Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate H281DRAFT_00385 H281DRAFT_00385 2-isopropylmalate synthase
Query= curated2:P05345 (381 letters) >FitnessBrowser__Burk376:H281DRAFT_00385 Length = 572 Score = 72.0 bits (175), Expect = 4e-17 Identities = 94/361 (26%), Positives = 146/361 (40%), Gaps = 42/361 (11%) Query: 9 TTLRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMG--DEEIARIQLVRRQLPD 66 T LRDG Q+ K+ + + L G +EV P+ D R + +PD Sbjct: 36 TDLRDGNQALFEPMNAERKMRMFKTLVQIGFKEIEVAFPSASQTDFNFVRELIEGGHIPD 95 Query: 67 AT---LMTWCRMNALE-----IRQSADLGIDWVDISIPASDKL-------RQYKLREPLA 111 ++T R + +E +R + + + + P K+ +L + A Sbjct: 96 DVTIEVLTQARDDLIERTFESLRGAPRAIVHLYNATAPEFRKIVFGLDQNGVKELAQKAA 155 Query: 112 VLLERLAMFIHLAH-TLGLKVCIGCEDASRASGQTLRAIAEVAQNAPA--ARLRYADTVG 168 ++RLA H TL + + + A+ ++ Q P A + TV Sbjct: 156 RTMKRLADAAPETHFTLQYSPEVFSGTELEFAKEVCDAVFDIWQPTPEHKAIVNLPATVE 215 Query: 169 LLDPFTTAAQIS------ALRDVWSGEIEMHAHNDLGMATANTLAAVSAGATSVNTTVLG 222 + P A QI A RD S + +H HND G A A AV AGA + + G Sbjct: 216 MATPNVYADQIEWMHRNLARRD--SLIVSVHPHNDRGTAVAAAELAVMAGADRIEGCLFG 273 Query: 223 LGERAGNAAAWKPSALGLERCLGVETGVHFSALPALCQRVAEAAQRAIDPQQPLVGELVF 282 GER GN AL L GV+ G+ FS + + + E Q + P+ P VG+LVF Sbjct: 274 NGERTGNVDL-VTLALNLYT-QGVDPGLDFSNINEIARTAEECTQLPVHPRHPYVGDLVF 331 Query: 283 THESGVHVAALLRD----------SESYQSIAPSLMGRSYRLVL--GKHSGRQAVNGVFD 330 T SG H A+ + Y I P+ +GR+Y V+ SG+ + + + Sbjct: 332 TAFSGSHQDAIKKGFAVQKPDAMWEVPYMPIDPNDLGRTYDSVIRVNSQSGKGGIAYLLE 391 Query: 331 Q 331 Q Sbjct: 392 Q 392 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: 370 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: 1 Length of query: 381 Length of database: 572 Length adjustment: 33 Effective length of query: 348 Effective length of database: 539 Effective search space: 187572 Effective search space used: 187572 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