Alignments for a candidate for aroA in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Shewanella amazonensis SB2B

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate 6937579 Sama_1734 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq)

Query= BRENDA::Q9KRB0
         (426 letters)



>FitnessBrowser__SB2B:6937579
          Length = 428

 Score =  606 bits (1563), Expect = e-178
 Identities = 299/426 (70%), Positives = 348/426 (81%)

Query: 1   MESLTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKL 60
           M+ L L+P+  ++G VN+PGSKS+SNRALLLA LASG T L NLLDSDDIRHMLNAL  L
Sbjct: 1   MDQLRLEPVSRVNGVVNIPGSKSISNRALLLATLASGETTLVNLLDSDDIRHMLNALKSL 60

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GVN+ LS DKT C + GLG    T +  ELFLGNAGTAMRPL AAL LG G++ LTGEPR
Sbjct: 61  GVNFTLSDDKTVCTLNGLGGPIQTDKAFELFLGNAGTAMRPLCAALTLGTGEFTLTGEPR 120

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

Query: 181 APLAQGKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPGQFLV 240
           APLA+G VTI + GELVSKPYIDITL +M +FGV V+N +YQ F I +GQ YVSPG+ LV
Sbjct: 181 APLAKGAVTIAVKGELVSKPYIDITLDLMAKFGVTVVNDNYQRFEIASGQHYVSPGKVLV 240

Query: 241 EGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVIARRG 300
           EGDASSASYFLAA AI GGEVKVTG+G+ ++QGD++FADAL  MGA IEWG+DY+IAR  
Sbjct: 241 EGDASSASYFLAAGAIGGGEVKVTGVGRLAVQGDVKFADALAAMGADIEWGEDYIIARGS 300

Query: 301 ELNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMATELRKVGATV 360
           +L+ +D+D NHIPDAAMTIAT ALFA+GTT + N+YNWR+KETDRLAAMATELRKVGA V
Sbjct: 301 KLHGIDMDMNHIPDAAMTIATAALFAEGTTRMSNIYNWRIKETDRLAAMATELRKVGAKV 360

Query: 361 EEGEDFIVITPPTKLIHAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCTSKTFPDYFDK 420
           EEG D+I ITPP K +HA IDTY+DHRMAMCFSL+A +D  VTINDP CTSKTFPDYF++
Sbjct: 361 EEGHDYIQITPPVKPVHAEIDTYNDHRMAMCFSLLAFADCGVTINDPGCTSKTFPDYFNR 420

Query: 421 FAQLSR 426
           FA L++
Sbjct: 421 FANLAK 426


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: 561
Number of extensions: 19
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: 428
Length adjustment: 32
Effective length of query: 394
Effective length of database: 396
Effective search space:   156024
Effective search space used:   156024
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 6937579 Sama_1734 (3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq))
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.11706.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.2e-144  466.7   0.0   3.6e-144  466.6   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937579  Sama_1734 3-phosphoshikimate 1-c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937579  Sama_1734 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.6   0.0  3.6e-144  3.6e-144       1     413 [.      14     425 ..      14     427 .. 0.95

  Alignments for each domain:
  == domain 1  score: 466.6 bits;  conditional E-value: 3.6e-144
                         TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgg.lkepe.ael 73 
                                       g ++ipgsKSis+Rallla La+get++ nlL+s+D++ +l+al++lG++++ ++ k +++ +g gg +++ +  el
  lcl|FitnessBrowser__SB2B:6937579  14 GVVNIPGSKSISNRALLLATLASGETTLVNLLDSDDIRHMLNALKSLGVNFTlSDdKTVCTLNGLGGpIQTDKaFEL 90 
                                       679*************************************************744477888999999755555689* PP

                         TIGR01356  74 dlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkggivelsg 149
                                        lgn+Gt++R+l ++l+l  ge++ltg++++++RPi++lv+aLr+lga+i++ +++g++Pl+i+++ l gg+ve++g
  lcl|FitnessBrowser__SB2B:6937579  91 FLGNAGTAMRPLCAALTLGTGEFTLTGEPRMEERPIGDLVDALRQLGADIRYLKNDGFPPLTINATgLAGGVVEIDG 167
                                       *****************999*********************************************98999******* PP

                         TIGR01356 150 saSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqk.evevegD 225
                                       s SsQ+++all+ apla+ avt+ + g +l+s+pyi+itL+l+++fgv+v +++ +++ +  gq+y ++ +v vegD
  lcl|FitnessBrowser__SB2B:6937579 168 SLSSQFLTALLMVAPLAKGAVTIAVKG-ELVSKPYIDITLDLMAKFGVTVVNDNYQRFEIASGQHYVSPgKVLVEGD 243
                                       ******************999999988.*************************99**********76666******* PP

                         TIGR01356 226 aSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqrdvevegasklkgvkvdidvdsliDel 302
                                       aSsA++flaa+ai g+ev+v+++g    qgd+++++ L +mGad+e+ e+  ++ +g skl+g++  +d+++++D++
  lcl|FitnessBrowser__SB2B:6937579 244 ASSASYFLAAGAIGGGEVKVTGVGRLAVQGDVKFADALAAMGADIEWGED-YIIARG-SKLHGID--MDMNHIPDAA 316
                                       **************************************************.588885.78*****..********** PP

                         TIGR01356 303 ptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamal 379
                                       +t+a++a+fAeg+tr+ ni ++R+kE+dR+aa+a+eL+k+G++vee++d+++i++   +   a++dty+DHR+am++
  lcl|FitnessBrowser__SB2B:6937579 317 MTIATAALFAEGTTRMSNIYNWRIKETDRLAAMATELRKVGAKVEEGHDYIQITPPV-KPVHAEIDTYNDHRMAMCF 392
                                       ********************************************************6.5556*************** PP

                         TIGR01356 380 avlglaaegeveiedaecvaksfPeFfevleqlg 413
                                       ++l++a   +v+i+d++c++k+fP++f+  ++l 
  lcl|FitnessBrowser__SB2B:6937579 393 SLLAFADC-GVTINDPGCTSKTFPDYFNRFANLA 425
                                       *****997.******************9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (428 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: 10.79
//
[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