Alignments for a candidate for aroA in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Shewanella oneidensis MR-1

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate 201548 SO2404 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI ptt file)

Query= BRENDA::Q9KRB0
         (426 letters)



>FitnessBrowser__MR1:201548
          Length = 426

 Score =  610 bits (1572), Expect = e-179
 Identities = 307/424 (72%), Positives = 344/424 (81%)

Query: 1   MESLTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKL 60
           M+ L L+P+  + GE+N+PGSKS+SNRALLLA LA GTT LTNLLDSDDIRHML +L +L
Sbjct: 1   MKQLRLEPVVQVRGEINIPGSKSISNRALLLATLAQGTTTLTNLLDSDDIRHMLASLKQL 60

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GV YRLS + T CE+ GLG    + Q   LFLGNAGTAMRPL AAL LGQG++ LTGEPR
Sbjct: 61  GVEYRLSHNNTVCELAGLGGVMSSKQAQTLFLGNAGTAMRPLCAALTLGQGEFTLTGEPR 120

Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQAGTVTIDGSISSQFLTAFLMS 180
           M+ERPIG LVDALRQ GA I YL+ + FPPL I  TGL  G V I G +SSQFLTA LM 
Sbjct: 121 MEERPIGDLVDALRQLGANIVYLKNDGFPPLTINATGLNGGDVEIVGDLSSQFLTALLMV 180

Query: 181 APLAQGKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPGQFLV 240
           APLA+G V I + GELVSKPYIDITL +M QFGV+VINH Y  F IPAGQ YVSPG+ LV
Sbjct: 181 APLAKGSVNIHVKGELVSKPYIDITLALMAQFGVKVINHHYARFEIPAGQHYVSPGKVLV 240

Query: 241 EGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVIARRG 300
           EGDASSASYFLAA AIKGGEVKVTG+G+ SIQGD++FAD LEKMGA IEWGDDY+IAR  
Sbjct: 241 EGDASSASYFLAAGAIKGGEVKVTGVGRLSIQGDVKFADVLEKMGADIEWGDDYIIARGA 300

Query: 301 ELNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMATELRKVGATV 360
            L AVDLD NHIPDAAMTIAT ALFAKGTT IRN+YNWR+KETDRLAAMATELRKVGA V
Sbjct: 301 PLTAVDLDMNHIPDAAMTIATAALFAKGTTVIRNIYNWRIKETDRLAAMATELRKVGAEV 360

Query: 361 EEGEDFIVITPPTKLIHAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCTSKTFPDYFDK 420
           EEG D+I ITPP  L  A IDTY+DHRMAMCFS++A +D  +TINDP CTSKTFPDYF +
Sbjct: 361 EEGNDYIKITPPAVLNTAQIDTYNDHRMAMCFSMLAFADCGITINDPDCTSKTFPDYFVQ 420

Query: 421 FAQL 424
           FA L
Sbjct: 421 FASL 424


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: 580
Number of extensions: 22
Number of successful extensions: 4
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: 426
Length adjustment: 32
Effective length of query: 394
Effective length of database: 394
Effective search space:   155236
Effective search space used:   155236
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 201548 SO2404 (3-phosphoshikimate 1-carboxyvinyltransferase (NCBI ptt file))
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.32192.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.6e-143  463.2   0.0   4.1e-143  463.1   0.0    1.0  1  lcl|FitnessBrowser__MR1:201548  SO2404 3-phosphoshikimate 1-carb


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201548  SO2404 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.1   0.0  4.1e-143  4.1e-143       1     412 [.      14     424 ..      14     426 .] 0.95

  Alignments for each domain:
  == domain 1  score: 463.1 bits;  conditional E-value: 4.1e-143
                       TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgg.lkepe.aeldl 75 
                                     gei+ipgsKSis+Rallla La+g+t++tnlL+s+D++ +l +l++lG++ + ++ + ++   g gg +  ++ ++l l
  lcl|FitnessBrowser__MR1:201548  14 GEINIPGSKSISNRALLLATLAQGTTTLTNLLDSDDIRHMLASLKQLGVEYRlSHnNTVCELAGLGGvMSSKQaQTLFL 92 
                                     89**************************************************54435556788888864444479**** PP

                       TIGR01356  76 gnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkggivelsgsaSs 153
                                     gn+Gt++R+l ++l+l +ge++ltg++++++RPi++lv+aLr+lga+i + +++g++Pl+i+++ l+gg ve+ g+ Ss
  lcl|FitnessBrowser__MR1:201548  93 GNAGTAMRPLCAALTLGQGEFTLTGEPRMEERPIGDLVDALRQLGANIVYLKNDGFPPLTINATgLNGGDVEIVGDLSS 171
                                     ****************************************************************9999*********** PP

                       TIGR01356 154 QyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqk.evevegDaSsAaf 231
                                     Q+++all+ apla+  v++++ g +l+s+pyi+itL+l+++fgv+v +++  ++ ++ gq+y ++ +v vegDaSsA++
  lcl|FitnessBrowser__MR1:201548 172 QFLTALLMVAPLAKGSVNIHVKG-ELVSKPYIDITLALMAQFGVKVINHHYARFEIPAGQHYVSPgKVLVEGDASSASY 249
                                     ***********999888888777.*************************99**********76666************* PP

                       TIGR01356 232 flaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqrdvevegasklkgvkvdidvdsliDelptlavlaa 310
                                     flaa+ai+g+ev+v+++g  s qgd+++++vLe+mGad+e+ ++  ++ +ga  l +v+   d+++++D+++t+a++a+
  lcl|FitnessBrowser__MR1:201548 250 FLAAGAIKGGEVKVTGVGRLSIQGDVKFADVLEKMGADIEWGDD-YIIARGA-PLTAVD--LDMNHIPDAAMTIATAAL 324
                                     ********************************************.6999975.587777..****************** PP

                       TIGR01356 311 fAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaege 389
                                     fA+g+t+i+ni ++R+kE+dR+aa+a+eL+k+G+evee++d+++i++  + l++a++dty+DHR+am++++l++a   +
  lcl|FitnessBrowser__MR1:201548 325 FAKGTTVIRNIYNWRIKETDRLAAMATELRKVGAEVEEGNDYIKITPP-AVLNTAQIDTYNDHRMAMCFSMLAFADC-G 401
                                     ************************************************.6************************998.* PP

                       TIGR01356 390 veiedaecvaksfPeFfevleql 412
                                     ++i+d+ c++k+fP++f   ++l
  lcl|FitnessBrowser__MR1:201548 402 ITINDPDCTSKTFPDYFVQFASL 424
                                     ****************9888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (426 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: 9.33
//
[ok]

This GapMind analysis is from Apr 09 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