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 3608293 Dshi_1696 2-isopropylmalate synthase/homocitrate synthase family protein (RefSeq)
Query= curated2:Q8TW28 (397 letters) >FitnessBrowser__Dino:3608293 Length = 545 Score = 159 bits (402), Expect = 2e-43 Identities = 121/380 (31%), Positives = 183/380 (48%), Gaps = 45/380 (11%) Query: 17 DEVIVYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVSEGERD------ 70 + + +YDTTLRDG+QT GV F+ +K +IA LD LG+ IE G+P + + + Sbjct: 3 ERLYLYDTTLRDGQQTQGVQFSTPEKQQIAAALDALGIDFIEGGWPGANPTDSEFFASAP 62 Query: 71 -----------AVRRIAHEGLNADILCLARTLRGDVDAALDCDVDGVITFIATSELHLKH 119 +R N D+L A L+ V + E H+ Sbjct: 63 TFDHARFAAFGMTKRAGFSAENDDVLA----------AVLNAGTQAVCLVGKSHEYHVTR 112 Query: 120 KLRMSREEVLERIADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRV 176 L +S E E IA +V + G F AE DG + + A E GA V Sbjct: 113 ALGISLAENTENIARSVAHLVAQGREAIFDAEHFFDGYLANPGYAVETLQAALEAGARWV 172 Query: 177 HATDTVGVMIPAAMRLFVAKI--REVVDLPIGVHCHDDFGMAVANSLAAVEAGAQAISTT 234 DT G +PA + A++ V +G+H H+D G AVAN+LAA++AGA+ + T Sbjct: 173 VLCDTNGGRLPAEVGRITAEVIAAGVPGDRLGIHTHNDTGNAVANALAAIDAGARQVQGT 232 Query: 235 VNGIGERAGNAALEEVI--MALKELYG--IDPGFNTEVLAELSRKVSEYSGI--DVPPNK 288 +NG+GER GNA L +I + LKE Y + G + L +L R I VP Sbjct: 233 LNGLGERCGNANLVTLIPTLLLKEPYASRFETGVSAAALRDLVRVSRTLDDILNRVPTKS 292 Query: 289 A-VVGENAFRHESGIHVAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELG 347 A VG +AF H++G+H +A+L++P TYE I P+ VG R I + G+ + +L + G Sbjct: 293 APYVGASAFAHKAGLHASAILKDPSTYEHIPPEAVGNARVIPMSNQAGQSNLRKRLADAG 352 Query: 348 VEPEE------EIVEEVLKR 361 + ++ +++EV +R Sbjct: 353 IAVQKGDMRLGALLDEVKRR 372 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: 492 Number of extensions: 22 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: 545 Length adjustment: 33 Effective length of query: 364 Effective length of database: 512 Effective search space: 186368 Effective search space used: 186368 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