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_035240746.1 Q366_RS15935 citramalate synthase
Query= curated2:Q8TW28 (397 letters) >NCBI__GCF_000745975.1:WP_035240746.1 Length = 544 Score = 179 bits (453), Expect = 2e-49 Identities = 122/352 (34%), Positives = 183/352 (51%), Gaps = 22/352 (6%) Query: 18 EVIVYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVSEGER---DAVRR 74 +V++YDTTLRDG Q + F+P KL+IA LD+ G+ IE G+P + G + D VR Sbjct: 9 KVLLYDTTLRDGMQGENIFFSPGDKLKIAMRLDDAGIHYIEGGWPGSNPGAQAFFDLVRD 68 Query: 75 IAHEGLNADILCLARTLR--------GDVDAALDCDVDGVITFIATSELHLKHKLRMSRE 126 + A I T R ++ A +D V F + +LH+ + +RE Sbjct: 69 TPFK--QAKICAFGSTRRQNSTCEKDSNIKALIDSGAPVVTIFGKSWDLHVSDIMNNTRE 126 Query: 127 EVLERIADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRVHATDTVG 183 E L I ++V Y K G V + AE DG + F A + G + DT G Sbjct: 127 ENLAMITESVSYLKARGREVLYDAEHFYDGYKANPGFALETLGAALKGGTRCLVLCDTNG 186 Query: 184 VMIPAAM----RLFVAKIREVVDLPIGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIG 239 +P + R +A ++ D+ GVH H+D MAVAN++ AV AGA + TVNG G Sbjct: 187 GCLPCDIDTITRETIAHFKDYEDVIFGVHTHNDCAMAVANAINAVHAGAIMVQGTVNGYG 246 Query: 240 ERAGNAALEEVI--MALKELYGIDPGFNTEVLAELSRKVSEYSGIDVPPNKAVVGENAFR 297 ER GNA L +I +ALK N L LSR VSE + + ++ VG +AF Sbjct: 247 ERCGNADLTALIPILALKMNRACISEKNLAKLQNLSRFVSETANMPPVASRPFVGRSAFT 306 Query: 298 HESGIHVAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELGVE 349 H+ G+HV+A+++ PR YE + P+ VG R++++ + +G+ + K +ELGV+ Sbjct: 307 HKGGVHVSAIMKNPRAYEHMSPEFVGNRRRVLVSEQSGKSNITYKAKELGVD 358 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: 463 Number of extensions: 30 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: 397 Length of database: 544 Length adjustment: 33 Effective length of query: 364 Effective length of database: 511 Effective search space: 186004 Effective search space used: 186004 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