Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_057509262.1 ABB28_RS14275 isocitrate lyase
Query= BRENDA::P9WKK7 (428 letters) >NCBI__GCF_001431535.1:WP_057509262.1 Length = 430 Score = 588 bits (1517), Expect = e-173 Identities = 287/425 (67%), Positives = 345/425 (81%), Gaps = 2/425 (0%) Query: 4 VGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDL 63 + T +AEQIQ +WDTNPRW + R Y+A DVV L+G+V EH+LAR GAE LW L + Sbjct: 1 MSTLPTAEQIQHDWDTNPRWHGIERNYTAADVVRLRGTVHVEHSLARMGAEKLWTYLQEK 60 Query: 64 EWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRR 123 ++VNALGALTGN A+QQV+AGL AIYLSGWQVA DANL+G YPDQSLYPA+SVP VV+R Sbjct: 61 DFVNALGALTGNQAMQQVKAGLNAIYLSGWQVAADANLAGQMYPDQSLYPADSVPAVVKR 120 Query: 124 INNALQRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWED 183 INN L RADQ+ EG ++ +L PIVAD EAGFGG LN +EL KA+I AG AG H+ED Sbjct: 121 INNTLLRADQLHHAEGKDEID-FLQPIVADAEAGFGGVLNAFELMKAMIEAGAAGVHFED 179 Query: 184 QLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDE 243 QLAS KKCGH+GGKVL+PT++ I L +ARLAADV VPT+++ARTDAEAA L+TSD+D Sbjct: 180 QLASVKKCGHMGGKVLVPTREAIEKLNAARLAADVLGVPTLLVARTDAEAADLLTSDIDA 239 Query: 244 RDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKA 303 DQPF TGERT EGFY+T+NG++ I+R AYAP+ADL+W ETG PDLE ARQF+EA+ A Sbjct: 240 NDQPFATGERTTEGFYKTRNGLDQAISRGLAYAPYADLVWCETGKPDLEFARQFAEAIHA 299 Query: 304 EYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAY 363 ++P ++LAYNCSPSFNWKK+LDDATIA FQ E+A G++FQFITLAGFHALNYSMF+LA+ Sbjct: 300 KFPGKLLAYNCSPSFNWKKNLDDATIATFQTEIAKYGYRFQFITLAGFHALNYSMFNLAH 359 Query: 364 GYAQNQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDP-NSSTTALTGST 422 GYA+ QMSA+VELQE EFAA +RG+TA KHQREVG GYFD + + SSTTALTGST Sbjct: 360 GYARRQMSAFVELQEAEFAAADRGFTAVKHQREVGTGYFDAVTQAIQQGQSSTTALTGST 419 Query: 423 EEGQF 427 EE QF Sbjct: 420 EEAQF 424 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: 588 Number of extensions: 16 Number of successful extensions: 3 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: 430 Length adjustment: 32 Effective length of query: 396 Effective length of database: 398 Effective search space: 157608 Effective search space used: 157608 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 24 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