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_011384529.1 AMB_RS10755 citramalate synthase
Query= curated2:Q8TW28 (397 letters) >NCBI__GCF_000009985.1:WP_011384529.1 Length = 546 Score = 185 bits (469), Expect = 3e-51 Identities = 129/366 (35%), Positives = 192/366 (52%), Gaps = 22/366 (6%) Query: 15 LPDEVIVYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVSEGERDAVRR 74 + + V +YDTTLRDG QT GV F+ K+ IA LD +G+ +E G+P + + DA Sbjct: 1 MAERVYLYDTTLRDGAQTQGVDFSAADKVRIARELDRIGIDYVEGGWPGANPTD-DAFFA 59 Query: 75 IAHEGLNADILCLARTLRGDVDAALDCDVDGVI-------TFIATS-ELHLKHKLRMSRE 126 + + T R A D ++ ++ T + S + + L + + Sbjct: 60 DPPAFKRSRLTAFGMTRRAGRSADNDPGLNALLVTPARVATMVGKSWDFQVTVALGIELD 119 Query: 127 EVLERIADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRVHATDTVG 183 E L +AD+V++A+ V F AE DG + + + A + GA V DT G Sbjct: 120 ENLRMVADSVQHARTKVEEVMFDAEHFFDGYKANPAYALAAAKAAYDAGARWVVLCDTNG 179 Query: 184 VMIPAAMRLFVAKIRE--VVDLPIGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIGER 241 +P MR V ++ + + +GVHCH+D AVANSLAAVEAG + I T+NG+GER Sbjct: 180 GTLPHEMRRIVGEVIKGGIPGSHLGVHCHNDSDTAVANSLAAVEAGVRQIQGTLNGLGER 239 Query: 242 AGNAALEEVIMALKELYGIDPGFNTEVLAEL---SRKVSEYSGIDVPPNKA--VVGENAF 296 GNA L +I AL G D G E L L SR + E +D PN+ VG++AF Sbjct: 240 CGNANLISIIPALMLKMGFDTGIAPEDLKNLVSVSRALDEV--LDRTPNRGQPYVGKSAF 297 Query: 297 RHESGIHVAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELGVEPEEEIVE 356 H+ G+HV+AV ++P+ YE +DP VG R IV+ GR +VA+L E+G++ + + Sbjct: 298 AHKGGLHVSAVAKDPKCYEHVDPASVGNMRHIVMSDQAGRSNLVARLTEIGID-LDSVKR 356 Query: 357 EVLKRI 362 E L R+ Sbjct: 357 ESLVRV 362 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: 537 Number of extensions: 33 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: 546 Length adjustment: 33 Effective length of query: 364 Effective length of database: 513 Effective search space: 186732 Effective search space used: 186732 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 09 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