Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate 5208774 Shew_1276 isocitrate lyase (RefSeq)
Query= BRENDA::P9WKK7 (428 letters) >FitnessBrowser__PV4:5208774 Length = 450 Score = 536 bits (1380), Expect = e-157 Identities = 275/434 (63%), Positives = 335/434 (77%), Gaps = 10/434 (2%) Query: 4 VGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHD- 62 + + + I+Q+W NPRW V R YSAEDVVAL+GS+V E+TLA RGAE LW+ ++ Sbjct: 17 ISRQQQIDAIKQDWAENPRWAGVRRPYSAEDVVALRGSIVPENTLATRGAEKLWQLVNGG 76 Query: 63 --LEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQV 120 +VN+LGALTG AVQQ +AG++AIYLSGWQVA DANL+G YPDQSLYPANSVP V Sbjct: 77 AKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPANSVPAV 136 Query: 121 VRRINNALQRADQIA---KIEG-DTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGV 176 V+RINN+ +RADQI +I+ D ++ PIVAD EAGFGG LN YEL K +I AG Sbjct: 137 VQRINNSFRRADQIQWSNEIDPQDERYTDYFLPIVADAEAGFGGVLNAYELMKNMIDAGA 196 Query: 177 AGSHWEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATL 236 AG H+EDQLAS KKCGH+GGKVL+PTQ+ ++ L SARLAADV+ VPT+VIARTDA AA L Sbjct: 197 AGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVSARLAADVSGVPTLVIARTDANAADL 256 Query: 237 ITSDVDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQ 296 +TSD D D+ FITGERT EGFYR GI+ I+R AYAP+ADLIW ET PDLE AR+ Sbjct: 257 LTSDCDPYDRDFITGERTSEGFYRVNAGIDQAISRGLAYAPYADLIWCETAKPDLEEARR 316 Query: 297 FSEAVKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNY 356 F+EA+ A+YPDQ+LAYNCSPSFNWKK+LDDATIA+FQ+EL+ MG+K+QFITLAG H + Y Sbjct: 317 FAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMGYKYQFITLAGIHNMWY 376 Query: 357 SMFDLAYGYAQNQ-MSAYVE-LQEREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNS 413 +MFDLAY YA+ + M YVE +QE EFAA ++GYT HQ+EVG GYFD++ + S Sbjct: 377 NMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDKVTNVIQGGES 436 Query: 414 STTALTGSTEEGQF 427 S TALTGSTEE QF Sbjct: 437 SVTALTGSTEEEQF 450 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: 615 Number of extensions: 18 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: 450 Length adjustment: 32 Effective length of query: 396 Effective length of database: 418 Effective search space: 165528 Effective search space used: 165528 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