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 8499505 DvMF_0275 putative alpha-isopropylmalate/homocitrate synthase family transferase (RefSeq)
Query= curated2:Q8TW28 (397 letters) >FitnessBrowser__Miya:8499505 Length = 540 Score = 174 bits (442), Expect = 4e-48 Identities = 128/394 (32%), Positives = 201/394 (51%), Gaps = 23/394 (5%) Query: 21 VYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVSEGERDAVRRIAHEGL 80 +YDTTLRDG Q+ ++ T KL+IA LDE+G+ +IE G+P + + + IA+ L Sbjct: 7 LYDTTLRDGSQSEDINLTAADKLKIALKLDEIGIDRIEGGWPGSNPVDVAFFKEIANYHL 66 Query: 81 -NADILCLARTLRGDVDAALDCDVDGVIT--------FIATSELHLKHKLRMSREEVLER 131 +A I T + A D ++ + F + E+H LR+ LE Sbjct: 67 KHAVISAFGSTHHPNFTADSDPNLRAIAESGARVASIFGKSCEVHAAEALRLDAARNLEI 126 Query: 132 IADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRVHATDTVGVMIPA 188 I D+V + K V F AE DG R + R A E GAD + DT G +P Sbjct: 127 IGDSVAFLKGKLAEVYFDAEHFFDGYRHNAAYALSALRRAHEAGADVLVLCDTNGGTLPH 186 Query: 189 AMRLFVAKIREVVD-LPIGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIGERAGNAAL 247 + V ++RE + +G+H H+D +AVANS+AAV+AGA I T+NG+GER GNA L Sbjct: 187 EVARIVTEVREALPGAAVGIHAHNDCELAVANSIAAVQAGAVQIQGTINGVGERCGNANL 246 Query: 248 EEVIMALKELYGID----PGFNTEVLAELSRKVSEYSGIDVPPNKAVVGENAFRHESGIH 303 +I L+ +G + P + L ++ VSE + I + VG +AF H+ G+H Sbjct: 247 CSIIPTLELKFGGEYTCLPEGRLQQLTAVAAYVSEVANIPPFSRQPYVGRSAFAHKGGVH 306 Query: 304 VAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELG--VEPEEEIVEEVLKR 361 V+AV + YE I P VG ++I++ + GR +V+ G ++ +E +V+ +L Sbjct: 307 VSAVNRKSSLYEHISPDVVGNRQRILITELAGRSNIVSLARRFGFHLDKDEPVVKGLLTE 366 Query: 362 IK---ALGDRRVRVTDSKLEEIVRNVLESRGDRD 392 +K +LG ++ +E ++ L RG R+ Sbjct: 367 LKKKASLG-YDYAAAEASVELLILRKLARRGVRE 399 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: 490 Number of extensions: 31 Number of successful extensions: 5 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: 540 Length adjustment: 33 Effective length of query: 364 Effective length of database: 507 Effective search space: 184548 Effective search space used: 184548 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