Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate 6938260 Sama_2380 isocitrate lyase (RefSeq)
Query= BRENDA::P9WKK7 (428 letters) >FitnessBrowser__SB2B:6938260 Length = 439 Score = 526 bits (1355), Expect = e-154 Identities = 267/435 (61%), Positives = 331/435 (76%), Gaps = 10/435 (2%) Query: 4 VGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHD- 62 + + + ++++W NPRWK V R Y+AE+VV+L+GS V E+T+A+RGA LW+ ++ Sbjct: 5 ISRQEQIDALKKDWAENPRWKGVRRPYTAEEVVSLRGSFVPENTVAQRGAAKLWDLVNGG 64 Query: 63 --LEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQV 120 +VN+LGALTG AVQQ +AG++AIYLSGWQVA DANL+G YPDQSLYPANSVP V Sbjct: 65 AKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPANSVPAV 124 Query: 121 VRRINNALQRADQIAKIEG----DTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGV 176 V RINN+ +RADQI G D ++ PIVAD EAGFGG LN YEL K++I AG Sbjct: 125 VGRINNSFRRADQIQWSNGVGPEDDKFVDYFLPIVADAEAGFGGVLNAYELMKSMIDAGA 184 Query: 177 AGSHWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATL 236 AG H+EDQLAS KKCGH+GGKVL+PTQ+ ++ L +ARLAADV+ V T+VIARTDA AA L Sbjct: 185 AGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTDANAADL 244 Query: 237 ITSDVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQ 296 +TSD D D FITGERT EGFYR + G++ IAR AYAP+ADLIW ET PDLE AR+ Sbjct: 245 LTSDCDPYDSDFITGERTSEGFYRVRAGLDQAIARGLAYAPYADLIWCETAKPDLEEARR 304 Query: 297 FSEAVKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNY 356 F+EA+ A+YPDQ+LAYNCSPSFNWKK+LDDATIAKFQ+ L+ MG+K+QFITLAG H + + Sbjct: 305 FAEAIHAKYPDQLLAYNCSPSFNWKKNLDDATIAKFQQALSDMGYKYQFITLAGIHNMWF 364 Query: 357 SMFDLAYGYAQNQ-MSAYVE-LQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPN-S 413 +MFDLAY YA+ + M YVE +QE EFAA +GYT HQ+EVG GYFD++ + S Sbjct: 365 NMFDLAYDYARGEGMKHYVEKVQEAEFAAASKGYTFVAHQQEVGTGYFDKMTNIIQGGAS 424 Query: 414 STTALTGSTEEGQFH 428 S TALTGSTEE QFH Sbjct: 425 SVTALTGSTEEEQFH 439 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: 593 Number of extensions: 20 Number of successful extensions: 5 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: 439 Length adjustment: 32 Effective length of query: 396 Effective length of database: 407 Effective search space: 161172 Effective search space used: 161172 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 Apr 09 2024. 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