Alignments for a candidate for aroA in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Cupriavidus basilensis 4G11

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate RR42_RS04475 RR42_RS04475 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q9KRB0
         (426 letters)



>FitnessBrowser__Cup4G11:RR42_RS04475
          Length = 436

 Score =  454 bits (1169), Expect = e-132
 Identities = 238/439 (54%), Positives = 306/439 (69%), Gaps = 16/439 (3%)

Query: 1   MESLTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKL 60
           ME LTL P    SG V LPGSKS+SNR LLLAALA G TR+ +LLDSDD R ML AL  L
Sbjct: 1   MEHLTLGPFTRASGTVRLPGSKSISNRVLLLAALAEGETRVCDLLDSDDTRVMLQALRTL 60

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GV +R   ++  C V G+G  F   +  ELF+GNAGTA+RPL AAL L  G Y L+G PR
Sbjct: 61  GVEWR--QEEGVCVVRGVGGKF-PNKAAELFMGNAGTAIRPLTAALALQGGSYKLSGVPR 117

Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQAGT-VTIDGSISSQFLTAFLM 179
           M ERPIG LVD LRQ GA + YL  E +PPL+I    ++    + + G +SSQFLTA LM
Sbjct: 118 MHERPIGDLVDGLRQIGASVAYLGTEGYPPLQISPARIRIDAPIRVRGDVSSQFLTALLM 177

Query: 180 SAPLAQGK---VTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPG 236
           + PLA      + I++VGEL+SKPY++ITL+++ +FG+++    +  F++PA  +Y SPG
Sbjct: 178 ALPLADAPGDTIEIEVVGELISKPYVEITLNLLARFGIEIRREGWSRFILPARAAYRSPG 237

Query: 237 QFLVEGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVI 296
           +  VEGDASSASYFLAA AI GG ++V G+G  SIQGD++FA+AL +MGA +  G +++ 
Sbjct: 238 EIFVEGDASSASYFLAAGAIGGGPLRVEGVGMASIQGDVKFAEALNRMGANVMAGANWIE 297

Query: 297 AR-----RGELNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMAT 351
            R      G LN ++LD NHIPDAAMT+A  ALFA+G T + N+ +WRVKETDR++AMA 
Sbjct: 298 VRGTERDDGRLNGIELDCNHIPDAAMTLAVAALFAEGPTTLTNIASWRVKETDRISAMAA 357

Query: 352 ELRKVGATVEEGEDFIVITPPTKLI----HAAIDTYDDHRMAMCFSLVALSDTPVTINDP 407
           ELRK+G  VEEG D++ +TPP +       A IDTYDDHRMAMCFSL A    PV IN+P
Sbjct: 358 ELRKLGVEVEEGADYLKVTPPAQSAWQTPAAGIDTYDDHRMAMCFSLAAFGPLPVRINEP 417

Query: 408 KCTSKTFPDYFDKFAQLSR 426
            C +KTFPDYF+ F  ++R
Sbjct: 418 GCVAKTFPDYFEVFGAVAR 436


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: 470
Number of extensions: 20
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: 436
Length adjustment: 32
Effective length of query: 394
Effective length of database: 404
Effective search space:   159176
Effective search space used:   159176
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 RR42_RS04475 RR42_RS04475 (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.15988.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-141  457.7   0.0   1.9e-141  457.6   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS04475  RR42_RS04475 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS04475  RR42_RS04475 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.6   0.0  1.9e-141  1.9e-141       1     410 [.      14     432 ..      14     436 .] 0.94

  Alignments for each domain:
  == domain 1  score: 457.6 bits;  conditional E-value: 1.9e-141
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgglkep 69 
                                               g +++pgsKSis+R+lllaaLaeget+v +lL+s+Dt+++l+alr lG++ ++e++++v++gvgg k+p
  lcl|FitnessBrowser__Cup4G11:RR42_RS04475  14 GTVRLPGSKSISNRVLLLAALAEGETRVCDLLDSDDTRVMLQALRTLGVEWRQEEGVCVVRGVGG-KFP 81 
                                               789*************************************************************8.666 PP

                                 TIGR01356  70 e..aeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlai 136
                                               +  ael +gn+Gt++R+lt++lal++g++ l+g +++++RPi++lv+ Lr++ga++ +  +eg++Pl+i
  lcl|FitnessBrowser__Cup4G11:RR42_RS04475  82 NkaAELFMGNAGTAIRPLTAALALQGGSYKLSGVPRMHERPIGDLVDGLRQIGASVAYLGTEGYPPLQI 150
                                               656****************************************************************** PP

                                 TIGR01356 137 sgp.lkg.givelsgsaSsQyksalllaaplalqa...vtleivgeklisrpyieitLkllksfgveve 200
                                               s   ++  + ++++g++SsQ+++all+a pla+ +    ++e+vg +lis+py+eitL+ll++fg+e++
  lcl|FitnessBrowser__Cup4G11:RR42_RS04475 151 SPArIRIdAPIRVRGDVSSQFLTALLMALPLADAPgdtIEIEVVG-ELISKPYVEITLNLLARFGIEIR 218
                                               *9988889**********************665441114566666.*********************** PP

                                 TIGR01356 201 eederkivvkggqkykqk.evevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGa 268
                                               +e  ++++++  ++y+++ e+ vegDaSsA++flaa+ai g+ ++ve++g++s qgd+++++ L++mGa
  lcl|FitnessBrowser__Cup4G11:RR42_RS04475 219 REGWSRFILPARAAYRSPgEIFVEGDASSASYFLAAGAIGGGPLRVEGVGMASIQGDVKFAEALNRMGA 287
                                               **99999999999999888************************************************** PP

                                 TIGR01356 269 dveveeqrdveveg....asklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRia 333
                                               +v   ++ ++ev+g       l+g++   d+++++D+++tlav+a+fAeg+t+++ni+++RvkE+dRi+
  lcl|FitnessBrowser__Cup4G11:RR42_RS04475 288 NVMAGAN-WIEVRGterdDGRLNGIE--LDCNHIPDAAMTLAVAALFAEGPTTLTNIASWRVKETDRIS 353
                                               *******.9****9875555677777..***************************************** PP

                                 TIGR01356 334 aiaeeLeklGveveeledgllieGkk.kelkg..avvdtydDHRiamalavlglaaegeveiedaecva 399
                                               a+a+eL+klGvevee++d+l++++ + + +++  a +dtydDHR+am+++++++    +v+i++++cva
  lcl|FitnessBrowser__Cup4G11:RR42_RS04475 354 AMAAELRKLGVEVEEGADYLKVTPPAqSAWQTpaAGIDTYDDHRMAMCFSLAAFGPL-PVRINEPGCVA 421
                                               *************************98666666699********************8.*********** PP

                                 TIGR01356 400 ksfPeFfevle 410
                                               k+fP++fev  
  lcl|FitnessBrowser__Cup4G11:RR42_RS04475 422 KTFPDYFEVFG 432
                                               ********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (436 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.97
//
[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