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 351386 BT1858 2-isopropylmalate synthase (NCBI ptt file)
Query= curated2:Q8TW28 (397 letters) >FitnessBrowser__Btheta:351386 Length = 499 Score = 196 bits (497), Expect = 2e-54 Identities = 130/375 (34%), Positives = 200/375 (53%), Gaps = 12/375 (3%) Query: 23 DTTLRDGEQTPGVSFTPEQKLEIAHLL-DELGVQQIEAGFPVVSEGERDAVRRIAHEGLN 81 DTTLRDGEQT GVSF P +KL IA LL ++L V ++E VSEGE +AV+ I Sbjct: 2 DTTLRDGEQTSGVSFVPHEKLMIARLLLEDLKVDRVEVASARVSEGEFEAVKMICDWAAR 61 Query: 82 ADILCLARTLRGDVDAALDCDVDG-----VITFIATSEL-HLKHKLRMSREEVLERIADT 135 ++L L G VD D VI + L H +L+ + EE + I + Sbjct: 62 RNLLQKVEVL-GFVDGHTSVDWIQRTGCRVINLLCKGSLKHCTQQLKKTPEEHIADIINV 120 Query: 136 VEYAKDHGLWVAFSAED---GTRTEFEFLERVYRTAEECGADRVHATDTVGVMIPAAMRL 192 V YA + + V ED G + E++ ++ ++ R DT+G++ P + Sbjct: 121 VHYADEQDIGVNVYLEDWSNGMKDSPEYVFQLMDGLKQTSIRRYMLPDTLGILNPLQVIE 180 Query: 193 FVAKIRE-VVDLPIGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIGERAGNAALEEVI 251 ++ K+++ + H H+D+ +AV+N LAAV +G + + TT+NG+GERAGNA L V Sbjct: 181 YMRKMKKRYPNTHFDFHAHNDYDLAVSNVLAAVLSGVRGLHTTINGLGERAGNAPLSSVQ 240 Query: 252 MALKELYGIDPGFNTEVLAELSRKVSEYSGIDVPPNKAVVGENAFRHESGIHVAAVLEEP 311 LK+ + + L ++SR V YSGI +P NK +VGEN F +G+H + Sbjct: 241 AILKDHFNAMTNIDESRLNDVSRVVESYSGIVIPANKPIVGENVFTQVAGVHADGDNKNN 300 Query: 312 RTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELGVEPEEEIVEEVLKRIKALGDRRVR 371 + P+ G R+ LGK +G+ + LE+LG+E +E+ + +V +RI LGD++ Sbjct: 301 LYCNDLLPERFGRKREYALGKTSGKANIRKNLEDLGLELDEDAMRKVTERIIELGDKKEL 360 Query: 372 VTDSKLEEIVRNVLE 386 VT L IV +VL+ Sbjct: 361 VTQEDLPYIVSDVLK 375 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: 419 Number of extensions: 20 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: 499 Length adjustment: 32 Effective length of query: 365 Effective length of database: 467 Effective search space: 170455 Effective search space used: 170455 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