Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19 (characterized, see rationale)
to candidate CA265_RS11640 CA265_RS11640 3-phosphoshikimate 1-carboxyvinyltransferase
Query= uniprot:L0FR45 (405 letters) >FitnessBrowser__Pedo557:CA265_RS11640 Length = 422 Score = 342 bits (877), Expect = 1e-98 Identities = 194/406 (47%), Positives = 259/406 (63%), Gaps = 25/406 (6%) Query: 17 IPLPSSKSESNRVLIVDALTEGQNQISNLAEARDTQTMIRLL----------AEDPETLD 66 I L SKSE NR LI+ AL++ ++ NL+ A DT T+ +L ++ +T+D Sbjct: 19 IQLTGSKSECNRALIISALSKKLVKVENLSNAADTVTLNGILNNLEEELEVEIQESKTVD 78 Query: 67 VLDAGTTMRFLTAYAALTNRRKTLTGTPRMCERPIGILVDALRAIGAKIEYKGKEGYPPM 126 V AGT MRFL+AY + N LTGT RM +RPIGIL +AL+ IGA I Y EG+PP+ Sbjct: 79 VGPAGTAMRFLSAYLSAKNGNFLLTGTERMKQRPIGILAEALKTIGADISYAEAEGFPPL 138 Query: 127 ETLGFEKQLTNKVQIRGDVSSQYISALLMNAPLLPEGLTLELTGKIGSKTYITMTLELMK 186 +G Q T +V+I+GD+SSQYISALLM AP+LP+GLTLE+ G++ SK Y+ MTL+++ Sbjct: 139 NIVGPLNQKTAEVKIKGDISSQYISALLMIAPILPQGLTLEIEGELTSKPYVDMTLDMLA 198 Query: 187 QFGIAYSFEGNTISIAPQSYKNTSFAVESDWSGASYWFSLLACADEGSFFLKGLKENSLQ 246 + GIA+S+ GN+ISI PQ++K + VE DWS ASYW+S+ A ADE L LKE SLQ Sbjct: 199 EVGIAHSWNGNSISIKPQAFKPGTLVVEPDWSAASYWYSIAALADEAEISLPALKEKSLQ 258 Query: 247 GDSKIVEIMDKLGVQSEFKDDGILLTKKAITGLG-------SYDFTHCPDLAQTVAVTCA 299 GDS+I IM G+ + D+GI AI+ LG D CPDLAQT+ V A Sbjct: 259 GDSQIKNIMKIFGIATSKTDNGI-----AISNLGLSLDTKEVLDLKTCPDLAQTIVVIAA 313 Query: 300 LIGQKSQFTGLESLRIKETDRIYALQQELAKFNAKLEEGENGAFTV-IPSTDIPANVTIE 358 +G+ FTGLE+L+IKETDRI ALQ ELAK L E +N +T+ + P +TI Sbjct: 314 ALGKNMAFTGLETLKIKETDRIAALQNELAKIGVTLTE-DNLVYTLNTDNLHFPDKITIA 372 Query: 359 TYDDHRMGMAFMPL-VTKTSVTLLDKEVVNKSYPSFWKHCVLAGIE 403 TY+DHRM MAF PL + V + + +VV KSYP +W+ AG + Sbjct: 373 TYEDHRMAMAFAPLALLINEVEIEEMQVVEKSYPYYWEDLKKAGFD 418 Lambda K H 0.316 0.133 0.376 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: 386 Number of extensions: 18 Number of successful extensions: 5 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: 405 Length of database: 422 Length adjustment: 31 Effective length of query: 374 Effective length of database: 391 Effective search space: 146234 Effective search space used: 146234 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate CA265_RS11640 CA265_RS11640 (3-phosphoshikimate 1-carboxyvinyltransferase)
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.24307.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-95 305.6 0.1 3.1e-95 305.4 0.1 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS11640 CA265_RS11640 3-phosphoshikimate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS11640 CA265_RS11640 3-phosphoshikimate 1-carboxyvinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 305.4 0.1 3.1e-95 3.1e-95 2 412 .. 18 415 .. 17 418 .. 0.93 Alignments for each domain: == domain 1 score: 305.4 bits; conditional E-value: 3.1e-95 TIGR01356 2 eikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgglkep 69 ei++ gsKS +Ral+++aL+++ ++v+nl +++Dt + +l++l + e + i++ lcl|FitnessBrowser__Pedo557:CA265_RS11640 18 EIQLTGSKSECNRALIISALSKKLVKVENLSNAADTVTLNGILNNLEEELE-----VEIQES------ 74 7999****************************************9987777.....666663...... PP TIGR01356 70 eaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlais 137 +++d+g +Gt++R+l++ l++ +g++ ltg e++k+RPi+ l eaL+ +ga+i+++e eg++Pl+i lcl|FitnessBrowser__Pedo557:CA265_RS11640 75 -KTVDVGPAGTAMRFLSAYLSAKNGNFLLTGTERMKQRPIGILAEALKTIGADISYAEAEGFPPLNIV 141 .58***************************************************************** PP TIGR01356 138 gp.lkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203 gp ++ + v+++g++SsQy+sall+ ap q+ tlei+g +l s+py+++tL++l++ g+ + + lcl|FitnessBrowser__Pedo557:CA265_RS11640 142 GPlNQKtAEVKIKGDISSQYISALLMIAPILPQGLTLEIEG-ELTSKPYVDMTLDMLAEVGIAHSWNG 208 **844459*********************************.*******************9999987 PP TIGR01356 204 erkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270 + +i++k+++ k+ ++ ve D S+A+++ +aa++ e e+ + l e+s+qgd +i ++++ +G lcl|FitnessBrowser__Pedo557:CA265_RS11640 209 N-SISIKPQA-FKPGTLVVEPDWSAASYWYSIAALADEaEISLPALKEKSLQGDSQIKNIMKIFGIAT 274 6.*****975.88889*************************************************998 PP TIGR01356 271 eveeqrdvevegasklkgvkv.d.idvdsliDelptlavlaafAegetriknieelRvkEsdRiaaia 336 + +++ + + + +l+ ++ + d+++++D+++t+ v+aa + +++e+l++kE+dRiaa+ lcl|FitnessBrowser__Pedo557:CA265_RS11640 275 SKTDN-GIAISN-LGLS-LDTkEvLDLKTCPDLAQTIVVIAAALGKNMAFTGLETLKIKETDRIAALQ 339 88888.699996.3443.3332337****************99999999******************* PP TIGR01356 337 eeLeklGveveeledgllieGkk.kelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfP 403 +eL+k+Gv+ +e + + + + + + ++ ty+DHR+ama+a l+l + eveie+ ++v+ks+P lcl|FitnessBrowser__Pedo557:CA265_RS11640 340 NELAKIGVTLTEDNLVYTLNTDNlHFPDKITIATYEDHRMAMAFAPLALLIN-EVEIEEMQVVEKSYP 406 ************999999999986666679*********************8.*************** PP TIGR01356 404 eFfevleql 412 +++e+l++ lcl|FitnessBrowser__Pedo557:CA265_RS11640 407 YYWEDLKKA 415 *****9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (422 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: 12.24 // [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