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) (characterized)
to candidate WP_011883818.1 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q9KRB0
         (426 letters)



>NCBI__GCF_000016205.1:WP_011883818.1
          Length = 434

 Score =  503 bits (1294), Expect = e-147
 Identities = 263/436 (60%), Positives = 324/436 (74%), Gaps = 13/436 (2%)

Query: 1   MESLTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKL 60
           M+ L L P    SG V LPGSKS+SNR LLLAALA G T +TNLLDSDD R ML+AL KL
Sbjct: 1   MDYLDLGPYSSASGTVRLPGSKSISNRVLLLAALAEGETTITNLLDSDDTRVMLDALGKL 60

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GV  RL+ D  TC V G   AF T +  +LFLGNAGTA+RPL AAL +  GDY + G PR
Sbjct: 61  GV--RLTRDADTCVVAGTRGAF-TARTADLFLGNAGTAVRPLTAALAVNGGDYRVHGVPR 117

Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQAGT-VTIDGSISSQFLTAFLM 179
           M ERPIG LVD LRQ GAQI+Y + E FPPLRI+   +     + + G +SSQFLTA LM
Sbjct: 118 MHERPIGDLVDGLRQIGAQIDYEQNEGFPPLRIKPAAITVDAPIRVRGDVSSQFLTALLM 177

Query: 180 SAPLAQ---GKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPG 236
           + PL +   GK+ +++ GEL+SKPYIDIT+ +ME+FGV V    +Q FV+PAG  Y SPG
Sbjct: 178 TLPLVKAKDGKIVVEVDGELISKPYIDITIRLMERFGVTVERDGWQRFVVPAGVRYRSPG 237

Query: 237 QFLVEGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVI 296
           + +VEGDASSASYFLAA A+ GG ++V G+G+ SIQGD+ FA+AL +MGA +  GDD++ 
Sbjct: 238 RIMVEGDASSASYFLAAGALGGGPLRVEGVGRASIQGDVGFANALMQMGANVSMGDDWIE 297

Query: 297 AR-----RGELNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMAT 351
            R      G+L+ +D+DFN IPDAAMTIA  ALFA GT+ +RN+ +WRVKETDR+AAMAT
Sbjct: 298 VRGIGHDHGKLDPIDMDFNLIPDAAMTIAVAALFASGTSTLRNIASWRVKETDRIAAMAT 357

Query: 352 ELRKVGATVEEGEDFIVITPPTKLI-HAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCT 410
           ELRK+GA VEEG D++V+TPP +L  +A IDTYDDHRMAMCFSLV+L   PV INDPKC 
Sbjct: 358 ELRKLGAVVEEGPDYLVVTPPQRLTPNATIDTYDDHRMAMCFSLVSLGGVPVRINDPKCV 417

Query: 411 SKTFPDYFDKFAQLSR 426
            KTFPDYFD+FA L++
Sbjct: 418 GKTFPDYFDRFAALAK 433


Lambda     K      H
   0.318    0.135    0.384 

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: 535
Number of extensions: 25
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: 426
Length of database: 434
Length adjustment: 32
Effective length of query: 394
Effective length of database: 402
Effective search space:   158388
Effective search space used:   158388
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_011883818.1 (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.3758509.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-140  454.1   0.0   2.4e-140  453.9   0.0    1.0  1  NCBI__GCF_000016205.1:WP_011883818.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016205.1:WP_011883818.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  453.9   0.0  2.4e-140  2.4e-140       1     413 [.      14     432 ..      14     434 .] 0.96

  Alignments for each domain:
  == domain 1  score: 453.9 bits;  conditional E-value: 2.4e-140
                             TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg.lkepeae 72 
                                           g +++pgsKSis+R+lllaaLaeget++tnlL+s+Dt+++l+al klG++ +++ +++v+ g +g +   +a 
  NCBI__GCF_000016205.1:WP_011883818.1  14 GTVRLPGSKSISNRVLLLAALAEGETTITNLLDSDDTRVMLDALGKLGVRLTRDADTCVVAGTRGaFTARTAD 86 
                                           789************************************************************99788888** PP

                             TIGR01356  73 ldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkg.g 143
                                           l lgn+Gt++R+lt++la+ +g++ + g +++++RPi++lv+ Lr++ga+i+++++eg++Pl+i+   +++ +
  NCBI__GCF_000016205.1:WP_011883818.1  87 LFLGNAGTAVRPLTAALAVNGGDYRVHGVPRMHERPIGDLVDGLRQIGAQIDYEQNEGFPPLRIKPAaITVdA 159
                                           *****************************************************************9988889* PP

                             TIGR01356 144 ivelsgsaSsQyksalllaap..lalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqk 214
                                            ++++g++SsQ+++all++ p  +a++++ +  v+++lis+pyi+it+ l+++fgv+ve++  +++vv+ g  
  NCBI__GCF_000016205.1:WP_011883818.1 160 PIRVRGDVSSQFLTALLMTLPlvKAKDGKIVVEVDGELISKPYIDITIRLMERFGVTVERDGWQRFVVPAGVR 232
                                           *********************766677777888999************************999********99 PP

                             TIGR01356 215 ykqk.evevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqrdveveg.... 282
                                           y+++ ++ vegDaSsA++flaa+a+ g+ ++ve++g +s qgd+ +++ L +mGa+v++ ++ ++ev+g    
  NCBI__GCF_000016205.1:WP_011883818.1 233 YRSPgRIMVEGDASSASYFLAAGALGGGPLRVEGVGRASIQGDVGFANALMQMGANVSMGDD-WIEVRGighd 304
                                           99888*********************************************************.9*****9865 PP

                             TIGR01356 283 asklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledglli 355
                                           + kl +++  +d++ ++D+++t+av+a+fA+g+++++ni+++RvkE+dRiaa+a+eL+klG+ vee++d+l++
  NCBI__GCF_000016205.1:WP_011883818.1 305 HGKLDPID--MDFNLIPDAAMTIAVAALFASGTSTLRNIASWRVKETDRIAAMATELRKLGAVVEEGPDYLVV 375
                                           55666666..*************************************************************** PP

                             TIGR01356 356 eGkkkelkg.avvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlg 413
                                           ++ + +l + a++dtydDHR+am++++++l    +v+i+d++cv k+fP++f+  ++l 
  NCBI__GCF_000016205.1:WP_011883818.1 376 TPPQ-RLTPnATIDTYDDHRMAMCFSLVSLGGV-PVRINDPKCVGKTFPDYFDRFAALA 432
                                           ***5.77766**********************8.*******************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (434 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: 17.24
//
[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