Alignments for a candidate for trpD_2 in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Sinorhizobium meliloti 1021

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate SMc00235 SMc00235 anthranilate phosphoribosyltransferase

Query= SwissProt::P83827
         (329 letters)



>FitnessBrowser__Smeli:SMc00235
          Length = 337

 Score =  263 bits (672), Expect = 5e-75
 Identities = 150/331 (45%), Positives = 195/331 (58%), Gaps = 7/331 (2%)

Query: 4   VKKAILGEVLEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAA 63
           V K    E L  E+A      +M+G  +P +  G L+AL +RGE   EI     AMR   
Sbjct: 8   VAKVAAREALSREDARAAFEIIMSGAATPSQIGGFLMALRVRGETVDEIVGAVGAMRARM 67

Query: 64  RPLRVHRRPLLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLE 123
            P+      + DIVGTGGDG G  N+STLAAL+ A  GV VAKHGNRA SS++G+AD L 
Sbjct: 68  LPVEAPDGAI-DIVGTGGDGAGTYNISTLAALIVAGAGVPVAKHGNRALSSKSGTADALS 126

Query: 124 ALGVDLEAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPA 183
            LGV+L+  P  +   I E G GF+FA+  H AMRHV P R ELG RT+FNLLGPL NPA
Sbjct: 127 CLGVNLDIGPAVISRCIAEAGLGFMFAQQHHSAMRHVGPTRVELGTRTIFNLLGPLANPA 186

Query: 184 GADAYVLGVFSPEWLAPMAEALERLGARGL-VVHGEGADEL-VLGENRVVEVGKGA---Y 238
           G    ++GV++P+W+ P+AE L  LG+  + VVHGEG DE+   G  +V  +  G    +
Sbjct: 187 GVRQQLVGVYAPQWVDPLAEVLRDLGSESVWVVHGEGLDEITTTGVTKVAALKDGTITNF 246

Query: 239 ALTPEEVGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTP 298
            LTP + GL+R  L+ALKGG    NAA  + +L G E     D     A A    AG+  
Sbjct: 247 ELTPADFGLERVSLDALKGGDGAHNAAALQAVLDGAENA-YRDISLANAAASLMIAGRAG 305

Query: 299 SLKEGVALAREVLASGEAYLLLERYVAFLRA 329
            L EG+ALAR+ L+SG A + L+R +    A
Sbjct: 306 DLSEGMALARQSLSSGGAKVALQRLITVSNA 336


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: 318
Number of extensions: 18
Number of successful extensions: 5
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: 337
Length adjustment: 28
Effective length of query: 301
Effective length of database: 309
Effective search space:    93009
Effective search space used:    93009
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 SMc00235 SMc00235 (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.21669.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.2e-120  387.9   1.0   2.4e-120  387.7   1.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc00235  SMc00235 anthranilate phosphorib


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00235  SMc00235 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.7   1.0  2.4e-120  2.4e-120       2     328 ..       9     331 ..       8     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 387.7 bits;  conditional E-value: 2.4e-120
                           TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivG 76 
                                          k++ ++ Ls+e+a+++++ imsg a+++qi+ +l+alrv+get++ei+g++ a+r+++  ve+   + ++DivG
  lcl|FitnessBrowser__Smeli:SMc00235   9 AKVAAREALSREDARAAFEIIMSGAATPSQIGGFLMALRVRGETVDEIVGAVGAMRARMLPVEA--PDGAIDIVG 81 
                                         588999********************************************************88..79******* PP

                           TIGR01245  77 TGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPky 151
                                         TGGDg+ t+NiST +al++a+aGv+vaKhGnr+ ssksG aD L+ lgvnl++ p+ + r+++e g+gF+fA ++
  lcl|FitnessBrowser__Smeli:SMc00235  82 TGGDGAGTYNISTLAALIVAGAGVPVAKHGNRALSSKSGTADALSCLGVNLDIGPAVISRCIAEAGLGFMFAQQH 156
                                         *************************************************************************** PP

                           TIGR01245 152 hpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEislt 226
                                         h+a+++v p+R eLg+rt+fNlLGPL+nPa ++ q++Gvy ++ v+ laevl+ lg++ + vvhg +glDEi++t
  lcl|FitnessBrowser__Smeli:SMc00235 157 HSAMRHVGPTRVELGTRTIFNLLGPLANPAGVRQQLVGVYAPQWVDPLAEVLRDLGSESVWVVHG-EGLDEITTT 230
                                         *****************************************************************.********* PP

                           TIGR01245 227 getkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagka 301
                                         g tkva lkdg+i++++l+p+dfgl+r +l++lkgg+ ++na++l++vl g e +a rdi ++Naaa l++ag+a
  lcl|FitnessBrowser__Smeli:SMc00235 231 GVTKVAALKDGTITNFELTPADFGLERVSLDALKGGDGAHNAAALQAVLDGAE-NAYRDISLANAAASLMIAGRA 304
                                         ***************************************************99.899****************** PP

                           TIGR01245 302 kdlkegvelakeaiksgkalekleelv 328
                                          dl+eg+ la+++++sg a   l++l+
  lcl|FitnessBrowser__Smeli:SMc00235 305 GDLSEGMALARQSLSSGGAKVALQRLI 331
                                         ********************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (337 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: 10.45
//
[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