Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_012971046.1 ALVIN_RS09180 isocitrate lyase
Query= BRENDA::P9WKK7 (428 letters) >NCBI__GCF_000025485.1:WP_012971046.1 Length = 435 Score = 510 bits (1313), Expect = e-149 Identities = 257/428 (60%), Positives = 324/428 (75%), Gaps = 10/428 (2%) Query: 11 EQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLE---WVN 67 + I+++W NPRW DV R YSA DVV L+GSV E+T A+ GAE LW+++ +VN Sbjct: 8 QAIERDWAENPRWTDVERGYSAADVVRLRGSVQPEYTYAKLGAEKLWKRIRGESKKGYVN 67 Query: 68 ALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNA 127 +GA+TG A+QQ +AG++AIYLSGWQVA D N S YPDQSLY +SVP +VRRINN+ Sbjct: 68 CMGAITGGQAMQQAKAGIEAIYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMVRRINNS 127 Query: 128 LQRADQIAKIEG----DTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWED 183 +RAD+I G D ++ PIVAD EAGFGG LN +EL K +IA G AG H+ED Sbjct: 128 FKRADEIQWSRGIGPGDEGYIDYFLPIVADAEAGFGGVLNAFELMKNMIANGAAGVHFED 187 Query: 184 QLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDE 243 QLA+ KKCGH+GGKVL+PT++ ++ L +ARLAADV VPT+++ARTDAEAA L+TSDVD+ Sbjct: 188 QLAAVKKCGHMGGKVLVPTREAVQKLIAARLAADVMGVPTLLLARTDAEAANLLTSDVDD 247 Query: 244 RDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKA 303 D+PF+TG RT EGFY KNG+E I+R AYAP+ADL+W ETGTPDL AR+F++AV Sbjct: 248 NDRPFVTGARTDEGFYVVKNGLEQAISRGLAYAPYADLVWCETGTPDLGFAREFAQAVLG 307 Query: 304 EYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAY 363 P+++LAYNCSPSFNWKK+LDD TIA+FQ+ELA MG+K+QFITLAG H++ Y+MFDLAY Sbjct: 308 ANPNKLLAYNCSPSFNWKKNLDDRTIARFQEELADMGYKYQFITLAGIHSMWYNMFDLAY 367 Query: 364 GYAQNQ-MSAYVE-LQEREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNSSTTALTG 420 YA+ + M YVE +Q EFAA E+GYT HQ+EVGAGYFD + T + SS TALTG Sbjct: 368 DYARGEGMRHYVEKVQGPEFAAREKGYTFVSHQQEVGAGYFDDVTTVIQGGQSSVTALTG 427 Query: 421 STEEGQFH 428 STEE QFH Sbjct: 428 STEEEQFH 435 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: 15 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: 435 Length adjustment: 32 Effective length of query: 396 Effective length of database: 403 Effective search space: 159588 Effective search space used: 159588 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