Align Isocitrate lyase; ICL; Isocitrase; Isocitratase; EC 4.1.3.1 (characterized)
to candidate CCNA_01841 CCNA_01841 isocitrate lyase
Query= SwissProt::O50078 (540 letters) >FitnessBrowser__Caulo:CCNA_01841 Length = 539 Score = 887 bits (2293), Expect = 0.0 Identities = 439/540 (81%), Positives = 480/540 (88%), Gaps = 1/540 (0%) Query: 1 MAHKKTYSQLRSELLARYPVGLTKGGVSIDDIVQLRLQSPYESHLDVARAMASVMRADMA 60 M +KTY++ R LLARYP G+T GGV +DDI+QL+LQ+ + +HLD+ARAMA VMRADMA Sbjct: 1 MTQRKTYAEHRDALLARYPQGVTPGGVDVDDIIQLKLQNTFNTHLDIARAMAPVMRADMA 60 Query: 61 AYDRDTGKFTQSLGCWSGFHAQQMIKAVKRLRGTTKGAYVYLSGWMVAGLRNRWGHLPDQ 120 YDRD+ KFTQSLGCWSGFHAQQMIKAVKRLRGTTKGAYVYLSGWMVAGLRNR+GHLPDQ Sbjct: 61 EYDRDSSKFTQSLGCWSGFHAQQMIKAVKRLRGTTKGAYVYLSGWMVAGLRNRFGHLPDQ 120 Query: 121 SMHEKTSVVDLIEEIYVSLRQADEVALNDLFNELKDARAKGATNKACEEIISRIDGFESH 180 SMHEKTSVVDLIEEIYVSLRQADEVA+NDLF L AR K A + I ID FE+H Sbjct: 121 SMHEKTSVVDLIEEIYVSLRQADEVAINDLFKALSAAR-KAGDQIAEQAAIKAIDNFETH 179 Query: 181 VVPIIADIDAGFGNEHATYLLAKEMIKAGACCLQIENQVSDAKQCGHQDGKVTVPREDFI 240 VVPIIADIDAGFGNEHATYLLAKEMIKAGACCLQIENQVSDAKQCGHQDGKVTVPREDFI Sbjct: 180 VVPIIADIDAGFGNEHATYLLAKEMIKAGACCLQIENQVSDAKQCGHQDGKVTVPREDFI 239 Query: 241 EKLRACRLAFEELGVDDGVIVARTDSLGASLTQKIPVSQQAGDFASSYIKWLKTEPITDA 300 EKLRACRLAFEELGVDDGVIVARTDSLGA LTQKIPVSQ+ GD AS YIKWLKTEP+T Sbjct: 240 EKLRACRLAFEELGVDDGVIVARTDSLGAGLTQKIPVSQEPGDLASDYIKWLKTEPVTPE 299 Query: 301 NPLSEGELAIWQSGNFARPIRMPNGLFSFREGTGRARVIEDCIASLKDGDADLIWIETDT 360 NPL +GELAI + G F +P+RMPNGLF+F++GTGR RVIEDCIA+L G ADL+WIETDT Sbjct: 300 NPLKDGELAIMKDGAFVKPVRMPNGLFAFQDGTGRQRVIEDCIANLTQGGADLLWIETDT 359 Query: 361 PNVDEIASMVAEIRKQVPDAKLVYNNSPSFNWTLNLRKQVRAQWISEGKIAEADYPDGTA 420 PNVDEIASMVAE+R+ VP+AKL YNNSPSFNWTLNLRKQVR QWI+EGKI + YPDG A Sbjct: 360 PNVDEIASMVAEVRRVVPNAKLTYNNSPSFNWTLNLRKQVRDQWIAEGKIHKDSYPDGNA 419 Query: 421 LMSAQYDTSELGREADDRLRQFQVDISARAGVFHNLITLPTFHLTAKSTDELSHGYFGED 480 LMSA+YD S+LGREAD+RL +FQVDI+ARAGVFHNLITLPTFHLTAKS DELS GYFGED Sbjct: 420 LMSAEYDKSDLGREADERLARFQVDIAARAGVFHNLITLPTFHLTAKSVDELSRGYFGED 479 Query: 481 RMLAYVATVQREEIRRSISAVRHQHEVGSDLGDTFKEMVSGDRALKAGGAHNTMNQFAAE 540 RM AYV TVQREEIRR +SAV+HQHEVGSDLGDTFKEMV+G+RALKAGG NTMNQFAAE Sbjct: 480 RMQAYVNTVQREEIRRGVSAVKHQHEVGSDLGDTFKEMVAGERALKAGGHANTMNQFAAE 539 Lambda K H 0.318 0.133 0.388 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: 1024 Number of extensions: 29 Number of successful extensions: 2 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: 540 Length of database: 539 Length adjustment: 35 Effective length of query: 505 Effective length of database: 504 Effective search space: 254520 Effective search space used: 254520 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 (21.7 bits) S2: 52 (24.6 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