Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_028311044.1 H566_RS0108095 isocitrate lyase
Query= BRENDA::P9WKK7 (428 letters) >NCBI__GCF_000482785.1:WP_028311044.1 Length = 430 Score = 587 bits (1514), Expect = e-172 Identities = 288/421 (68%), Positives = 345/421 (81%), Gaps = 2/421 (0%) Query: 8 KSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVN 67 + A+Q+Q++W+ NPRWK + R YSAEDVV L+GS+ EHTLA+RGAE LW + +VN Sbjct: 6 EQAQQLQKDWNENPRWKGIQRGYSAEDVVRLRGSIQIEHTLAKRGAEKLWNLITTEPFVN 65 Query: 68 ALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNA 127 ALGALTGN A+QQV+AGLKAIYLSGWQVAGDANL+G YPDQSLYPANSVP VVRRINN Sbjct: 66 ALGALTGNQAMQQVKAGLKAIYLSGWQVAGDANLAGEMYPDQSLYPANSVPAVVRRINNT 125 Query: 128 LQRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLAS 187 QRADQI EG + + APIVAD EAGFGG LN +EL K++I AG AG H+EDQLAS Sbjct: 126 FQRADQIQWSEGKGDTD-FFAPIVADAEAGFGGVLNAFELMKSMIEAGAAGVHFEDQLAS 184 Query: 188 EKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQP 247 KKCGH+GGKVL+PT+ + L +ARLAADV VPTV++ARTDAEAA LIT+DVD+ D+P Sbjct: 185 VKKCGHMGGKVLVPTRDAVAKLVAARLAADVMGVPTVLVARTDAEAADLITTDVDDNDKP 244 Query: 248 FITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPD 307 F+TGERT EGF+RTK G+E I+R AYAP+ADLIW ETG PDLE A+ F+EA+ ++P Sbjct: 245 FLTGERTVEGFFRTKPGLEQAISRGLAYAPYADLIWCETGKPDLEYAKNFAEAIHKKFPG 304 Query: 308 QMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQ 367 +ML+YNCSPSFNWKK+LDDATIAKFQKEL AMG+KFQFITLAGFHALNYSMF+LA+GYA+ Sbjct: 305 KMLSYNCSPSFNWKKNLDDATIAKFQKELGAMGYKFQFITLAGFHALNYSMFNLAHGYAR 364 Query: 368 NQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNSSTTALTGSTEEGQ 426 QM A+VELQ+ EFAA ++G+TA KHQREVG GYFD + ++ SSTTAL GSTE+ Q Sbjct: 365 EQMKAFVELQQAEFAAADKGFTAVKHQREVGTGYFDAVTQCIEGGQSSTTALKGSTEDEQ 424 Query: 427 F 427 F Sbjct: 425 F 425 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: 655 Number of extensions: 24 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