Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_043771407.1 U743_RS06375 isocitrate lyase
Query= BRENDA::P9WKK7 (428 letters) >NCBI__GCF_000733765.1:WP_043771407.1 Length = 437 Score = 500 bits (1287), Expect = e-146 Identities = 255/429 (59%), Positives = 320/429 (74%), Gaps = 12/429 (2%) Query: 11 EQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHD---LEWVN 67 +Q++ +W TNPRWK V R YSA DVV L+GSV E+TLAR+GAE LW ++ +VN Sbjct: 8 KQLENDWATNPRWKGVKRPYSATDVVRLRGSVQPEYTLARQGAEKLWNLVNGGAKKGYVN 67 Query: 68 ALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNA 127 + GA++ A+QQ +AGL+A+YLSGWQVA D N S YPDQSLY +SVP +VRRINN Sbjct: 68 SFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPAMVRRINNT 127 Query: 128 LQRADQIA---KIEGDTSVEN---WLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHW 181 QRAD+I +G+ S ++ + PIVAD EAGFGG LN +EL K +I G AG+H+ Sbjct: 128 FQRADEIQWKKLCDGEMSEKDAIDYFLPIVADAEAGFGGVLNGFELMKNMIRNGAAGAHY 187 Query: 182 EDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDV 241 EDQLA+ KKCGH+GGKVL+PT++ I L +ARLAADV +VPT+V ARTDAEAA LITSD Sbjct: 188 EDQLAAVKKCGHMGGKVLVPTKEAIEKLVAARLAADVLNVPTLVFARTDAEAANLITSDH 247 Query: 242 DERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAV 301 D D PF+TG+RT EGFYR KNG+E I+R AYAPFAD++W ETGTPDL A++F++AV Sbjct: 248 DANDAPFLTGDRTAEGFYRVKNGLEQAISRGVAYAPFADMVWCETGTPDLGFAKEFADAV 307 Query: 302 KAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDL 361 + E P Q+LAYNCSPSFNWKK+LDD TIAKFQ+EL++ G+K+QFITLAG H Y+ F+ Sbjct: 308 RKENPGQLLAYNCSPSFNWKKNLDDKTIAKFQEELSSYGYKYQFITLAGIHINWYNTFEF 367 Query: 362 AYGYAQNQ-MSAYVEL-QEREFAAEERGYTATKHQREVGAGYFDRIATTVDPN-SSTTAL 418 A+ YAQ + M Y E+ Q+ EF A E+GYT HQ+EVGAGYFD + T + SS TAL Sbjct: 368 AHKYAQGEGMKHYTEMVQQPEFEAREKGYTFVSHQQEVGAGYFDDVTTVIQGGASSVTAL 427 Query: 419 TGSTEEGQF 427 TGSTEE QF Sbjct: 428 TGSTEEEQF 436 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: 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: 437 Length adjustment: 32 Effective length of query: 396 Effective length of database: 405 Effective search space: 160380 Effective search space used: 160380 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