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_012675635.1 PERMA_RS05365 citramalate synthase
Query= SwissProt::Q57926 (406 letters) >NCBI__GCF_000021565.1:WP_012675635.1 Length = 524 Score = 199 bits (505), Expect = 2e-55 Identities = 129/389 (33%), Positives = 200/389 (51%), Gaps = 19/389 (4%) Query: 30 KDIYIYDTTLRDGEQTPGVCFTKEQKLEIARKLDELGLKQIEAGFPIVSEREADIVKTIA 89 K + IYDTTLRDG Q GV + E KL I KLD+ G+ IE G+P + ++ K + Sbjct: 3 KKVLIYDTTLRDGTQAEGVNVSVEDKLRITEKLDDFGIHYIEGGWPGSNPKDDQYFKEVK 62 Query: 90 NEGLNADILALCRALKKD---------IDKAIECDVDGIITFIATSPLHLKYKFNNKSLD 140 L +A + ++ + ++ + I F + +H+ L+ Sbjct: 63 KLNLKNSKIAAFGSTRRAYLKVEDDPLVQNLVKAETPVITIFGKSWDIHVTQALKT-DLE 121 Query: 141 EILEMGVEAVEYAKEHGLFVAFSAE---DATRTPIEDLIKVHKAAEEAGADRVHIADTTG 197 + LEM + V++ K+H V F E D ++ E +KV AA E GAD + +ADT G Sbjct: 122 KNLEMVFDTVQFLKKHTDEVVFIGEHFFDGYKSNPEYAVKVLNAASEGGADFLVLADTNG 181 Query: 198 CATPQSMEFICKTLKENLKKAHIGVHCHNDFGFAVINSIYGLIGGAKAVSTTVNGIGERA 257 P +E I K +KE +G+H HND AV NSI ++ GA V T+NG GER Sbjct: 182 GTLPNEIERIIKEVKERGINNRLGIHAHNDSDTAVWNSIVAVLNGAVQVHGTINGFGERC 241 Query: 258 GNAALEELIMALTVL--YDVDLGLNLEVLPELCRMVEEYSGIKMPKNKPIVGELVFAHES 315 GNA L +I LT+ Y+ N++ L E+ V + + +PKN P VG+ FAH+ Sbjct: 242 GNANLCSIIPDLTLKLGYETIPRENIKRLKEISNFVADLVNLPVPKNMPYVGDSAFAHKG 301 Query: 316 GIHVDAVIENPLTYEPFLPEKIGLKRNILLGKHSGCRAVAYKLKLMGIDYDRE--MLCEI 373 G+H AVI+N YE PE++G +R IL+ +G + YK + +GI D + + E+ Sbjct: 302 GVHASAVIKNSRLYEHIDPEQVGNRRKILVSDLAGKSNIIYKARELGIQLDEKDPRIAEL 361 Query: 374 VKKVKEIREEGKFITDEVFKEIVEEVLRK 402 V+++K++ G E + +E ++RK Sbjct: 362 VREIKQLENYGYHF--EAAEASLELLIRK 388 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: 515 Number of extensions: 29 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: 406 Length of database: 524 Length adjustment: 33 Effective length of query: 373 Effective length of database: 491 Effective search space: 183143 Effective search space used: 183143 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