Alignments for a candidate for trpD_2 in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Magnetospirillum magneticum AMB-1

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_011385239.1 AMB_RS14410 anthranilate phosphoribosyltransferase

Query= SwissProt::P83827
         (329 letters)



>NCBI__GCF_000009985.1:WP_011385239.1
          Length = 346

 Score =  260 bits (665), Expect = 3e-74
 Identities = 162/335 (48%), Positives = 204/335 (60%), Gaps = 15/335 (4%)

Query: 3   AVKKAILGEV-----LEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMAR 57
           A+ K ILG V     L E +A EV   +M+G+ +P +  GLL+ L +RGE   EI   AR
Sbjct: 9   ALMKEILGRVAVGASLSETQAEEVFEIIMSGDATPAQIGGLLLGLRVRGETVEEITGAAR 68

Query: 58  AMREAARPLRVHRRP-LLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRA 116
            MR  A+ L++   P  +DIVGTGGD  G  N+ST A+ V AA GV VAKHGNRA SS++
Sbjct: 69  IMR--AKALKIEAPPGSVDIVGTGGDEAGTFNISTAASFVVAACGVPVAKHGNRAVSSKS 126

Query: 117 GSADLLEALGVDLEAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLL 176
           G++D+L ALGV+++A    V E + E   GFL A   H AMRHVA  R ELG RT+FNLL
Sbjct: 127 GASDVLTALGVNIDADFALVHETLWENKVGFLMAPRHHNAMRHVAGPRGELGTRTIFNLL 186

Query: 177 GPLTNPAGADAYVLGVFSPEWLAPMAEALERLGA-RGLVVHG-EGADEL-VLGENRVVEV 233
           GPL+NPAG    V+GVF+  W+ P+A  L RLGA    VVHG +G DEL   G  RV E 
Sbjct: 187 GPLSNPAGTTRQVVGVFAERWVEPLARVLGRLGAEHAWVVHGTDGLDELTTTGPTRVAEY 246

Query: 234 GKG---AYALTPEEVGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAG 290
             G    +++TPEEVGLKRA    LKGG    NAA  + LLKGE+ G   D V L A A 
Sbjct: 247 KGGEVRLFSVTPEEVGLKRAAPADLKGGDSATNAAAMKALLKGEQ-GAYRDIVVLNAAAA 305

Query: 291 FYAAGKTPSLKEGVALAREVLASGEAYLLLERYVA 325
              AGK  +L +G   A + +  GEA  +L R +A
Sbjct: 306 LVVAGKVDTLGDGARAAEQAIDRGEAEAVLHRMIA 340


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: 358
Number of extensions: 21
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: 346
Length adjustment: 28
Effective length of query: 301
Effective length of database: 318
Effective search space:    95718
Effective search space used:    95718
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_011385239.1 AMB_RS14410 (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.30369.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-122  393.0   0.8   6.8e-122  392.8   0.8    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011385239.1  AMB_RS14410 anthranilate phospho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011385239.1  AMB_RS14410 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.8   0.8  6.8e-122  6.8e-122       3     329 ..      17     340 ..      15     341 .. 0.98

  Alignments for each domain:
  == domain 1  score: 392.8 bits;  conditional E-value: 6.8e-122
                                 TIGR01245   3 klldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseel 71 
                                               +++ + +Lse++ae++++ imsg+a++aqi+ +l  lrv+get+eei+g+a+++r+ka k+e+      
  lcl|NCBI__GCF_000009985.1:WP_011385239.1  17 RVAVGASLSETQAEEVFEIIMSGDATPAQIGGLLLGLRVRGETVEEITGAARIMRAKALKIEA--PPGS 83 
                                               5666789******************************************************88..6999 PP

                                 TIGR01245  72 vDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarslee 140
                                               vDivGTGGD++ t+NiSTa+++v+aa+Gv+vaKhGnr+vssksG++DvL algvn++++ + v+++l e
  lcl|NCBI__GCF_000009985.1:WP_011385239.1  84 VDIVGTGGDEAGTFNISTAASFVVAACGVPVAKHGNRAVSSKSGASDVLTALGVNIDADFALVHETLWE 152
                                               ********************************************************************* PP

                                 TIGR01245 141 vgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvk 209
                                               + +gFl+AP++h+a+++va+ R eLg+rt+fNlLGPL+nPa  ++qv+Gv+ +  ve la+vl +lg++
  lcl|NCBI__GCF_000009985.1:WP_011385239.1 153 NKVGFLMAPRHHNAMRHVAGPRGELGTRTIFNLLGPLSNPAGTTRQVVGVFAERWVEPLARVLGRLGAE 221
                                               ********************************************************************* PP

                                 TIGR01245 210 ralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegk 278
                                               +a vvhg dglDE+++tg+t+vae k ge++ ++++pe+ glkra   +lkgg+ + na+++k++l+g+
  lcl|NCBI__GCF_000009985.1:WP_011385239.1 222 HAWVVHGTDGLDELTTTGPTRVAEYKGGEVRLFSVTPEEVGLKRAAPADLKGGDSATNAAAMKALLKGE 290
                                               ****************************************************************99999 PP

                                 TIGR01245 279 ekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                               + +a rdivvlNaaaal+vagk+++l +g+++a++ai+ g+a ++l++++a
  lcl|NCBI__GCF_000009985.1:WP_011385239.1 291 Q-GAYRDIVVLNAAAALVVAGKVDTLGDGARAAEQAIDRGEAEAVLHRMIA 340
                                               8.9*******************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (346 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: 10.40
//
[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