Alignments for a candidate for trpD_2 in Methyloferula stellata AR4 AR4T

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Methyloferula stellata AR4 AR4T

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_020175705.1 A3OQ_RS0112360 anthranilate phosphoribosyltransferase

Query= SwissProt::P83827
         (329 letters)



>NCBI__GCF_000385335.1:WP_020175705.1
          Length = 338

 Score =  262 bits (669), Expect = 1e-74
 Identities = 161/334 (48%), Positives = 198/334 (59%), Gaps = 12/334 (3%)

Query: 1   MDAVK----KAILGEVLEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMA 56
           MDA K    K + G  L+  EA      +++GEV+  +  G L+ L  RGE   EI    
Sbjct: 1   MDAFKPFLAKTVSGAPLDRAEARAAFDLILSGEVTQAQIGGFLIGLRQRGETVDEITGAV 60

Query: 57  RAMREAARPLRVHRRPLLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRA 116
            A+R   R +      + DIVGTGGDG G  N+STLAAL+ AA GV VAKHGNRAASS++
Sbjct: 61  SALRAQMRRVEAPGNAI-DIVGTGGDGHGTYNVSTLAALIVAACGVPVAKHGNRAASSKS 119

Query: 117 GSADLLEALGVDLEAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLL 176
           GS+D+L ALGV L   P  V   I E G GF+ A+  H AMRHVA  RAELG RT+FNLL
Sbjct: 120 GSSDVLAALGVKLGLAPADVSRCIAEAGIGFMMAQAHHEAMRHVAGARAELGTRTIFNLL 179

Query: 177 GPLTNPAGADAYVLGVFSPEWLAPMAEALERLGA-RGLVVHG-EGADEL-VLGENRVVEV 233
           GPL+NPAG    +LGVFS  WL P+AE L  LG  +  VVHG +G DE+   G  +VV +
Sbjct: 180 GPLSNPAGVKHMLLGVFSAAWLQPLAEVLRELGTEKAWVVHGADGLDEISTTGPTQVVAL 239

Query: 234 GKG---AYALTPEEVGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAG 290
             G   A+ +TPEE GL RA L  LKGG    NAA    +LKG +  P  D     + A 
Sbjct: 240 EGGKIRAFEITPEEAGLPRAALADLKGGDAAHNAAALTAVLKGAQT-PYRDIALFNSAAA 298

Query: 291 FYAAGKTPSLKEGVALAREVLASGEAYLLLERYV 324
              AGK  +L+EGVALA   L SG+A  +L R V
Sbjct: 299 LVIAGKAANLQEGVALADAALRSGKAADVLARLV 332


Lambda     K      H
   0.317    0.136    0.380 

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: 343
Number of extensions: 16
Number of successful extensions: 4
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: 329
Length of database: 338
Length adjustment: 28
Effective length of query: 301
Effective length of database: 310
Effective search space:    93310
Effective search space used:    93310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_020175705.1 A3OQ_RS0112360 (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.1275575.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-120  388.2   2.4     2e-120  388.0   2.4    1.0  1  NCBI__GCF_000385335.1:WP_020175705.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000385335.1:WP_020175705.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.0   2.4    2e-120    2e-120       2     329 ..       9     333 ..       8     334 .. 0.98

  Alignments for each domain:
  == domain 1  score: 388.0 bits;  conditional E-value: 2e-120
                             TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDi 74 
                                            k +++  L+++ea+++++ i+sge+++aqi+ +l+ lr +get++ei+g++ alr+++++ve+    +++Di
  NCBI__GCF_000385335.1:WP_020175705.1   9 AKTVSGAPLDRAEARAAFDLILSGEVTQAQIGGFLIGLRQRGETVDEITGAVSALRAQMRRVEA--PGNAIDI 79 
                                           57788999******************************************************88..699**** PP

                             TIGR01245  75 vGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlf 147
                                           vGTGGDg  t+N+ST +al++aa+Gv+vaKhGnr++ssksGs+DvL algv+l l p+ v r+++e gigF++
  NCBI__GCF_000385335.1:WP_020175705.1  80 VGTGGDGHGTYNVSTLAALIVAACGVPVAKHGNRAASSKSGSSDVLAALGVKLGLAPADVSRCIAEAGIGFMM 152
                                           ************************************************************************* PP

                             TIGR01245 148 APkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedgl 220
                                           A ++h+a+++va+ R eLg+rt+fNlLGPL+nPa +k+ +lGv+s+  ++ laevl++lg+++a vvhg+dgl
  NCBI__GCF_000385335.1:WP_020175705.1 153 AQAHHEAMRHVAGARAELGTRTIFNLLGPLSNPAGVKHMLLGVFSAAWLQPLAEVLRELGTEKAWVVHGADGL 225
                                           ************************************************************************* PP

                             TIGR01245 221 DEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaa 293
                                           DEis+tg+t+v+ l+ g+i+ ++++pe+ gl+ra l +lkgg+a++na++l++vl+g + ++ rdi ++N aa
  NCBI__GCF_000385335.1:WP_020175705.1 226 DEISTTGPTQVVALEGGKIRAFEITPEEAGLPRAALADLKGGDAAHNAAALTAVLKGAQ-TPYRDIALFNSAA 297
                                           *********************************************************98.899********** PP

                             TIGR01245 294 alyvagkakdlkegvelakeaiksgkalekleelva 329
                                           al++agka++l+egv la +a++sgka+++l++lv+
  NCBI__GCF_000385335.1:WP_020175705.1 298 ALVIAGKAANLQEGVALADAALRSGKAADVLARLVD 333
                                           *******************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (338 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.51
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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