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.20808.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.10
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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:

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:

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:

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:

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