Align Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 (characterized)
to candidate Ac3H11_2326 Methylisocitrate lyase (EC 4.1.3.30)
Query= SwissProt::D4GTL3 (345 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2326 Length = 289 Score = 134 bits (338), Expect = 2e-36 Identities = 79/261 (30%), Positives = 133/261 (50%), Gaps = 12/261 (4%) Query: 21 RELREMLNTQDFVFAPGMYHALDARLAEMTGHDAAYMSGYSTVLGQFGFPDLEMVTMTEM 80 ++L+ + + V PG ++AL AR+ G +A Y++G FG PD + +T++ Sbjct: 8 QQLKALAQARRGVIVPGAFNALSARVVADLGFEAIYVTGAGVTNMWFGLPDQAFMGLTDI 67 Query: 81 VENAKRMVEATNLPVIADCDTGYGGIHNVRRAVREYEKAGVAAVHIEDQTTPKRCGHIAG 140 ++ R+ +A LP+I D DTG+G N AVR E+AG + +EDQ +PKRCGH G Sbjct: 68 ADHTARIRDAVELPLIVDADTGFGNALNTYHAVRTLERAGADCIQLEDQVSPKRCGHFNG 127 Query: 141 KQIVSREKAKARFEAAVDAKQSEDTVVIARTDAYGSSNGDWDEHVERGRIYADAGVDIVW 200 K+++ ++ + +AAVDA++ T+++ARTDA + ++ VER + + +AG DI++ Sbjct: 128 KEVIGTDEMLGKIKAAVDARRDAGTLILARTDACATQG--FEAAVERAQRFQEAGADILF 185 Query: 201 PEMPNPSREDAVAYAEEIHETHPDLKLAFNYSSSFAWSEEEDPLTFQELGDLGYKYIFIT 260 E AV +EI +LA + + + +EL LGY + Sbjct: 186 VE--------AVTTLDEIRAL--PQRLAAPQLMNMVIGGKTPITSAEELATLGYGLVLYA 235 Query: 261 LFGLHSGAHAVYEDFKKLAEQ 281 L + + L EQ Sbjct: 236 NAALQGAVAGMQKALTVLREQ 256 Lambda K H 0.315 0.132 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: 232 Number of extensions: 14 Number of successful extensions: 1 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: 345 Length of database: 289 Length adjustment: 27 Effective length of query: 318 Effective length of database: 262 Effective search space: 83316 Effective search space used: 83316 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: 42 (22.0 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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