Alignments for a candidate for aroA in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Acidovorax sp. GW101-3H11

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate Ac3H11_2576 5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) / Cytidylate kinase (EC 2.7.4.25)

Query= BRENDA::Q9KRB0
         (426 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2576
          Length = 676

 Score =  436 bits (1120), Expect = e-126
 Identities = 240/435 (55%), Positives = 309/435 (71%), Gaps = 22/435 (5%)

Query: 4   LTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKLGVN 63
           L L P++  +GEV+LPGSKS+SNR LLLAAL++GTT + +LL SDD R ML+AL ++G  
Sbjct: 7   LDLPPLQAAAGEVHLPGSKSISNRVLLLAALSNGTTTVHDLLASDDTRVMLDALRQIGCT 66

Query: 64  YRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPRMKE 123
             +    +T  + GLG     + P +LFLGNAGTAMRPL AAL L  G++ L+G PRM E
Sbjct: 67  --VDEAGSTVRITGLGGRLPQS-PAKLFLGNAGTAMRPLTAALALLGGEFELSGVPRMHE 123

Query: 124 RPIGHLVDALRQAGAQIEYLEQENFPPLRI-QGTGLQ----AGTVTIDGSISSQFLTAFL 178
           RPIG L+DALRQ G QI+YL  E +PPL+I  G G+     A  + + G +SSQFLTA L
Sbjct: 124 RPIGDLIDALRQLGCQIDYLGNEGYPPLKIAHGQGVPSLALAEPIRVRGDVSSQFLTALL 183

Query: 179 MSAPLAQGK--VTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPG 236
           M+ PLA G   + I++VGEL+SKPYI ITL ++ +FG+ V + ++Q F IPAG  Y SPG
Sbjct: 184 MALPLAAGTQAIVIEVVGELISKPYIAITLQLLARFGIVVGHQNWQRFTIPAGSRYQSPG 243

Query: 237 QFLVEGDASSASYFLAAAAIK-GGE----VKVTGIGKNSIQGDIQFADALEKMGAQIEWG 291
              VE DASSASYF+A  AI  GGE    +K+ G+G +SIQGDI+F +A   MGA +  G
Sbjct: 244 SIHVEADASSASYFIALGAIATGGEAQKSIKIQGVGLDSIQGDIRFVEAARAMGAVVTGG 303

Query: 292 DDYVIARRGE--LNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAM 349
            +++   RG   L A++LD NHIPDAAMT+A  AL+A+GTT + N+ +WRVKETDR+AAM
Sbjct: 304 PNWLQIERGAWPLKAIELDCNHIPDAAMTLAVMALYAEGTTTLTNIASWRVKETDRIAAM 363

Query: 350 ATELRKVGATVEEGEDFIVITPPTKLIH---AAIDTYDDHRMAMCFSLVALSDT--PVTI 404
           ATELRK+GATVEEG D+I +TPPT+      A+I TYDDHR+AMCFSL A +    PV I
Sbjct: 364 ATELRKLGATVEEGADYIRVTPPTQAADWKAASIHTYDDHRVAMCFSLAAFNPARLPVRI 423

Query: 405 NDPKCTSKTFPDYFD 419
            DPKC +KTFPDYF+
Sbjct: 424 EDPKCVAKTFPDYFE 438


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: 692
Number of extensions: 26
Number of successful extensions: 12
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: 676
Length adjustment: 35
Effective length of query: 391
Effective length of database: 641
Effective search space:   250631
Effective search space used:   250631
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: 52 (24.6 bits)

Align candidate Ac3H11_2576 (5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) / Cytidylate kinase (EC 2.7.4.25))
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.8491.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   4.6e-136  439.8   0.0   5.9e-136  439.5   0.0    1.1  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2576  5-Enolpyruvylshikimate-3-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2576  5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) / Cytidyla
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.5   0.0  5.9e-136  5.9e-136       1     412 [.      17     443 ..      17     446 .. 0.94

  Alignments for each domain:
  == domain 1  score: 439.5 bits;  conditional E-value: 5.9e-136
                                        TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelvieg 62 
                                                      ge+++pgsKSis+R+lllaaL++g+t+v++lL s+Dt+++l+alr++G +v e++ ++ i+g
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2576  17 GEVHLPGSKSISNRVLLLAALSNGTTTVHDLLASDDTRVMLDALRQIGCTVDEAGSTVRITG 78 
                                                      799*************************************************99******** PP

                                        TIGR01356  63 vgglkepe..aeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgae 122
                                                       gg + p+  a+l lgn+Gt++R+lt++lal++ge++l+g +++++RPi++l++aLr+lg++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2576  79 LGG-RLPQspAKLFLGNAGTAMRPLTAALALLGGEFELSGVPRMHERPIGDLIDALRQLGCQ 139
                                                      **9.5555559*************************************************** PP

                                        TIGR01356 123 ieskeeegslPlaisgp.....lkg.givelsgsaSsQyksalllaap..lalqavtleivg 176
                                                      i++  +eg++Pl+i  +     l + + ++++g++SsQ+++all+a p    +qa  +e+vg
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2576 140 IDYLGNEGYPPLKIAHGqgvpsLALaEPIRVRGDVSSQFLTALLMALPlaAGTQAIVIEVVG 201
                                                      **************644476776667999*******************53345566667777 PP

                                        TIGR01356 177 eklisrpyieitLkllksfgveveeederkivvkggqkykqk.evevegDaSsAafflaaaa 237
                                                       +lis+pyi itL+ll++fg+ v +++ ++++++ g  y+++ +++ve+DaSsA++f+a++a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2576 202 -ELISKPYIAITLQLLARFGIVVGHQNWQRFTIPAGSRYQSPgSIHVEADASSASYFIALGA 262
                                                      .************************999********9988888******************* PP

                                        TIGR01356 238 itge.....evtvenlgenstqgdkaiiivLeemGadveveeqrdveveg.asklkgvkvdi 293
                                                      i+ +      ++++++g +s qgd ++++  ++mGa v+   + ++++e+ a  lk+++   
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2576 263 IATGgeaqkSIKIQGVGLDSIQGDIRFVEAARAMGAVVTGGPN-WLQIERgAWPLKAIE--L 321
                                                      *876566678*********************************.9***98677888888..* PP

                                        TIGR01356 294 dvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledglli 355
                                                      d+++++D+++tlav+a++Aeg+t+++ni+++RvkE+dRiaa+a+eL+klG++vee++d++ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2576 322 DCNHIPDAAMTLAVMALYAEGTTTLTNIASWRVKETDRIAAMATELRKLGATVEEGADYIRV 383
                                                      ************************************************************** PP

                                        TIGR01356 356 eGkk..kelkgavvdtydDHRiamalavlglaae.geveiedaecvaksfPeFfevleql 412
                                                      ++ +  + +k a+++tydDHR+am+++++++  +  +v+ied++cvak+fP++fe+l ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2576 384 TPPTqaADWKAASIHTYDDHRVAMCFSLAAFNPArLPVRIEDPKCVAKTFPDYFEALFSV 443
                                                      ***99999***********************98868*******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (676 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: 10.96
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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