Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate AO356_22080 AO356_22080 isocitrate lyase
Query= BRENDA::P9WKK7 (428 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 AO356_22080 isocitrate lyase Length = 441 Score = 541 bits (1395), Expect = e-158 Identities = 268/430 (62%), Positives = 331/430 (76%), Gaps = 14/430 (3%) Query: 13 IQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLH---------DL 63 ++++W NPRWK V R YSA DVV L+GSV EHT A+ GAE LW + + Sbjct: 12 LEKDWAENPRWKGVKRNYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVTQGAKPAFRPEK 71 Query: 64 EWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRR 123 ++VN +GALTG AVQQV+AG++AIYLSGWQVA D N + YPDQSLYP +SVP VV+R Sbjct: 72 DFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLYPVDSVPTVVKR 131 Query: 124 INNALQRADQI----AKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGS 179 INN+ +RADQI K GD ++ APIVAD EAGFGG LN YEL K++I AG AG Sbjct: 132 INNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELMKSMIEAGAAGV 191 Query: 180 HWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITS 239 H+EDQLAS KKCGH+GGKVL+PTQ+ ++ LT+ARLAADVA VPT+++ARTDA AA L+TS Sbjct: 192 HFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGVPTIILARTDANAADLLTS 251 Query: 240 DVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSE 299 D D DQPF+TG RT+EGFY+ + G++ IAR AYAP+ADLIW ET PDL+ AR+F+E Sbjct: 252 DCDPYDQPFVTGTRTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAKPDLDEARRFAE 311 Query: 300 AVKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMF 359 A+K EYPDQ+L+YNCSPSFNWKK+LDDATIAKFQ+EL+AMG+K QFITLAG H + +SMF Sbjct: 312 AIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAGIHNMWHSMF 371 Query: 360 DLAYGYAQNQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNSSTTAL 418 +LA+ YA+N M+AYV+LQE+EFA +GYT HQ+EVG GYFD + T + SS TAL Sbjct: 372 NLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTVIQGGTSSVTAL 431 Query: 419 TGSTEEGQFH 428 TGSTEE QFH Sbjct: 432 TGSTEEEQFH 441 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: 632 Number of extensions: 14 Number of successful extensions: 4 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: 441 Length adjustment: 32 Effective length of query: 396 Effective length of database: 409 Effective search space: 161964 Effective search space used: 161964 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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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