Align Homocitrate synthase AksA; (R)-homo(2)citrate synthase; (R)-homo(3)citrate synthase; EC 2.3.3.14; EC 2.3.3.- (characterized)
to candidate WP_027179522.1 G496_RS0112155 citramalate synthase
Query= SwissProt::Q57926 (406 letters) >NCBI__GCF_000429985.1:WP_027179522.1 Length = 538 Score = 167 bits (424), Expect = 5e-46 Identities = 116/376 (30%), Positives = 183/376 (48%), Gaps = 25/376 (6%) Query: 29 LKDIYIYDTTLRDGEQTPGVCFTKEQKLEIARKLDELGLKQIEAGFPIVSEREADIVKTI 88 +K + IYDTTLRDG Q+ + + + K+ + KLDELG+ IE G+P + + + I Sbjct: 1 MKTVKIYDTTLRDGTQSEEINLSVQDKIRLTIKLDELGIHYIEGGWPGSNPTDEEFFNEI 60 Query: 89 ANEGLNADILALCRALK---------KDIDKAIECDVDGIITFIATSPLHLKYKFNNKSL 139 N L +A + K+++ I+ + F T H+ K L Sbjct: 61 KNYNLKTAKVAAFGSTHNVRTTPEKDKNLNALIKSKAKALTIFGKTWDFHVTEALGIK-L 119 Query: 140 DEILEMGVEAVEYAKEHGLFVAFSAE---DATRTPIEDLIKVHKAAEEAGADRVHIADTT 196 D LE+ ++ Y + + F AE D + E + KAA GAD + + DT Sbjct: 120 DRNLELITNSLSYLRSQVEDLFFDAEHFFDGFKNNSEYALSCLKAAVAGGADILVLCDTN 179 Query: 197 GCATPQSMEFICKTLKENLKKAHIGVHCHNDFGFAVINSIYGLIGGAKAVSTTVNGIGER 256 G P + I + +K+N+ +A +G+H HND AV NSI + GA + T+NG GER Sbjct: 180 GGTLPNEVAEIIREVKKNIPEAQLGIHAHNDCELAVANSITAVENGAVQIQGTMNGYGER 239 Query: 257 AGNAALEELIMALTVLYDVDLGL------NLEVLPELCRMVEEYSGIKMPKNKPIVGELV 310 GNA + +I L D+ +G + L E+ V E + ++ +P VG+ Sbjct: 240 CGNANICSIIPNL----DLKMGYKSIGKEKIAKLTEVSAYVAEIANLRPFMRQPYVGQGA 295 Query: 311 FAHESGIHVDAVIENPLTYEPFLPEKIGLKRNILLGKHSGCRAVAYKLKLMGIDY--DRE 368 FAH+ GIHV AV++N TYE PE++G R +LL +G + +K + G D D Sbjct: 296 FAHKGGIHVSAVLKNTKTYEHVTPEEVGNTRRVLLSDLAGASNILFKARQYGYDLAKDDP 355 Query: 369 MLCEIVKKVKEIREEG 384 + I+ ++KE + G Sbjct: 356 SVQTILTEIKEREKMG 371 Lambda K H 0.320 0.138 0.398 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: 480 Number of extensions: 23 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: 406 Length of database: 538 Length adjustment: 33 Effective length of query: 373 Effective length of database: 505 Effective search space: 188365 Effective search space used: 188365 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