Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate BPHYT_RS13280 BPHYT_RS13280 2-isopropylmalate synthase
Query= curated2:P05345 (381 letters) >FitnessBrowser__BFirm:BPHYT_RS13280 Length = 572 Score = 70.5 bits (171), Expect = 1e-16 Identities = 102/388 (26%), Positives = 159/388 (40%), Gaps = 49/388 (12%) Query: 9 TTLRDGEQSPGVAFRTSEKVAIAEALYAAGITAMEVGTPAMG--DEEIARIQLVRRQLPD 66 T LRDG QS K+ + + L G +EV P+ D R + +PD Sbjct: 36 TDLRDGNQSLFEPMDAQRKMRMFKTLVQIGFKEIEVAFPSASQTDFNFVRELIEGGHIPD 95 Query: 67 AT---LMTWCRMNALEIRQSADLGIDWVDISIPAS------------DKLRQYKLREPLA 111 ++T R + +E + G+ + + + +K +L + A Sbjct: 96 DVTIEVLTQARDDLIERTFESLRGVPRAIVHLYNATAPEFRKIVFNLEKSGVKELAQNAA 155 Query: 112 VLLERLAMFI---HLAHTLGLKVCIGCEDASRASGQTLRAIAEVAQNAPA--ARLRYADT 166 ++R+A + +V G E + + A+ +V Q P A + T Sbjct: 156 RTMKRIAATMPETQFTFQYSPEVFSGTE--IEFAKEVCDAVFDVWQPTPEHKAIVNLPAT 213 Query: 167 VGLLDPFTTAAQIS------ALRDVWSGEIEMHAHNDLGMATANTLAAVSAGATSVNTTV 220 V + P A QI A RD S I +H HND G A A AV AGA + + Sbjct: 214 VEMSTPNIYADQIEWMHRNLARRD--SLIISVHPHNDRGTAVAAAELAVMAGADRIEGCL 271 Query: 221 LGLGERAGNAAAWKPSALGLERCLGVETGVHFSALPALCQRVAEAAQRAIDPQQPLVGEL 280 G GER GN AL L GV+ G+ FS + + + E Q I P+ P VG+L Sbjct: 272 FGNGERTGNVDL-VTLALNLYT-QGVDPGLDFSNINEVARTAEECTQLPIHPRHPYVGDL 329 Query: 281 VFTHESGVHVAALLRD----------SESYQSIAPSLMGRSYRLVL--GKHSGRQAVNGV 328 VFT SG H A+ + Y I P+ +GR+Y V+ SG+ + + Sbjct: 330 VFTAFSGSHQDAIKKGFAVQKPDAVWEVPYMPIDPADLGRTYDSVIRVNSQSGKGGIAYL 389 Query: 329 FDQMGYHLNAAQINQL--LPAIRRFAEN 354 +Q GY + + Q+ A++RF ++ Sbjct: 390 LEQ-GYGVVLPRRLQVDFSSAVQRFTDD 416 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: 17 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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