Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_044411821.1 NA59_RS09995 citrate synthase
Query= BRENDA::P31660 (389 letters) >NCBI__GCF_000934765.1:WP_044411821.1 Length = 397 Score = 243 bits (620), Expect = 7e-69 Identities = 134/379 (35%), Positives = 220/379 (58%), Gaps = 13/379 (3%) Query: 22 LSGVPAGNTALCTVGKSGNDLHYRGYDILDLAKHCEFEEVAHLLIHGKLPTRDELAAYKT 81 L+GVPA + + + L YRGYDI++LA+ FEE LL+ G+LPT ELA + Sbjct: 7 LAGVPATESKISYIDGQKGVLTYRGYDIMELAEKSSFEETTLLLLFGELPTTSELADFDQ 66 Query: 82 KLKALRGLPANVRTVLEALPAASHPMDVMRTGVSALGCTLPEKE---GHTVSGA--RDIA 136 +L+ R + N+R +++ LP +HPM +++ V++L P E G T + D+ Sbjct: 67 QLRDHRRVKYNIREIMKNLPETTHPMHMLQVVVASLASFYPSTEYMKGGTENQGYINDVT 126 Query: 137 DKLLASLSSILLYWYHYSHNGERIQPETDDDSIGGHFLHLLHGEKPSQSWEKAMHISLVL 196 K++A +++++ W H + + I+P D + +FL+++ GE+P W + + L+L Sbjct: 127 VKIIAHMATLVASWEHMRNGYDPIEPRKDLN-YAENFLYMVTGEEPDPDWARLLDACLIL 185 Query: 197 YAEHEFNASTFTSRVIAGTGSDMYSAIIGAIGALRGPKHGGANEVSLEIQQRYETPDEAE 256 +AEH NASTFT+ V T ++ S I AI +L GP HGGAN++ +E+ ++ P+ A Sbjct: 186 HAEHTINASTFTTMVTGSTLANPCSVISSAIASLSGPLHGGANQMVIEMLEKIGRPENAR 245 Query: 257 ADIRKRVENKEVVIGFGHPVYTIADPRHQVIKRVAKQL----SQEGGSLKMYNIADRLET 312 A I R+ NK+V+ G GH Y DPR ++++++++L S+ G M+ A +E Sbjct: 246 AYIEDRLANKKVIWGMGHREYKTKDPRATILQKLSEKLLTKKSKSGELSVMFETALEVER 305 Query: 313 VMWE---SKKMFPNLDWFSAVSYNMMGVPTEMFTPLFVIARVTGWAAHIIEQRQDNKIIR 369 + E K ++PN+D++S + Y MG +MFT +F +AR GW AH EQ Q+NKI R Sbjct: 306 ICEELLGHKGVYPNVDFYSGILYKEMGFDPKMFTSIFAVARSAGWMAHWREQLQNNKIFR 365 Query: 370 PSANYVGPEDRPFVALDKR 388 P+ Y G + ++ LD+R Sbjct: 366 PTQVYTGAGNSCYLPLDQR 384 Lambda K H 0.317 0.134 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: 389 Number of extensions: 19 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: 389 Length of database: 397 Length adjustment: 31 Effective length of query: 358 Effective length of database: 366 Effective search space: 131028 Effective search space used: 131028 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