Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate AO353_15925 AO353_15925 2-isopropylmalate synthase
Query= curated2:P05345 (381 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15925 Length = 559 Score = 63.5 bits (153), Expect = 1e-14 Identities = 90/362 (24%), Positives = 142/362 (39%), Gaps = 48/362 (13%) Query: 11 LRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMG--DEEIARIQLVRRQLPDAT 68 LRDG QS +K+ + L A G+ +E PA D + R + +PD T Sbjct: 40 LRDGNQSLIEPMDAVKKLRFWKTLVAVGVKEIEASFPAASQTDFDFVRTLIEGGHIPDDT 99 Query: 69 ---LMTWCRMNALE-----IRQSADLGIDWVDISIPASDKLRQYKLREPL-AVLLERLAM 119 ++T R + +E +R + + + + P+ ++ + ++ + A+ + + Sbjct: 100 TIQVLTQGREDLIERTFESLRGAKKAIVHLYNATCPSFRRIVFNQDKDGIKAIAVNAAKL 159 Query: 120 FIHLAH-------TLGLKVCIGCEDASRASGQTLRAIAEVAQNAPAAR--LRYADTVGLL 170 F+ A T + + A+ EV P + L TV Sbjct: 160 FVKYAAQQPDTEWTFEYSPETFSATELEFAKEVCDAVIEVWNPTPEHKVILNLPATVECA 219 Query: 171 DPFTTAAQISALRDVWSGE---------IEMHAHNDLGMATANTLAAVSAGATSVNTTVL 221 P A QI W G I +H HND G A T + AGA V + Sbjct: 220 TPNIYADQIE-----WFGRHINRRDSVIISLHTHNDRGTGVAATELGLMAGADRVEGCLF 274 Query: 222 GLGERAGNAAAWKPSALGLERCLGVETGVHFSALPALCQRVAEAAQRAIDPQQPLVGELV 281 G GER GN AL L GV+ + FS + + + V E Q + P+ P VG+LV Sbjct: 275 GNGERTGNVDL-VTVALNL-YTQGVDPELDFSDIDGVRKVVEECNQIPVHPRHPYVGDLV 332 Query: 282 FTHESGVHVAALLRD----------SESYQSIAPSLMGRSYRLVL--GKHSGRQAVNGVF 329 T SG H A+ + Y I P+ +GRSY V+ SG+ + + Sbjct: 333 HTAFSGSHQDAIRKGFAQQKPDALWEVPYLPIDPADIGRSYEAVIRVNSQSGKGGIAYLL 392 Query: 330 DQ 331 +Q Sbjct: 393 EQ 394 Lambda K H 0.319 0.132 0.384 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: 408 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 381 Length of database: 559 Length adjustment: 33 Effective length of query: 348 Effective length of database: 526 Effective search space: 183048 Effective search space used: 183048 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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