Alignments for a candidate for aroA in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Desulfatibacillum aliphaticivorans DSM 15576

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_028315505.1 G491_RS0117440 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::A2T9R8
         (514 letters)



>NCBI__GCF_000429905.1:WP_028315505.1
          Length = 419

 Score =  295 bits (755), Expect = 2e-84
 Identities = 175/430 (40%), Positives = 255/430 (59%), Gaps = 15/430 (3%)

Query: 82  QLVLQPIKQISGTVRLPGSKSISNRVLLLAALAEGTTVVKNLLDSDDIRYMVGALKGLGI 141
           Q+ ++P+ +   T  +PGSKS ++R+L+ AALA+G + VKN L S+D    + AL  +G+
Sbjct: 4   QITIRPMGKTELTAMVPGSKSYTHRMLICAALADGLSQVKNGLVSEDTLLTMNALNKMGV 63

Query: 142 ELEERWDKGEMVVKGCGGQFSAEGGELFLGNAGTAMRPLTAAVAAAGRGKFVLDGTARMR 201
            +  R + G   V G GG        + LGN+GT +R L  AVAA G G + L GT RM+
Sbjct: 64  SV--RREGGGFWVNGSGGSLDRYEDPIHLGNSGTTLR-LMCAVAAMGVGTYTLTGTERMQ 120

Query: 202 ERPIQDLVDGLVQLGVDAKCPLGTGCPPVEVNAQGLPSGKVQLKGSVSSQYLTALLMAAP 261
           +RPI DL   L QLGV  +     GCPP+++    +  GKV +   VSSQYL+ALL+ AP
Sbjct: 121 QRPILDLAQALEQLGVPVETT--NGCPPIKIQGTAVKGGKVSINCGVSSQYLSALLLIAP 178

Query: 262 LSKGTEGIEIVITDELVSQPYVDMTVQIMERFGVTVERLNGLQHMRIPPNQTYKTSGEAF 321
            ++  +G+EI +T+  VS+PY+DMTV +M+  GV ++R +G     +P    Y+ +GE  
Sbjct: 179 YTQ--DGMEITVTEGPVSKPYIDMTVSVMKAMGVEIKR-DGHTWFSVPGQSQYQ-AGEYM 234

Query: 322 VEGDASSASYFLAGATITGGTVVVEGCGSASVQGDVRFAEVMGLMGAKVEWSLYSIKITG 381
           VE DAS ASYF   A ITG T+ V G  SAS QGD RFA ++  MG +++ +   + +  
Sbjct: 235 VEADASGASYFWGAAAITGATIRVAGTHSASCQGDSRFAYILKSMGCRLDETNEGLAVA- 293

Query: 382 PSAFGKPLQGIDHDCNDIPDAAMTLAVAALFADKPTTIRNVYNWRVKETERMVAIVNETR 441
               G+ L+GI  D  ++PD A TLAV A FA   T I NV + + KE++R+ A++ E +
Sbjct: 294 ----GRDLKGITVDMGNMPDVAPTLAVVAAFAKGETRIENVGHLKAKESDRITAVITELK 349

Query: 442 KLGATVEEGRDYCVITPPKQIQSAAIDTYDDHRMAMAFSLAACGPVPVTINDPGCTRKTF 501
           K+G       D   I   K  Q A IDTYDDHR+AM+F++A      V I +P C  K+F
Sbjct: 350 KMGVQASCTDDSMTIIGGKP-QGAVIDTYDDHRIAMSFAVAGLLTPGVIIKNPSCVDKSF 408

Query: 502 PDYFRVLESV 511
           P+++   E +
Sbjct: 409 PNFWEEWEKL 418


Lambda     K      H
   0.318    0.134    0.388 

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: 549
Number of extensions: 27
Number of successful extensions: 8
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: 514
Length of database: 419
Length adjustment: 33
Effective length of query: 481
Effective length of database: 386
Effective search space:   185666
Effective search space used:   185666
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: 51 (24.3 bits)

Align candidate WP_028315505.1 G491_RS0117440 (3-phosphoshikimate 1-carboxyvinyltransferase)
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

# 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/TIGR01356.hmm
# target sequence database:        /tmp/gapView.13623.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01356  [M=415]
Accession:   TIGR01356
Description: aroA: 3-phosphoshikimate 1-carboxyvinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-138  447.4   0.0   2.8e-138  447.1   0.0    1.0  1  lcl|NCBI__GCF_000429905.1:WP_028315505.1  G491_RS0117440 3-phosphoshikimat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429905.1:WP_028315505.1  G491_RS0117440 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.1   0.0  2.8e-138  2.8e-138       4     412 ..      18     418 ..      15     419 .] 0.97

  Alignments for each domain:
  == domain 1  score: 447.1 bits;  conditional E-value: 2.8e-138
                                 TIGR01356   4 kipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg.lkepea 71 
                                                +pgsKS++hR+l+ aaLa+g ++v+n L seDtl t++al+k+G++v++e++ + ++g gg l + e+
  lcl|NCBI__GCF_000429905.1:WP_028315505.1  18 MVPGSKSYTHRMLICAALADGLSQVKNGLVSEDTLLTMNALNKMGVSVRREGGGFWVNGSGGsLDRYED 86 
                                               58**********************************************************99999999* PP

                                 TIGR01356  72 eldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp. 139
                                                ++lgnsGtt+Rl+ +v+a+  g+++ltg e++++RPi +l +aL++lg+ +e ++  g++P++i+g+ 
  lcl|NCBI__GCF_000429905.1:WP_028315505.1  87 PIHLGNSGTTLRLMCAVAAMGVGTYTLTGTERMQQRPILDLAQALEQLGVPVETTN--GCPPIKIQGTa 153
                                               *******************888*******************************876..8*********9 PP

                                 TIGR01356 140 lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkiv 208
                                               +kgg+v +++ +SsQy+salll ap+++++ ++++++  ++s+pyi++t+ ++k+ gve++++ ++ ++
  lcl|NCBI__GCF_000429905.1:WP_028315505.1 154 VKGGKVSINCGVSSQYLSALLLIAPYTQDGMEITVTE-GPVSKPYIDMTVSVMKAMGVEIKRDGHTWFS 221
                                               999**********************999888888777.99**********************9998888 PP

                                 TIGR01356 209 vkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqrd 277
                                               v+g+ +y+  e+ ve+DaS A++f  aaaitg +++v + +++s qgd +++++L++mG++++ +++  
  lcl|NCBI__GCF_000429905.1:WP_028315505.1 222 VPGQSQYQAGEYMVEADASGASYFWGAAAITGATIRVAGTHSASCQGDSRFAYILKSMGCRLDETNE-G 289
                                               8888889999*********************************************************.7 PP

                                 TIGR01356 278 vevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGvev 346
                                               + v g ++lkg++  +d+ +++D +ptlav+aafA+getri+n+ +l++kEsdRi a+ +eL+k+Gv++
  lcl|NCBI__GCF_000429905.1:WP_028315505.1 290 LAVAG-RDLKGIT--VDMGNMPDVAPTLAVVAAFAKGETRIENVGHLKAKESDRITAVITELKKMGVQA 355
                                               ****6.68*****..****************************************************** PP

                                 TIGR01356 347 eeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleql 412
                                                 + d+++i G+  + +gav+dtydDHRiam++av+gl    +v+i++++cv+ksfP+F+e +e+l
  lcl|NCBI__GCF_000429905.1:WP_028315505.1 356 SCTDDSMTIIGG--KPQGAVIDTYDDHRIAMSFAVAGLLTP-GVIIKNPSCVDKSFPNFWEEWEKL 418
                                               ************..6*************************9.********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (419 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.82
//
[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