Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate Pf6N2E2_279 Isocitrate lyase (EC 4.1.3.1)
Query= BRENDA::P9WKK7 (428 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_279 Length = 441 Score = 543 bits (1398), Expect = e-159 Identities = 269/430 (62%), Positives = 332/430 (77%), Gaps = 14/430 (3%) Query: 13 IQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLH---------DL 63 ++++W NPRWK V R YSA DVV L+GSV EHTLA+ GAE LW + + Sbjct: 12 LEKDWAENPRWKGVKRNYSAADVVRLRGSVQPEHTLAKMGAEKLWNLVTQGAKPAFRPEK 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 AIKKEYPDQILSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAGIHNMWHSMF 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: 639 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:
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