Align (R)-citramalate synthase (EC 2.3.1.182) (characterized)
to candidate WP_066328410.1 BLR17_RS00960 2-isopropylmalate synthase
Query= reanno::Btheta:351386 (499 letters) >NCBI__GCF_900100165.1:WP_066328410.1 Length = 507 Score = 601 bits (1550), Expect = e-176 Identities = 297/498 (59%), Positives = 383/498 (76%), Gaps = 2/498 (0%) Query: 1 MDTTLRDGEQTSGVSFVPHEKLMIARLLLEDLKVDRVEVASARVSEGEFEAVKMICDWAA 60 MDTTLRDGEQTSGVSF EKL IA+LLLE+L+VDR+E+ASARVSEGEFE VK I WA Sbjct: 9 MDTTLRDGEQTSGVSFSAAEKLTIAQLLLEELQVDRIEIASARVSEGEFEGVKGIMTWAE 68 Query: 61 RRNLLQKVEVLGFVDGHTSVDWIQRTGCRVINLLCKGSLKHCTQQLKKTPEEHIADIINV 120 + K+EVL FVD S++W++++G +V NLL KGSL H T QLKKTPE+H ++I Sbjct: 69 TKGYTDKIEVLTFVDKGLSIEWMKKSGAKVQNLLTKGSLNHLTHQLKKTPEQHFSEIAES 128 Query: 121 VHYADEQDIGVNVYLEDWSNGMKDSPEYVFQLMDGLKQTSIRRYMLPDTLGILNPLQVIE 180 + A E I NVYLEDWSNGM++S EYV+Q +D + ++R +LPDTLG+L P + E Sbjct: 129 IALATENGIATNVYLEDWSNGMRNSSEYVYQYLDFISTQPVKRILLPDTLGVLIPSETFE 188 Query: 181 YMRKMKKRYPNTHFDFHAHNDYDLAVSNVLAAVLSGVRGLHTTINGLGERAGNAPLSSVQ 240 Y+ ++ KRYPN HFDFHAHNDYDL+V+NV+ A+ +GV GLH T+NG+GERAGNAPL+S Sbjct: 189 YISEITKRYPNIHFDFHAHNDYDLSVANVMEALKAGVHGLHVTVNGMGERAGNAPLASTI 248 Query: 241 AILKDHFNAM-TNIDESRLNDVSRVVESYSGIVIPANKPIVGENVFTQVAGVHADGDNKN 299 A++ D + + E+ L VS++VE+++G IPANKPIVG+NVFTQ AG+HADGDNKN Sbjct: 249 AVINDFMPEIEIGVKETSLYSVSKLVETFTGYRIPANKPIVGDNVFTQTAGIHADGDNKN 308 Query: 300 NLYCNDLLPERFGRKREYALGKTSGKANIRKNLEDLGLELDEDAMRKVTERIIELGDKKE 359 NLY NDLLPERFGRKR+YALGKTSGKANI KNL++LGL+L+++ ++ VT+RIIELGDKKE Sbjct: 309 NLYFNDLLPERFGRKRKYALGKTSGKANIEKNLQELGLQLNQEDLKLVTQRIIELGDKKE 368 Query: 360 LVTQEDLPYIVSDVLKHGAIGEKVKLKSYFVNLAHGLKPMATLKIEINGKEYEESSSGDG 419 VT+EDLPYI+SDVL EK+ ++SY ++ A G++P TL ++I+G+ EE + GDG Sbjct: 369 TVTKEDLPYIISDVLDSHTYQEKITVESYLLSHAKGMRPSTTLCLKIDGQIIEEHAQGDG 428 Query: 420 QYDAFVRALRKIYKVTLGRKFPMLTNYAVSIPPGGRTDAFVQTVITWNYDEQVFRTRGLD 479 Q+DAF+ AL KIYK T P L +YAV IPPG +DA +T+ITW D + F+TRGLD Sbjct: 429 QFDAFMNALAKIYK-TKKMTLPKLIDYAVRIPPGSSSDALCETIITWVNDGKEFKTRGLD 487 Query: 480 ADQTEAAIKATMKMLNLL 497 +DQT AAI AT KMLN++ Sbjct: 488 SDQTVAAIIATQKMLNVV 505 Lambda K H 0.318 0.135 0.390 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: 727 Number of extensions: 21 Number of successful extensions: 3 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: 499 Length of database: 507 Length adjustment: 34 Effective length of query: 465 Effective length of database: 473 Effective search space: 219945 Effective search space used: 219945 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: 52 (24.6 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