515DRAFT_2112 anthranilate phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2112  N515DRAFT_2112 anthranilate phosphoribosyltransferase (EC 2.4.2.18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.8   1.6  6.9e-129  6.9e-129       1     329 [.      16     343 ..      16     344 .. 0.99

  Alignments for each domain:
  == domain 1  score: 415.8 bits;  conditional E-value: 6.9e-129
                                    TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke 66 
                                                  l++ ++++++ ++e+ +lm++im+ge+s+   aAi++ lrvk et+ ei+g+a+++re a+kve+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2112  16 LQRTIEHREIFHDEMIELMRQIMRGEVSPLMTAAIITGLRVKKETIGEITGAARVMRELAEKVEAA 81 
                                                  578999************************************************************ PP

                                    TIGR01245  67 eseelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspe 132
                                                  +++++vDivGTGGDg++++NiSTas++vaaaaG++vaKhG rsvssksGsaDvLealg++++l p+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2112  82 PHAHFVDIVGTGGDGASSFNISTASMFVAAAAGARVAKHGGRSVSSKSGSADVLEALGASIDLAPA 147
                                                  ****************************************************************** PP

                                    TIGR01245 133 kvarsleevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvev 198
                                                  +va++++e++igF+fAP++hpa+k vapvRke+gvrt+fN+LGPL+nPa a++ ++Gv+++dlv +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2112 148 RVAQCMDETDIGFMFAPNHHPAMKVVAPVRKEMGVRTLFNILGPLTNPAGAPNILMGVFHPDLVGI 213
                                                  ****************************************************************** PP

                                    TIGR01245 199 laevlknlgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsa 264
                                                   ++vl++lg+++alvv g+dg+DEisl ++t v el+dge++ey+++pedfgl++a+ ++l++++a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2112 214 QVRVLQQLGARHALVVWGRDGMDEISLGASTLVGELRDGEVREYEVEPEDFGLAMASSRNLRVENA 279
                                                  ****************************************************************** PP

                                    TIGR01245 265 eenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                                  +e+ ++l e+leg+  +  +div lNa+aaly+a++a ++++g+ela+++i sg+a +k++++va
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2112 280 AESRAMLLEALEGRR-GVPHDIVCLNAGAALYAADVAPSIAAGIELARATIASGAARAKMDAFVA 343
                                                  **************9.6669***************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (351 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: 11.00
//
[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