Align Homocitrate synthase AksA; EC 2.3.3.14; (R)-homo(2)citrate synthase; EC 2.3.3.-; (R)-homo(3)citrate synthase; EC 2.3.3.- (uncharacterized)
to candidate WP_028584513.1 G494_RS0110500 citramalate synthase
Query= curated2:O27667 (391 letters) >NCBI__GCF_000429965.1:WP_028584513.1 Length = 530 Score = 168 bits (425), Expect = 4e-46 Identities = 116/374 (31%), Positives = 192/374 (51%), Gaps = 22/374 (5%) Query: 20 ITIYDTTLRDGEQTPGVCLGTEEKLEIARKLDELGIHQIESGFPVVSEQERVSVKSIANE 79 I IYDTTLRDG Q L E+K++I +LD LG+ IE G+P + KS+ Sbjct: 5 IEIYDTTLRDGTQAENFNLSVEDKVKICLQLDRLGVDYIEGGWPGSNPLAIDFFKSMKQV 64 Query: 80 GL-NAEILALCRTK-------KD-DIDAAIDCDVDGVITFMATSDLHLKHKLKLTREEAL 130 L +A + A T+ KD ++ A ++ V F + D+H+ L++ ++ L Sbjct: 65 ELKHARLTAFGSTRHFQNPADKDANLQALLEAGTPAVTIFGKSWDIHVTEALRIGLDDNL 124 Query: 131 NVCMNSIEYAKDHGLFLAFSAE---DATRTDLDFLKQIYRKAENYGADRVHIADTVGAIS 187 + +S+ Y + L + AE D + + ++ +A GA+ + + DT G Sbjct: 125 ELIQDSLAYLRPRVEHLLYDAEHFFDGFKHNKEYCLATLARAVAGGAETLVLCDTNGGTL 184 Query: 188 PQGMDYLVREL-----RRDIKVDIALHCHNDFGMALSNSIAGLLAGGTAVSTTVNGIGER 242 PQ + ++ E+ R+ V + +H HND A++N++ + G V T+NG GER Sbjct: 185 PQEIPAIITEVQAFMERQPRPVKLGIHAHNDSETAVANALISVDLGVRQVQGTINGFGER 244 Query: 243 AGNTSLEELIMAL--RIIYEVDLGFNIGVLYELSRLVEKHTRMKVPENKPIVGRNVFRHE 300 GN++L +I AL ++ +G I LY SRLV++ + + +P VG + F H+ Sbjct: 245 CGNSNLTSIIPALVFKMGCSCKVGERIEQLYTTSRLVDELANLPHDQYQPYVGESAFAHK 304 Query: 301 SGIHVDAVIEEPLTYEPFLPEMIGHQRKIVLGKHSGCRAVKAKLEEYGIDVTRDE--LCR 358 GIHV AV PLTYE PE +G+ R+I++ +G V +K ++G+ + D+ + Sbjct: 305 GGIHVSAVQRNPLTYEHIEPEKVGNIRRILISDQAGRANVLSKARKFGVPIEADDPLMSS 364 Query: 359 IVEEVKKNREKGKY 372 I+ E+ KNRE Y Sbjct: 365 IISEL-KNRENLGY 377 Lambda K H 0.320 0.138 0.395 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: 443 Number of extensions: 28 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: 391 Length of database: 530 Length adjustment: 33 Effective length of query: 358 Effective length of database: 497 Effective search space: 177926 Effective search space used: 177926 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 10 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