Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate 7024797 Shewana3_1975 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq)
Query= BRENDA::Q9KRB0 (426 letters) >FitnessBrowser__ANA3:7024797 Length = 426 Score = 610 bits (1574), Expect = e-179 Identities = 306/424 (72%), Positives = 344/424 (81%) Query: 1 MESLTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKL 60 M+ L L+P+ + GE+N+PGSKS+SNRALLLA LA GTT LTNLLDSDDIRHML +L +L Sbjct: 1 MKQLRLEPVVQVRGEINIPGSKSISNRALLLATLAKGTTTLTNLLDSDDIRHMLASLKQL 60 Query: 61 GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120 GV YRLS + T CE+ GLG + LFLGNAGTAMRPL AAL LG+G++ LTGEPR Sbjct: 61 GVEYRLSQNNTVCELTGLGGVISSDTAQTLFLGNAGTAMRPLCAALTLGRGEFTLTGEPR 120 Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQAGTVTIDGSISSQFLTAFLMS 180 M+ERPIG LVDAL+Q GA I YL+ + FPPL I TGL G V I G +SSQFLTA LM Sbjct: 121 MEERPIGDLVDALKQLGANIVYLKNDGFPPLTINATGLNGGDVEIAGDLSSQFLTALLMV 180 Query: 181 APLAQGKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPGQFLV 240 APLA+G V I + GELVSKPYIDITL +M QFGVQVINHDY F IPAGQ YVSPG+ LV Sbjct: 181 APLAKGSVNIHVKGELVSKPYIDITLALMAQFGVQVINHDYARFEIPAGQQYVSPGKVLV 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 PLTAVDLDMNHIPDAAMTIATAALFAKGTTTIRNIYNWRIKETDRLAAMATELRKVGALV 360 Query: 361 EEGEDFIVITPPTKLIHAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCTSKTFPDYFDK 420 EEG D+I ITPP L A IDTY+DHRMAMCFS++A +D +TINDP CTSKTFPDYF + Sbjct: 361 EEGHDYIQITPPVVLNTAEIDTYNDHRMAMCFSMMAFADCGITINDPDCTSKTFPDYFAQ 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: 585 Number of extensions: 23 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 7024797 Shewana3_1975 (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.15381.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-143 462.6 0.0 6.5e-143 462.4 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7024797 Shewana3_1975 3-phosphoshikimate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7024797 Shewana3_1975 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 462.4 0.0 6.5e-143 6.5e-143 1 413 [. 14 425 .. 14 426 .] 0.95 Alignments for each domain: == domain 1 score: 462.4 bits; conditional E-value: 6.5e-143 TIGR01356 1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgglkepe..ael 73 gei+ipgsKSis+Rallla La+g+t++tnlL+s+D++ +l +l++lG++ + ++ + ++ +g gg+ ++ ++l lcl|FitnessBrowser__ANA3:7024797 14 GEINIPGSKSISNRALLLATLAKGTTTLTNLLDSDDIRHMLASLKQLGVEYRlSQnNTVCELTGLGGVISSDtaQTL 90 89*************************************************964435566789999844444579** PP TIGR01356 74 dlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkggivelsg 149 lgn+Gt++R+l ++l+l +ge++ltg++++++RPi++lv+aL++lga+i + +++g++Pl+i+++ l+gg ve++g lcl|FitnessBrowser__ANA3:7024797 91 FLGNAGTAMRPLCAALTLGRGEFTLTGEPRMEERPIGDLVDALKQLGANIVYLKNDGFPPLTINATgLNGGDVEIAG 167 ******************************************************************9999******* PP TIGR01356 150 saSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqk.evevegD 225 + SsQ+++all+ apla+ v++++ g +l+s+pyi+itL+l+++fgv+v ++d ++ ++ gq+y ++ +v vegD lcl|FitnessBrowser__ANA3:7024797 168 DLSSQFLTALLMVAPLAKGSVNIHVKG-ELVSKPYIDITLALMAQFGVQVINHDYARFEIPAGQQYVSPgKVLVEGD 243 ***************999888888777.*************************************76666******* PP TIGR01356 226 aSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemGadveveeqrdvevegasklkgvkvdidvdsliDel 302 aSsA++flaa+ai+g+ev+v+++g s qgd+++++vLe+mGad+e+ ++ ++ +ga l +v+ d+++++D++ lcl|FitnessBrowser__ANA3:7024797 244 ASSASYFLAAGAIKGGEVKVTGVGRLSIQGDVKFADVLEKMGADIEWGDD-YIIARGA-PLTAVD--LDMNHIPDAA 316 **************************************************.6999975.587777..********** PP TIGR01356 303 ptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamal 379 +t+a++a+fA+g+t+i+ni ++R+kE+dR+aa+a+eL+k+G+ vee++d+++i++ l++a++dty+DHR+am++ lcl|FitnessBrowser__ANA3:7024797 317 MTIATAALFAKGTTTIRNIYNWRIKETDRLAAMATELRKVGALVEEGHDYIQITPP-VVLNTAEIDTYNDHRMAMCF 392 ********************************************************.6******************* PP TIGR01356 380 avlglaaegeveiedaecvaksfPeFfevleqlg 413 +++++a +++i+d+ c++k+fP++f ++l+ lcl|FitnessBrowser__ANA3:7024797 393 SMMAFADC-GITINDPDCTSKTFPDYFAQFASLK 425 *****997.*******************999886 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: 10.72 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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