Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_076478392.1 BW971_RS08040 isocitrate lyase
Query= BRENDA::P9WKK7 (428 letters) >NCBI__GCF_900156495.1:WP_076478392.1 Length = 428 Score = 748 bits (1930), Expect = 0.0 Identities = 360/428 (84%), Positives = 398/428 (92%) Query: 1 MSVVGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQL 60 MS VG P++A++IQ++WDTNPRWK VTR Y+AE V LQGSV+E HTLA+RGAE+LW+ + Sbjct: 1 MSTVGKPRTADEIQKDWDTNPRWKGVTREYTAEQVAELQGSVLEAHTLAKRGAELLWDGV 60 Query: 61 HDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQV 120 + ++NALGALTGN AVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQV Sbjct: 61 NGENYINALGALTGNQAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQV 120 Query: 121 VRRINNALQRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSH 180 VRRINNA+ RAD+IA++E D +V+NW+ PIVADGEAGFGGALNVYELQKA+IAAG AG+H Sbjct: 121 VRRINNAMLRADEIARVEDDKAVDNWVVPIVADGEAGFGGALNVYELQKAMIAAGAAGTH 180 Query: 181 WEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSD 240 WEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVAD PTVVIARTDAEAATLITSD Sbjct: 181 WEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADTPTVVIARTDAEAATLITSD 240 Query: 241 VDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEA 300 VDERD+PFITG+RT EGFY + GIEPCIARAKAYAP++DLIWMETG PDLE AR+F+EA Sbjct: 241 VDERDKPFITGDRTVEGFYNVQKGIEPCIARAKAYAPYSDLIWMETGKPDLELARKFAEA 300 Query: 301 VKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFD 360 VK+E+PDQ+LAYNCSPSFNWK+HLDDATIAKFQ EL AMGFKFQFITLAGFHALNYSMFD Sbjct: 301 VKSEFPDQLLAYNCSPSFNWKQHLDDATIAKFQNELGAMGFKFQFITLAGFHALNYSMFD 360 Query: 361 LAYGYAQNQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNSSTTALTG 420 LAYGYA+ QMSAYV+LQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPN+ST AL G Sbjct: 361 LAYGYAREQMSAYVDLQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNTSTAALKG 420 Query: 421 STEEGQFH 428 STEEGQFH Sbjct: 421 STEEGQFH 428 Lambda K H 0.316 0.130 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: 753 Number of extensions: 14 Number of successful extensions: 1 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: 428 Length of database: 428 Length adjustment: 32 Effective length of query: 396 Effective length of database: 396 Effective search space: 156816 Effective search space used: 156816 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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