Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate 200655 SO1484 isocitrate lyase (NCBI ptt file)
Query= BRENDA::P9WKK7 (428 letters) >FitnessBrowser__MR1:200655 Length = 440 Score = 528 bits (1361), Expect = e-154 Identities = 265/427 (62%), Positives = 334/427 (78%), Gaps = 10/427 (2%) Query: 11 EQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLE---WVN 67 + I+++W NPRWK+V R Y+AE+VVAL+GS+V E+T+A+RGA LW+ ++ +VN Sbjct: 14 DAIKKDWAENPRWKNVRRPYTAEEVVALRGSIVPENTIAKRGAAKLWDLVNGGSKKGYVN 73 Query: 68 ALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNA 127 +LGALTG AVQQ +AG++AIYLSGWQVA DANL+G YPDQSLYPANSVP VV RINN+ Sbjct: 74 SLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGTMYPDQSLYPANSVPAVVSRINNS 133 Query: 128 LQRADQIAKIEG----DTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWED 183 +RADQI G D + ++ PI+AD EAGFGG LN +EL K++I AG AG H+ED Sbjct: 134 FRRADQIQWSNGVNPEDENFVDYFLPIIADAEAGFGGVLNAFELMKSMIDAGAAGVHFED 193 Query: 184 QLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDE 243 QLAS KKCGH+GGKVL+PTQ+ ++ L +ARLAADV+ V T+VIARTDA AA L+TSD D Sbjct: 194 QLASVKKCGHMGGKVLVPTQEAVQKLVAARLAADVSGVETLVIARTDANAADLLTSDCDP 253 Query: 244 RDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKA 303 D+ F+TGERT EGFYR G++ I+R AYAP+ADLIW ET PDLE AR+F+EA+ A Sbjct: 254 YDRDFVTGERTNEGFYRVNAGLDQAISRGLAYAPYADLIWCETAKPDLEEARRFAEAIHA 313 Query: 304 EYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAY 363 +YPDQ+LAYNCSPSFNWKK+LDDATIA+FQ+ L+ MG+K+QFITLAG H + Y+MFDLAY Sbjct: 314 QYPDQLLAYNCSPSFNWKKNLDDATIARFQQALSDMGYKYQFITLAGIHNMWYNMFDLAY 373 Query: 364 GYAQNQ-MSAYVE-LQEREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNSSTTALTG 420 YA+ + M YVE +QE EFAA ++GYT HQ+EVG GYFD++ T + +SS TALTG Sbjct: 374 DYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVGTGYFDQVTTVIQGGHSSVTALTG 433 Query: 421 STEEGQF 427 STEE QF Sbjct: 434 STEEEQF 440 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: 612 Number of extensions: 23 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: 440 Length adjustment: 32 Effective length of query: 396 Effective length of database: 408 Effective search space: 161568 Effective search space used: 161568 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