Alignments for a candidate for aroA in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Burkholderia vietnamiensis G4

Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS (uncharacterized)
to candidate WP_011882219.1 3-phosphoshikimate 1-carboxyvinyltransferase

Query= curated2:A0B7Z0
         (421 letters)



>NCBI__GCF_000016205.1:WP_011882219.1
          Length = 460

 Score =  229 bits (584), Expect = 1e-64
 Identities = 161/429 (37%), Positives = 233/429 (54%), Gaps = 20/429 (4%)

Query: 9   SISGTVCAPPSKSYTHRAVLITALSD-SGCVHRPLISADTRATISACDAFGADVKLRGDS 67
           S+ G    P SK  T RA+L   L+D +  VH  L   +T A   AC A GA +      
Sbjct: 15  SLKGYAVTPSSKPETQRAILAATLADGTSIVHNDLRCVETSAMKQACRALGARIDEHAGY 74

Query: 68  LEIQGVSGAPRTPENVIDVLNSGTTLRFMSAVAALTDG-AVLTGDSSIRSRPNGPLLKAL 126
           LEI+GV  A    + V+D + SG   R  +A+ +  D  A++TGD+ +R+R   PL  AL
Sbjct: 75  LEIRGVGRALHLGQRVVDAIGSGLVFRTFTALTSFADSPAIITGDTILRTRVMKPLFDAL 134

Query: 127 NELGAEAFSIRGNDRAPLVI-RGRLRGGSTSLDGSVSSQFLSALLIACPLSSGETTISIK 185
            ELGA    I    +AP+V   G LRGG  ++ G+VSSQF++A+L A PL+     I+I+
Sbjct: 135 EELGARIECIGEAGKAPVVNWGGGLRGGRCTVPGNVSSQFITAILFAAPLADKPVEIAIE 194

Query: 186 GELKSRPYAEMTLDILRKAG--AEICTDGDIFRMRGGQSYRLAEYTVPGDFSSASYPLAA 243
           GEL S  Y   T+  LR +G   ++  D  + R++ G +Y+ AEY + GD++S+SY + A
Sbjct: 195 GELLSISYIRQTIATLRHSGIQVDVTDDFSLIRVQPG-NYQAAEYRIGGDYTSSSYLIGA 253

Query: 244 AALAGSATVEGLFPSR--QGDSAIVDILREMGAEVSWDMESGEVRV--SGADLRG-REID 298
           AAL     V G   S   QG+ AI+D+++ +G  V +D    E+ +  S + L G  E D
Sbjct: 254 AALFPGTFVLGNLGSESLQGERAIIDVVQALGLSVHFDDTRNELTLVNSHSQLTGDYEFD 313

Query: 299 ASQTPDLVPTLAVLGAVAEGRTVIKNAEHVRHKETDRIHAMAVELKKMGANIRER----- 353
           AS  P++VPTLA +GA  +G   +      R  ++ RI AM  EL KMG +I+       
Sbjct: 314 ASDFPNIVPTLAAIGAYVKGTFRVVGGSITRLHKSPRIKAMVSELGKMGVDIKGLFKDGV 373

Query: 354 PDGLEIDG-GDLH--GADLHGYHDHRIVMALTLAGIVAGD-TRIDTAESVDVSYPGFFED 409
            DG EI G G+ +  G DL  + DHRI M+L +A + A    R++    V+ S+P FF  
Sbjct: 374 YDGFEIRGTGEPYPGGVDLSSWGDHRIFMSLFIASLRARQPNRLEGYRDVNCSFPDFFTQ 433

Query: 410 MRRLGANVR 418
              LGA  R
Sbjct: 434 FEHLGAAYR 442


Lambda     K      H
   0.316    0.133    0.375 

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: 441
Number of extensions: 35
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: 421
Length of database: 460
Length adjustment: 32
Effective length of query: 389
Effective length of database: 428
Effective search space:   166492
Effective search space used:   166492
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_011882219.1 (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.17445.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.9e-94  302.2   0.0    3.3e-94  302.0   0.0    1.0  1  lcl|NCBI__GCF_000016205.1:WP_011882219.1  3-phosphoshikimate 1-carboxyviny


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016205.1:WP_011882219.1  3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.0   0.0   3.3e-94   3.3e-94       5     414 ..      22     439 ..      18     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: 302.0 bits;  conditional E-value: 3.3e-94
                                 TIGR01356   5 ipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg.lkepeae 72 
                                                p+sK  ++Ra+l+a La+g+++v+n L++  t a+ +a+r+lGa++ e+ + l i+gvg  l+  +++
  lcl|NCBI__GCF_000016205.1:WP_011882219.1  22 TPSSKPETQRAILAATLADGTSIVHNDLRCVETSAMKQACRALGARIDEHAGYLEIRGVGRaLHLGQRV 90 
                                               59**********************************************99*********9999999*** PP

                                 TIGR01356  73 ldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.l 140
                                               +d+  sG ++R  t++ ++a+++ ++tgd  l+ R +++l +aL+elga+ie+  e+g++P++  g+ l
  lcl|NCBI__GCF_000016205.1:WP_011882219.1  91 VDAIGSGLVFRTFTALTSFADSPAIITGDTILRTRVMKPLFDALEELGARIECIGEAGKAPVVNWGGgL 159
                                               **************************************************************9988889 PP

                                 TIGR01356 141 kggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede.rkiv 208
                                               +gg  ++ g++SsQ+++a+l+aapla+++v++ i+g +l+s +yi++t+++l++ g++v+++d+ + i+
  lcl|NCBI__GCF_000016205.1:WP_011882219.1 160 RGGRCTVPGNVSSQFITAILFAAPLADKPVEIAIEG-ELLSISYIRQTIATLRHSGIQVDVTDDfSLIR 227
                                               99*********************************9.***************************9**** PP

                                 TIGR01356 209 vkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqr. 276
                                               v++g+ y+  e+++ gD+ s ++++ aaa+ +++ ++ nlg++s+qg++aii+v++++G +v+++++r 
  lcl|NCBI__GCF_000016205.1:WP_011882219.1 228 VQPGN-YQAAEYRIGGDYTSSSYLIGAAALFPGTFVLGNLGSESLQGERAIIDVVQALGLSVHFDDTRn 295
                                               ***98.88888*******************************************************999 PP

                                 TIGR01356 277 .dvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGv 344
                                                 + v+++s+l g   + d++++++ +ptla+++a+ +g+ r+ + +  R++ s Ri+a+++eL k+Gv
  lcl|NCBI__GCF_000016205.1:WP_011882219.1 296 eLTLVNSHSQLTGDY-EFDASDFPNIVPTLAAIGAYVKGTFRVVGGSITRLHKSPRIKAMVSELGKMGV 363
                                               655566688886544.9**************************************************** PP

                                 TIGR01356 345 eveel.....edgllieGkk.kelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfe 407
                                               +++ l      dg++i+G+      g  +++++DHRi m+l +++l+a+++ ++e+   v+ sfP+Ff 
  lcl|NCBI__GCF_000016205.1:WP_011882219.1 364 DIKGLfkdgvYDGFEIRGTGePYPGGVDLSSWGDHRIFMSLFIASLRARQPNRLEGYRDVNCSFPDFFT 432
                                               **85322223899******8556666899**************************************** PP

                                 TIGR01356 408 vleqlga 414
                                                 e+lga
  lcl|NCBI__GCF_000016205.1:WP_011882219.1 433 QFEHLGA 439
                                               **99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (460 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 13.03
//
[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