Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate N515DRAFT_4123 N515DRAFT_4123 isocitrate lyase
Query= BRENDA::P9WKK7 (428 letters) >FitnessBrowser__Dyella79:N515DRAFT_4123 Length = 433 Score = 591 bits (1523), Expect = e-173 Identities = 282/421 (66%), Positives = 347/421 (82%), Gaps = 2/421 (0%) Query: 9 SAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLEWVNA 68 +AEQI +W NPRW V R Y+A DVV L+G+V EH++AR GAE LW+ L ++VNA Sbjct: 7 TAEQITLDWQNNPRWNGVRRNYTAADVVRLRGTVPVEHSIARHGAERLWKSLQQEDFVNA 66 Query: 69 LGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNAL 128 LGALTGN A+QQV+AGLKAIYLSGWQVA DANL+G YPDQSLYPANSVPQVV+RINN L Sbjct: 67 LGALTGNQAMQQVKAGLKAIYLSGWQVAADANLAGEMYPDQSLYPANSVPQVVKRINNTL 126 Query: 129 QRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQLASE 188 RADQ+ EG+ ++ W+ PIVAD EAGFGG LN +EL KA+I AG +G H+EDQLAS Sbjct: 127 LRADQLHHAEGNDEID-WMVPIVADAEAGFGGVLNAFELMKAMIEAGASGVHFEDQLASV 185 Query: 189 KKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERDQPF 248 KKCGH+GGKVL+PT++ + LT+ARLAADV VPT+++ARTDA+AA L+TSD+D+ D+PF Sbjct: 186 KKCGHMGGKVLVPTREAVDKLTAARLAADVLGVPTLLVARTDADAADLLTSDIDDNDRPF 245 Query: 249 ITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEYPDQ 308 +TGERT EGF+R + G++ I+R AYAP+ADL+W ET P+LE AR+F+EA+ A++P + Sbjct: 246 VTGERTVEGFFRVRPGLDQAISRGLAYAPYADLVWCETSKPNLEEARRFAEAIHAQFPGK 305 Query: 309 MLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGYAQN 368 +LAYNCSPSFNWKK+LDDATIA+FQ+EL AMG+KFQFITLAGFH+LNY MFDLA+GYA+ Sbjct: 306 LLAYNCSPSFNWKKNLDDATIARFQRELGAMGYKFQFITLAGFHSLNYGMFDLAHGYARR 365 Query: 369 QMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDP-NSSTTALTGSTEEGQF 427 QMSA+VELQEREFAA ERG+TA KHQREVG GYFD++ + SSTTAL GSTEE QF Sbjct: 366 QMSAFVELQEREFAAAERGFTAVKHQREVGTGYFDQVTQAIQQGQSSTTALKGSTEEAQF 425 Query: 428 H 428 H Sbjct: 426 H 426 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: 621 Number of extensions: 21 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: 433 Length adjustment: 32 Effective length of query: 396 Effective length of database: 401 Effective search space: 158796 Effective search space used: 158796 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