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_012756813.1 RLEG_RS05790 citramalate synthase
Query= curated2:Q8TW28 (397 letters) >NCBI__GCF_000023185.1:WP_012756813.1 Length = 537 Score = 175 bits (443), Expect = 3e-48 Identities = 130/398 (32%), Positives = 196/398 (49%), Gaps = 32/398 (8%) Query: 15 LPDEVIVYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVSEGERDAVRR 74 + + + ++DTTLRDG+QTPG+ F+ E K+ IA +LDE G+ +E G+P D Sbjct: 1 MKERIYLFDTTLRDGQQTPGIDFSVEDKIAIAAMLDEFGLDYVEGGYP--GANPTDTAFF 58 Query: 75 IAHEGLNADILCLARTLRGDVDAALDCDVDGV-------ITFIATS-ELHLKHKLRMSRE 126 A + T R V + D + G+ I F+A S + H+ L + E Sbjct: 59 SEKRTSQASFVAFGMTKRAGVSVSNDPGIAGLLQAKSDAICFVAKSWDYHVAVALGCTNE 118 Query: 127 EVLERIADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRVHATDTVG 183 E LE IA++V+ A G E DG + + +TA E GA V DT G Sbjct: 119 ENLECIAESVKAAVGAGKEAIVDCEHFFDGFKANPAYALACAKTAYESGARWVVLCDTNG 178 Query: 184 VMIPAAMRLFVAKI--REVVDLPIGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIGER 241 P +R V + V +G+H H+D G AVANSLAAV+AG + I T+NGIGER Sbjct: 179 GTQPPEVRAIVEAVIASGVPGHCLGIHAHNDTGQAVANSLAAVDAGVRQIQGTLNGIGER 238 Query: 242 AGNAALEEVI--MALKELYGIDPGFNTEV-------LAELSRKVSEYSGIDVPPNKAVVG 292 GNA L +I +ALK Y + F T + L LS E VG Sbjct: 239 CGNANLVTLIPTLALKSAY--NSRFETAIDEERLLNLTRLSHAFDELLNRSPDHQMPYVG 296 Query: 293 ENAFRHESGIHVAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELGVE--- 349 +AF ++GIH +A+L++PRTYE + P+ VG RK+++ G+ + L+ G+E Sbjct: 297 ASAFATKAGIHASALLKDPRTYEHVPPETVGNFRKVMVSDQGGKANFINALKRRGIEVAK 356 Query: 350 --PEEEIVEEVLKRIKALGDRRVRVTDSKLEEIVRNVL 385 P+ +++ ++K +++G D+ E + R L Sbjct: 357 DDPKLDLLISIVKERESIG-YAYEGADASFELLARRTL 393 Lambda K H 0.317 0.135 0.380 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: 465 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: 397 Length of database: 537 Length adjustment: 33 Effective length of query: 364 Effective length of database: 504 Effective search space: 183456 Effective search space used: 183456 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 (21.6 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