GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroA in Shewanella loihica PV-4

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate 5209482 Shew_1952 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq)

Query= BRENDA::Q9KRB0
         (426 letters)



>FitnessBrowser__PV4:5209482
          Length = 426

 Score =  595 bits (1535), Expect = e-175
 Identities = 300/426 (70%), Positives = 339/426 (79%)

Query: 1   MESLTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKL 60
           M+ L L PI  + G VN+PGSKS+SNRALLLA LA G TRLTNLLDSDDIRHML AL +L
Sbjct: 1   MKQLRLNPISKVHGTVNIPGSKSISNRALLLATLAEGKTRLTNLLDSDDIRHMLTALKQL 60

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GVNY+LS +   CEVEGL    ++     LFLGNAGTAMRPL AAL LG G++ LTGEPR
Sbjct: 61  GVNYQLSDNNRVCEVEGLSGVINSDTAQTLFLGNAGTAMRPLCAALTLGSGEFTLTGEPR 120

Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQAGTVTIDGSISSQFLTAFLMS 180
           M+ERPIG LVDAL   GA I YL+Q  FPPL I  TGL  G V I G +SSQFLTA LM 
Sbjct: 121 MEERPIGDLVDALNALGADIRYLKQPGFPPLTINATGLNGGDVEIAGDLSSQFLTALLMV 180

Query: 181 APLAQGKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPGQFLV 240
            PLA+ +V IKI GELVSKPYIDIT+ +M QFGV VINHDYQ F IPAGQ YVSPG  LV
Sbjct: 181 TPLAKAQVNIKIKGELVSKPYIDITIALMAQFGVTVINHDYQRFEIPAGQKYVSPGTVLV 240

Query: 241 EGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVIARRG 300
           EGDASSASYFLAA AI+GGEVKVTG+G  SIQGD++FA+ LE MGAQIEWGDD++IAR  
Sbjct: 241 EGDASSASYFLAAGAIQGGEVKVTGVGLKSIQGDVKFAEVLEAMGAQIEWGDDFIIARSA 300

Query: 301 ELNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMATELRKVGATV 360
            L+ VDLD NHIPDAAMTIAT ALFA GTT +RN+YNWR+KETDRLAAMATELRKVGA V
Sbjct: 301 PLHGVDLDMNHIPDAAMTIATAALFATGTTTLRNIYNWRIKETDRLAAMATELRKVGAEV 360

Query: 361 EEGEDFIVITPPTKLIHAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCTSKTFPDYFDK 420
           EEG D+I +T P +L  A IDTY+DHRMAMCFSL+A +D  +TINDP CTSKTFPDYF +
Sbjct: 361 EEGHDYIRVTAPAQLNTADIDTYNDHRMAMCFSLMAFADCGITINDPDCTSKTFPDYFAQ 420

Query: 421 FAQLSR 426
           FA L++
Sbjct: 421 FAALAQ 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: 606
Number of extensions: 26
Number of successful extensions: 3
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 5209482 Shew_1952 (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.32168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.9e-143  464.1   0.0   2.2e-143  464.0   0.0    1.0  1  lcl|FitnessBrowser__PV4:5209482  Shew_1952 3-phosphoshikimate 1-c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209482  Shew_1952 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.0   0.0  2.2e-143  2.2e-143       1     412 [.      14     424 ..      14     426 .] 0.96

  Alignments for each domain:
  == domain 1  score: 464.0 bits;  conditional E-value: 2.2e-143
                        TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgglkepe..aeld 74 
                                      g ++ipgsKSis+Rallla Laeg+t++tnlL+s+D++ +l al++lG++ + ++ + ++ +eg  g+  ++  ++l 
  lcl|FitnessBrowser__PV4:5209482  14 GTVNIPGSKSISNRALLLATLAEGKTRLTNLLDSDDIRHMLTALKQLGVNYQlSDnNRVCEVEGLSGVINSDtaQTLF 91 
                                      789***********************************************99755477789***99944444579*** PP

                        TIGR01356  75 lgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkggivelsgsa 151
                                      lgn+Gt++R+l ++l+l sge++ltg++++++RPi++lv+aL++lga+i++ ++ g++Pl+i+++ l+gg ve++g+ 
  lcl|FitnessBrowser__PV4:5209482  92 LGNAGTAMRPLCAALTLGSGEFTLTGEPRMEERPIGDLVDALNALGADIRYLKQPGFPPLTINATgLNGGDVEIAGDL 169
                                      *****************************************************************9999********* PP

                        TIGR01356 152 SsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqk.evevegDaSs 228
                                      SsQ+++all+  pla+ +v+++i g +l+s+pyi+it++l+++fgv+v ++d +++ ++ gqky ++ +v vegDaSs
  lcl|FitnessBrowser__PV4:5209482 170 SSQFLTALLMVTPLAKAQVNIKIKG-ELVSKPYIDITIALMAQFGVTVINHDYQRFEIPAGQKYVSPgTVLVEGDASS 246
                                      **********************999.*************************************77666********** PP

                        TIGR01356 229 AafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqrdvevegasklkgvkvdidvdsliDelptla 306
                                      A++flaa+ai+g+ev+v+++g +s qgd+++++vLe+mGa++e+ ++ +++ + +  l+gv+   d+++++D+++t+a
  lcl|FitnessBrowser__PV4:5209482 247 ASYFLAAGAIQGGEVKVTGVGLKSIQGDVKFAEVLEAMGAQIEWGDD-FIIAR-SAPLHGVD--LDMNHIPDAAMTIA 320
                                      ***********************************************.89999.678****9..************** PP

                        TIGR01356 307 vlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlgl 384
                                      ++a+fA g+t+++ni ++R+kE+dR+aa+a+eL+k+G+evee++d++ ++   ++l++a +dty+DHR+am+++++++
  lcl|FitnessBrowser__PV4:5209482 321 TAALFATGTTTLRNIYNWRIKETDRLAAMATELRKVGAEVEEGHDYIRVTAP-AQLNTADIDTYNDHRMAMCFSLMAF 397
                                      ****************************************************.6************************ PP

                        TIGR01356 385 aaegeveiedaecvaksfPeFfevleql 412
                                      a   +++i+d+ c++k+fP++f   ++l
  lcl|FitnessBrowser__PV4:5209482 398 ADC-GITINDPDCTSKTFPDYFAQFAAL 424
                                      998.******************998876 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: 00:00:00.02
# Mc/sec: 7.71
//
[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:

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:

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:

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:

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