Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19 (characterized, see rationale)
to candidate 8501011 DvMF_1748 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq)
Query= uniprot:Q72EV5_DESVH (439 letters) >FitnessBrowser__Miya:8501011 Length = 450 Score = 620 bits (1599), Expect = 0.0 Identities = 315/445 (70%), Positives = 349/445 (78%), Gaps = 7/445 (1%) Query: 2 EPVVVTAPPSKSLSHRALIGAALAAGESTVEHVLESRDLTCTADILRAAGAHIERRAPGS 61 E V V APPSKS+SHR LIGAALAAG+S VEHVLESRD+ TADILRAAGA IER+ G Sbjct: 6 ETVTVAAPPSKSVSHRMLIGAALAAGDSVVEHVLESRDIERTADILRAAGARIERQGDGR 65 Query: 62 YLVRGVAGTPAGGFEAPVSCDVHESGTTCRLLTAVLAAGMGRFRIHGAPRMHERPIGELT 121 + V GVAGTPAGGF+APVSCDVHESGTTCRLLTAVLAAG G+FRIHGAPRMHERPIGEL Sbjct: 66 FAVSGVAGTPAGGFDAPVSCDVHESGTTCRLLTAVLAAGKGQFRIHGAPRMHERPIGELV 125 Query: 122 DALASLGVQIAFEARAGFPPLVIDAAGMRGGEVSIGMDESSQYLSGLLLAAPLTQGMTVN 181 D L GV++ +E R G PPL+ID+ GM GG +IG+ ESSQYLSGLLLAAPLT G+T+ Sbjct: 126 DVLRGRGVRVTYEGREGCPPLLIDSDGMSGGSTAIGLGESSQYLSGLLLAAPLTSGLTIE 185 Query: 182 VAGKSVVSWPYVGLTLQTLEDFGIDFTVETRDAVDAPWGAVDWRSLHEAVPGLVRFRVRP 241 V+G VVSWPYV LTLQ LEDFGI F VETR+ W A DWR L E PGLVRF V P Sbjct: 186 VSGDKVVSWPYVALTLQALEDFGIGFRVETRETPRGKWQADDWRMLREVRPGLVRFVVSP 245 Query: 242 GMYRAGSYRVEGDWSGASYFLAAGAVGPRPVRVEGLRVDSLQGDRALLDILTAMGADIRP 301 G+YRAG+YRVEGDWS ASYFLAAGAVGPRPVRV GLRVDSLQGDRA+LDIL MGA Sbjct: 246 GVYRAGNYRVEGDWSNASYFLAAGAVGPRPVRVAGLRVDSLQGDRAMLDILGRMGARFER 305 Query: 302 GEGHVVVHPAPLHGVEVDMGHCPDLVPTVAAVAAFATGRTVVRNVAHLRIKESDRIAAPV 361 + VVV P+ L GVEVDMGHCPDLVPTVAA AAFA G T +RNVAHLRIKE DR++AP Sbjct: 306 ADNGVVVAPSSLTGVEVDMGHCPDLVPTVAATAAFAQGVTTIRNVAHLRIKECDRLSAPA 365 Query: 362 GELRRAGVNAEERADGLVVQGGALATEPGTL-------FSAHGDHRMAMSLALLGLGGVD 414 ELR+AGV EE DGL+V G + P + F ++GDHRMAMSLALLG GV Sbjct: 366 AELRKAGVRVEELDDGLIVHGSLRSGGPAPVIDEKVMPFLSYGDHRMAMSLALLGFAGVH 425 Query: 415 VRLDDPSCVSKSFPHFWELWEKVRA 439 V LDDP+CV+KSFPHFW WEKVRA Sbjct: 426 VVLDDPACVAKSFPHFWNEWEKVRA 450 Lambda K H 0.320 0.137 0.413 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: 715 Number of extensions: 30 Number of successful extensions: 2 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: 439 Length of database: 450 Length adjustment: 32 Effective length of query: 407 Effective length of database: 418 Effective search space: 170126 Effective search space used: 170126 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 (21.8 bits) S2: 51 (24.3 bits)
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