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

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.5792.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: 00:00:00.01
# Mc/sec: 10.27
//
[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