Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_086510845.1 BZY95_RS15540 isocitrate lyase
Query= BRENDA::Q9I0K4 (531 letters) >NCBI__GCF_002151265.1:WP_086510845.1 Length = 531 Score = 861 bits (2225), Expect = 0.0 Identities = 429/529 (81%), Positives = 475/529 (89%), Gaps = 1/529 (0%) Query: 3 AYQNEIKAVAALKEKNGSSWSAINPEYAARMRIQNRFKTGLDIAKYTAAIMRKDMAEYDA 62 +Y+++IKA+A L+E W++I+PE AARMR QNRFKTGLDIAKYTA IMR+DMA YDA Sbjct: 2 SYKDDIKALAQLREAQQGKWASISPENAARMRAQNRFKTGLDIAKYTAKIMREDMAAYDA 61 Query: 63 DSSVYTQSLGCWHGFIGQQKLISIKKHLKTTNKRYLYLSGWMVAALRSDFGPLPDQSMHE 122 DSS YTQSLGCWHGFIGQQKLISIKKH TT +RYLYLSGWMVAALRS+FGPLPDQSMHE Sbjct: 62 DSSQYTQSLGCWHGFIGQQKLISIKKHFGTTKRRYLYLSGWMVAALRSEFGPLPDQSMHE 121 Query: 123 KTAVSGLIEELYTFLRQADARELDLLFTGLDAARAAGDKAKEAELLAQIDNFETHVVPII 182 KT+V+GLIEELYTFLRQADA EL+ LF L+AA+ AGDKAK EL+A+IDN ETHVVPII Sbjct: 122 KTSVAGLIEELYTFLRQADAWELNHLFRDLEAAQKAGDKAKAEELIAKIDNHETHVVPII 181 Query: 183 ADIDAGFGNAEATYLLAKKMIEAGACCIQIENQVSDEKQCGHQDGKVTVPHIDFLAKINA 242 ADIDAGFGNAEATYLLAKKMIEAGACCIQ+ENQVSDEKQCGHQDGKVTVPH DFLAKINA Sbjct: 182 ADIDAGFGNAEATYLLAKKMIEAGACCIQLENQVSDEKQCGHQDGKVTVPHEDFLAKINA 241 Query: 243 VRYAFLELGVDDGVIVARTDSLGAGLTKQIAVTNEPGDLGDLYNSFLDCEEI-SESELGN 301 VRYAFLELGVDDGVIVARTDSLGAGLT++IAVT EPGDLGD YNSFLD + I S +++ N Sbjct: 242 VRYAFLELGVDDGVIVARTDSLGAGLTQKIAVTKEPGDLGDQYNSFLDGDVIESATDIDN 301 Query: 302 GDVVIKREGKLLRPKRLASNLFQFRKGTGEDRCVLDCITSLQNGADLLWIETEKPHVGQI 361 GDVVIK+ GKL++ KRLAS L+QF+ GTGEDR VLDCITSLQNGADLLWIETEKPHVGQI Sbjct: 302 GDVVIKQNGKLVKVKRLASGLYQFKPGTGEDRVVLDCITSLQNGADLLWIETEKPHVGQI 361 Query: 362 KAMVDRIREVIPNAKLVYNNSPSFNWTLNFRQQVFDAFVAEGKDVSAYDRNKLMSVEYDD 421 K MVDRIR+V+P+AKLVYNNSPSFNWTLNFRQQVFDA+ EGKDVSAYDR LMS EYD+ Sbjct: 362 KGMVDRIRQVVPDAKLVYNNSPSFNWTLNFRQQVFDAWEKEGKDVSAYDRANLMSAEYDN 421 Query: 422 TELAKVADEKIRTFQRDGSAHAGIFHHLITLPTYHTAALSTDNLAKGYFADEGMLAYVKG 481 TEL K+ADE + FQRD + AGIFHHLITLPTYHTAALSTDNLAKGYF EGMLAYV G Sbjct: 422 TELGKLADEWTQNFQRDAAREAGIFHHLITLPTYHTAALSTDNLAKGYFGAEGMLAYVAG 481 Query: 482 VQRQELRQGIACVKHQNMAGSDIGDNHKEYFAGEAALKASGKDNTMNQF 530 VQR+E+R+GIA VKHQ+MAGS+IGD+HKE+F GEAALKA GKDNTMNQF Sbjct: 482 VQRREIREGIATVKHQDMAGSNIGDDHKEFFHGEAALKAGGKDNTMNQF 530 Lambda K H 0.318 0.134 0.388 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: 939 Number of extensions: 26 Number of successful extensions: 2 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: 531 Length of database: 531 Length adjustment: 35 Effective length of query: 496 Effective length of database: 496 Effective search space: 246016 Effective search space used: 246016 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 (21.7 bits) S2: 52 (24.6 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