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 GFF1624 PGA1_c16460 2-isopropylmalate synthase/homocitrate synthase-like protein
Query= curated2:Q8TW28 (397 letters) >FitnessBrowser__Phaeo:GFF1624 Length = 543 Score = 169 bits (428), Expect = 2e-46 Identities = 134/373 (35%), Positives = 189/373 (50%), Gaps = 32/373 (8%) Query: 17 DEVIVYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVS---EGERDAVR 73 + + +YDTTLRDG+QT GV F+ +K++IA LD LGV IE G+P + G DA Sbjct: 4 ERLYLYDTTLRDGQQTQGVQFSTTEKVQIATALDGLGVDYIEGGWPGANPTDSGFFDAAP 63 Query: 74 RIAHEGLNADILCLARTLRG-------DVDAA-LDCDVDGVITFIATSELHLKHKLRMSR 125 R A + T R DV AA L+ V + + H+ H L ++ Sbjct: 64 RT-----RATMTAFGMTKRAGRSAENDDVLAAVLNAGTAAVCLVGKSHDYHVTHALGITL 118 Query: 126 EEVLERIADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRVHATDTV 182 EE L+ I ++ + G F AE DG + ++ R A E GA V DT Sbjct: 119 EENLDNIRASIAHLVAQGREALFDAEHFFDGYKDNPDYALAACRAALEAGARWVVLCDTN 178 Query: 183 GVMIPAAMRLFVAKIREVVDLP---IGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIG 239 G +P + VA++ LP +G+H H+D AVA SLAAV+AGA+ I T+NG+G Sbjct: 179 GGTLPGDVGRIVAEVI-AAGLPGDHLGIHTHNDTENAVACSLAAVDAGARQIQGTLNGLG 237 Query: 240 ERAGNAALEEVI--MALKELYG--IDPGFNTE---VLAELSRKVSEYSGIDVPPNKAVVG 292 ER GNA L +I + LK Y D G + E L LSR + E A VG Sbjct: 238 ERCGNANLTTLIPTLLLKPPYADQFDIGVSHEGLSTLTALSRMLDEILNRVPTKQAAYVG 297 Query: 293 ENAFRHESGIHVAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELG--VEP 350 +AF H++G+H +A+L++P TYE IDP VG R I + G+ + +L E G VE Sbjct: 298 ASAFAHKAGLHASAILKDPSTYEHIDPALVGNARIIPMSNQAGQSNLRRRLSEAGLRVEN 357 Query: 351 EEEIVEEVLKRIK 363 + + +L+RIK Sbjct: 358 GDPALARILERIK 370 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: 503 Number of extensions: 19 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: 543 Length adjustment: 33 Effective length of query: 364 Effective length of database: 510 Effective search space: 185640 Effective search space used: 185640 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