Alignments for a candidate for trpD_2 in Desulfuromonas acetexigens

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Desulfuromonas acetexigens

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_092056124.1 BQ4888_RS07920 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>NCBI__GCF_900111775.1:WP_092056124.1
          Length = 349

 Score =  286 bits (732), Expect = 5e-82
 Identities = 154/345 (44%), Positives = 215/345 (62%), Gaps = 12/345 (3%)

Query: 8   ALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREF 67
           A+ + +E +++   EM+ +M QIM GE + A ++A +T LR+K ET+ EI GAA VMR+ 
Sbjct: 5   AIAKIVERKDLTETEMIAVMDQIMGGEATPAQIAAFITALRMKGETVDEITGAARVMRDR 64

Query: 68  SRRVEV------------TDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGN 115
           +  + V             D+  ++D+VGTGGDG++TFNIST   FV AA G KVAKHGN
Sbjct: 65  ATPIRVGKVLDIDREDINLDQETILDVVGTGGDGTNTFNISTTVSFVVAACGVKVAKHGN 124

Query: 116 RSVSSKSGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGV 175
           RSVSS  GSAD LE LG  +++ PE+V   + + GIGF++AP  H AMK     R+E+G+
Sbjct: 125 RSVSSLCGSADVLEKLGVNLDVTPEKVEECIRELGIGFLFAPALHGAMKYAIGPRKEVGI 184

Query: 176 RTIFNILGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGA 235
           RTIFNILGPLTNPAG+   ++GV+   LV   A+VL  LG  R  VV+G DGMDE++L  
Sbjct: 185 RTIFNILGPLTNPAGADCQVLGVYQEALVEPLAQVLARLGCRRGFVVYGMDGMDEITLTG 244

Query: 236 GTLVGELRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVA 295
            T V E+RDG+V  + + PEDFG++      L+  +A  +  ++  VL     P  D+V 
Sbjct: 245 PTRVAEIRDGKVKVFTIEPEDFGLSRCPMSALQGGNAVGNAEIVRSVLQGETSPRRDVVL 304

Query: 296 LNAGAALYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340
           LNA  AL  AG A+ I  G+  AR+ + +G A A +DA    T +
Sbjct: 305 LNAAYALVAAGAAEDIPAGLALAREAIDEGRALAKVDALAGMTNE 349


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: 311
Number of extensions: 16
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 WP_092056124.1 BQ4888_RS07920 (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.8921.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     7e-131  422.4   0.9   1.6e-130  421.2   0.9    1.5  1  lcl|NCBI__GCF_900111775.1:WP_092056124.1  BQ4888_RS07920 anthranilate phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900111775.1:WP_092056124.1  BQ4888_RS07920 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.2   0.9  1.6e-130  1.6e-130       2     328 ..       7     344 ..       6     346 .. 0.95

  Alignments for each domain:
  == domain 1  score: 421.2 bits;  conditional E-value: 1.6e-130
                                 TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekee... 67 
                                                k++++kdL+e+e+ ++m++im gea++aqiaA+++alr+kget++ei+g+a+++r++a+ +++ +   
  lcl|NCBI__GCF_900111775.1:WP_092056124.1   7 AKIVERKDLTETEMIAVMDQIMGGEATPAQIAAFITALRMKGETVDEITGAARVMRDRATPIRVGKvld 75 
                                               799********************************************************9887532111 PP

                                 TIGR01245  68 .........seelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnl 127
                                                        +e ++D+vGTGGDg++t+NiST+ ++v+aa+GvkvaKhGnrsvss +GsaDvLe+lgvnl
  lcl|NCBI__GCF_900111775.1:WP_092056124.1  76 idredinldQETILDVVGTGGDGTNTFNISTTVSFVVAACGVKVAKHGNRSVSSLCGSADVLEKLGVNL 144
                                               1112222226789******************************************************** PP

                                 TIGR01245 128 elspekvarsleevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlv 196
                                               +++pekv+++++e+gigFlfAP+ h a+k++++ Rke+g+rt+fN+LGPL+nPa a+ qvlGvy++ lv
  lcl|NCBI__GCF_900111775.1:WP_092056124.1 145 DVTPEKVEECIRELGIGFLFAPALHGAMKYAIGPRKEVGIRTIFNILGPLTNPAGADCQVLGVYQEALV 213
                                               ********************************************************************* PP

                                 TIGR01245 197 evlaevlknlgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsae 265
                                               e la+vl +lg +r +vv g dg+DEi+ltg+t+vae++dg+++ +t++pedfgl r+++++l+gg+a 
  lcl|NCBI__GCF_900111775.1:WP_092056124.1 214 EPLAQVLARLGCRRGFVVYGMDGMDEITLTGPTRVAEIRDGKVKVFTIEPEDFGLSRCPMSALQGGNAV 282
                                               ********************************************************************* PP

                                 TIGR01245 266 enaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelv 328
                                                nae++++vl+g+  +++rd+v+lNaa al++ag+a+d+ +g+ la+eai++g+al+k+++l+
  lcl|NCBI__GCF_900111775.1:WP_092056124.1 283 GNAEIVRSVLQGET-SPRRDVVLLNAAYALVAAGAAEDIPAGLALAREAIDEGRALAKVDALA 344
                                               ************99.889***************************************998876 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 3.76
//
[ok]

This GapMind analysis is from Apr 10 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