Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_018231851.1 THITHI_RS0104340 2-methylcitrate synthase
Query= BRENDA::Q2Z1A8 (398 letters) >NCBI__GCF_000378965.1:WP_018231851.1 Length = 385 Score = 611 bits (1576), Expect = e-179 Identities = 286/382 (74%), Positives = 334/382 (87%) Query: 16 TASEPAAPRVKKSVALSGVTAGNTALCTVGRTGNDLHYRGYDILDIAETCEFEEIAHLLV 75 T + PR KKSVALSG AGNTA+CTVGRTGNDLHYRGYDILD A+ EFEEIAHLL+ Sbjct: 4 TDTTQTKPRPKKSVALSGTVAGNTAICTVGRTGNDLHYRGYDILDFADKAEFEEIAHLLI 63 Query: 76 HGKLPTKSELAAYKAKLKSLRGLPANVKAALEWVPASAHPMDVMRTGVSVLGTVLPEKED 135 HG LP ++ELAAYK +L++LRGLPA ++ LE +P SAHPMDVMRT VS+LGT+ PEKED Sbjct: 64 HGTLPDRAELAAYKERLRALRGLPAALRTVLEQIPPSAHPMDVMRTAVSMLGTLEPEKED 123 Query: 136 HNTPGARDIADRLMASLGSMLLYWYHYSHNGRRIEVETDDDSIGGHFLHLLHGEKPSALW 195 GAR I DRL+ASLGS LLYWYH++HNGRRI+VETDDDS+GGHFLHL+HG PS W Sbjct: 124 MTVAGARQIGDRLLASLGSALLYWYHFAHNGRRIDVETDDDSLGGHFLHLMHGRAPSEPW 183 Query: 196 ERAMHTSLNLYAEHEFNASTFTARVIAGTGSDMYSSISGAIGALRGPKHGGANEVAFEIQ 255 RAMHTSLNLYAEHEFNASTFT+RV+AGT +D+YS+I+GAIGALRGPKHGGANEVA +IQ Sbjct: 184 VRAMHTSLNLYAEHEFNASTFTSRVVAGTNADLYSAITGAIGALRGPKHGGANEVACDIQ 243 Query: 256 KRYDNPDEAQADITRRVGNKEVVIGFGHPVYTTGDPRNQVIKEVAKKLSKDAGSMKMFDI 315 RYD+PD+A+ADI RVG KE++IGFGHPVYTTGDPRN+VIK VAK+LS+D +M MF + Sbjct: 244 LRYDDPDQAEADIRERVGRKEIIIGFGHPVYTTGDPRNEVIKAVAKRLSEDRHTMTMFAV 303 Query: 316 AERLETVMWDIKKMFPNLDWFSAVSYHMMGVPTAMFTPLFVIARTSGWAAHIIEQRIDNK 375 A+RLE+VMWD+KKMFPNLDWFSAVSYHMMG+PTA+FTP+FVI+RT+GW AH+IEQR+D K Sbjct: 304 ADRLESVMWDLKKMFPNLDWFSAVSYHMMGIPTALFTPIFVISRTTGWVAHVIEQRLDGK 363 Query: 376 IIRPSANYTGPENLKFVPIGKR 397 IIRPSANYTGPEN K+VPI KR Sbjct: 364 IIRPSANYTGPENRKWVPIDKR 385 Lambda K H 0.317 0.133 0.396 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: 555 Number of extensions: 15 Number of successful extensions: 1 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: 398 Length of database: 385 Length adjustment: 31 Effective length of query: 367 Effective length of database: 354 Effective search space: 129918 Effective search space used: 129918 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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