Align 3-phosphoshikimate 1-carboxyvinyltransferase; EC 2.5.1.19 (characterized, see rationale)
to candidate WP_055435130.1 ASC41_RS02805 3-phosphoshikimate 1-carboxyvinyltransferase
Query= uniprot:I9A2E3 (408 letters) >NCBI__GCF_001418085.1:WP_055435130.1 Length = 411 Score = 309 bits (792), Expect = 9e-89 Identities = 183/406 (45%), Positives = 259/406 (63%), Gaps = 19/406 (4%) Query: 13 TTIQLPSSKSISNRALIINALGNRTFQLENLSDCDDTQVMIHALNDGKNTIDIMAAGTAM 72 + IQ+ SKS SNR L++ AL +EN+S+ DD+Q+M AL + IDI AGTAM Sbjct: 14 SAIQITGSKSESNRLLLLQALYPE-INIENVSNSDDSQLMTKALAATEQVIDIHHAGTAM 72 Query: 73 RFLTAYLSVTPGTR-IITGTQRMQQRPIQVLVNALRELGAEIEYIINDGYPPLRITGHKL 131 RFLTAY + IITG++RM++RPI++LV+AL +LGA+I Y N+GYPPL I G +L Sbjct: 73 RFLTAYFATQNNRETIITGSKRMKERPIKILVDALNQLGADISYKENEGYPPLLIKGKQL 132 Query: 132 QKDTISLPGNVSSQYISALLMIAPILSNGLTLTLTGEIISRPYINLTLQLMNDFGARAKW 191 K+ +SL NVSSQYISALL+IA L NGL LTL G+I S PYIN+TL L+++ K+ Sbjct: 133 TKNKVSLDANVSSQYISALLLIASKLENGLELTLNGKITSVPYINMTLSLLSELNIETKF 192 Query: 192 ------LNEYQLKVEPQPYQSIPFYVESDWSAASYWYQIAALSN-KAEIILPGLFETSYQ 244 + Q K+EP+ VESDWS+ASY+Y I AL+ I + + S Q Sbjct: 193 EGNVITVKPLQKKLEPK-----TLTVESDWSSASYFYSIVALAEVGTSIEISSYKKDSLQ 247 Query: 245 GDSKVAEIFQLLGIESIYGNKTVTLKKTDKITER--LDYDFINQPDLAQTFVVTCALMNI 302 GDS +AEI++ G+ +++ +K V L K +++ + +D++ N PD+AQT VT + + Sbjct: 248 GDSALAEIYKSFGVSTVFQDKGVLLTKENEVNKETAIDFNLANSPDIAQTIAVTAFALGL 307 Query: 303 PFRFSGLQSLKIKETDRMAALIQEMGKLGYILHETDDRILSWEGERCEMTADVAIDTYED 362 +GL +LKIKETDR+ AL E+ KLG + T++ + + + +VAI TY D Sbjct: 308 ESNLTGLHTLKIKETDRLEALKTEIEKLGGAVDITNETLHLKVTNK--IKENVAIATYND 365 Query: 363 HRMAMAFAPACVVMPEIRINNPQVVSKSYPYYWEDLKKAGFIIEEV 408 HRMAMAFAP + P + I + VVSKSYP +W+DLK+ GF I+ + Sbjct: 366 HRMAMAFAPLALKTP-LEIEDYMVVSKSYPTFWDDLKQLGFDIKAI 410 Lambda K H 0.320 0.135 0.391 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: 379 Number of extensions: 15 Number of successful extensions: 9 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: 408 Length of database: 411 Length adjustment: 31 Effective length of query: 377 Effective length of database: 380 Effective search space: 143260 Effective search space used: 143260 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: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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