Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate Ac3H11_2831 Isocitrate lyase (EC 4.1.3.1)
Query= BRENDA::P9WKK7 (428 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2831 Length = 443 Score = 491 bits (1263), Expect = e-143 Identities = 247/426 (57%), Positives = 314/426 (73%), Gaps = 10/426 (2%) Query: 13 IQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHD---LEWVNAL 69 ++++W TNPRWK V R YSA DVV L+GS+ EHTLA+RGAE LW++++ +VNA Sbjct: 18 LEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEKLWDKINGGAKKGYVNAF 77 Query: 70 GALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQ 129 GA++ A+QQ +AGL+A+YLSGWQVA D N S YPDQSLY +SVP +VRRINN + Sbjct: 78 GAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMVRRINNTFK 137 Query: 130 RADQI----AKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQL 185 RAD+I GD ++ PIVAD EAGFGG LN +EL K +I +G AG H+EDQL Sbjct: 138 RADEIQWGRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELMKNMIQSGAAGVHFEDQL 197 Query: 186 ASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERD 245 A+ KKCGH+GGKVL+PTQ+ L SAR AADV V T+V+ARTDAEAA LITSD D D Sbjct: 198 AAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLARTDAEAANLITSDHDAND 257 Query: 246 QPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEY 305 +PF+TGERT+EGFYR KNG+E I+R AYAP+ADL+W ETG PD+ AR+F++AV A Sbjct: 258 KPFLTGERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGVPDIGFAREFAQAVHAAC 317 Query: 306 PDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGY 365 P ++L+YNCSPSFNWKK+L+D IA FQ++L+A+G+K+QFITLAG H ++ F A+ Y Sbjct: 318 PGKLLSYNCSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITLAGIHINWFNTFQFAHAY 377 Query: 366 AQNQ-MSAYVEL-QEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNSSTT-ALTGST 422 A + M YV + QE EFAA ++GYT HQ+EVGAGYFD + T + SS+ ALTGST Sbjct: 378 ANGEGMKHYVNMVQEPEFAARDKGYTFVSHQQEVGAGYFDDVTTVIQGGSSSVKALTGST 437 Query: 423 EEGQFH 428 EE QFH Sbjct: 438 EEEQFH 443 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: 599 Number of extensions: 28 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: 443 Length adjustment: 32 Effective length of query: 396 Effective length of database: 411 Effective search space: 162756 Effective search space used: 162756 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