Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate WP_028584095.1 G494_RS0107890 2-isopropylmalate synthase
Query= curated2:P05345 (381 letters) >NCBI__GCF_000429965.1:WP_028584095.1 Length = 563 Score = 71.6 bits (174), Expect = 5e-17 Identities = 99/365 (27%), Positives = 148/365 (40%), Gaps = 42/365 (11%) Query: 11 LRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMGDEEIARIQLV---RRQLPDA 67 LRDG Q+ EK+ + E L A G +EVG PA E ++L+ +R P Sbjct: 38 LRDGNQALVQPMNLEEKLEMFELLTAIGFKEIEVGFPAASQVEFDFMRLLIDGQRIPPGV 97 Query: 68 TLMTWCRMNALEIRQS--ADLGIDWVDISIPASDKLRQYKL------REPLAVLLERLAM 119 + + A IR++ + +G + + + S Q + RE + + + + Sbjct: 98 VIQALTQSRAALIRKTFASFVGAEEAIVHLYNSTSTLQRDVVFRKGRREIIELGMAGARL 157 Query: 120 FIHLAHTLGLKVCIGCEDASRASGQT------LRAIAEVAQNAPA--ARLRYADTVGLLD 171 A +++ S + AI EV + P L TV + Sbjct: 158 IREQARDSDVRIRYEYSPESFTGTELEFALEICEAIMEVWEPTPENPVILNLPATVEMST 217 Query: 172 PFTTAAQISAL-RDVWSGE---IEMHAHNDLGMATANTLAAVSAGATSVNTTVLGLGERA 227 P A QI R++ S E I +H HND G A A T A+ AGA V T+ G GER Sbjct: 218 PNIYADQIEWFCRNLSSRECALISIHGHNDRGTAVAATELALMAGADRVEGTLFGNGERT 277 Query: 228 GNAAAWKPSALGLER-CLGVETGVHFSALPALCQRVAEAAQRAIDPQQPLVGELVFTHES 286 GN +L L GV + S + + + + P+ P GELV+T S Sbjct: 278 GNVDL---VSLALNMFTQGVNPNLDLSNINKVINVYERCTKMNVPPRHPYAGELVYTAFS 334 Query: 287 GVH-------VAALLRDSES-----YQSIAPSLMGRSYRLV--LGKHSGRQAVNGVFD-Q 331 G H + ALL ES Y I P +GR+Y + + SG+ V V D + Sbjct: 335 GSHQDAINKGMDALLAHPESLWEVPYLPIDPQDVGRTYESIIRINSQSGKGGVAYVMDKE 394 Query: 332 MGYHL 336 G+ L Sbjct: 395 FGFKL 399 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: 396 Number of extensions: 26 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: 563 Length adjustment: 33 Effective length of query: 348 Effective length of database: 530 Effective search space: 184440 Effective search space used: 184440 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 10 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