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 SMc02546 SMc02546 alpha-isopropylmalate/homocitrate synthase family transferase
Query= curated2:Q8TW28 (397 letters) >FitnessBrowser__Smeli:SMc02546 Length = 538 Score = 177 bits (450), Expect = 5e-49 Identities = 123/375 (32%), Positives = 193/375 (51%), Gaps = 27/375 (7%) Query: 17 DEVIVYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVSEGERDAVRRIA 76 + + ++DTTLRDG+QTPG+ F+ E K+ IA LLD+ G+ +E G+P + + + + Sbjct: 4 ERIYLFDTTLRDGQQTPGIDFSVEDKIAIASLLDQFGMDYVEGGYPGANPTDTEFFK--C 61 Query: 77 HEGLNADILCLARTLRGDVDAALDCDVDGVIT-------FIATS-ELHLKHKLRMSREEV 128 A + T R V A+ D + +++ +A S + H++ L + EE Sbjct: 62 RRTDKASFVAFGMTKRAGVSASNDPGLSALLSAKSDAICLVAKSWDYHVEVALGCTNEEN 121 Query: 129 LERIADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRVHATDTVGVM 185 L+ I +VE G E DG + + +TA E GA V DT G Sbjct: 122 LDNIRASVEAVVASGREAMVDCEHFFDGYKANSAYALACAKTAFEAGARWVVLCDTNGGT 181 Query: 186 IPAAMRLFVAKI--REVVDLPIGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIGERAG 243 P +R V+ + V +G+H H+D G AVANSLAAVEAG + I T+NGIGER G Sbjct: 182 QPPEIREIVSAVIAEGVPGANLGIHAHNDTGQAVANSLAAVEAGVRQIQGTLNGIGERCG 241 Query: 244 NAALEEVI--MALKELYG--IDPGFNTEVLAELSRKVSEYSGI---DVPPNKAVVGENAF 296 NA L +I +ALKE Y + G + E L EL++ + + P VG +AF Sbjct: 242 NANLVTLIATLALKETYSSRFETGIDAERLQELTKLAHAFDELLNRSPDPQAPYVGASAF 301 Query: 297 RHESGIHVAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELGV-----EPE 351 ++GIH +A+L++PRTYE + P+ VG RK+++ G+ + L+ G+ +P Sbjct: 302 ATKAGIHASALLKDPRTYEHVAPESVGNLRKVMVSDQGGKANFINALKRRGITVSKDDPR 361 Query: 352 EEIVEEVLKRIKALG 366 + + ++K +A G Sbjct: 362 LDKLISIVKEREATG 376 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: 452 Number of extensions: 24 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: 538 Length adjustment: 33 Effective length of query: 364 Effective length of database: 505 Effective search space: 183820 Effective search space used: 183820 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