Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate Ga0059261_1963 Ga0059261_1963 Isocitrate lyase
Query= BRENDA::Q9I0K4 (531 letters) >FitnessBrowser__Korea:Ga0059261_1963 Length = 531 Score = 846 bits (2185), Expect = 0.0 Identities = 422/528 (79%), Positives = 460/528 (87%), Gaps = 2/528 (0%) Query: 4 YQNEI-KAVAALKEKNGSSWSAINPEYAARMRIQNRFKTGLDIAKYTAAIMRKDMAEYDA 62 YQ+EI +A A + +NG W+ I+ E ARMR+QNRFKTGLDIAKYTA IMR+DMA YDA Sbjct: 3 YQDEIARANAPIAAENGR-WNGIDAESVARMRLQNRFKTGLDIAKYTAGIMRRDMAAYDA 61 Query: 63 DSSVYTQSLGCWHGFIGQQKLISIKKHLKTTNKRYLYLSGWMVAALRSDFGPLPDQSMHE 122 D S YTQSLGCWHGFI QQKLISIKKH TT RYLYLSGWMVAALRSDFGPLPDQSMHE Sbjct: 62 DPSAYTQSLGCWHGFIAQQKLISIKKHFGTTKGRYLYLSGWMVAALRSDFGPLPDQSMHE 121 Query: 123 KTAVSGLIEELYTFLRQADARELDLLFTGLDAARAAGDKAKEAELLAQIDNFETHVVPII 182 KT+V LIEELYTFL+QADAREL LF LD AR G++ + A + IDNFETHVVPII Sbjct: 122 KTSVPALIEELYTFLKQADARELGGLFRDLDKAREGGNEVEAARIQNAIDNFETHVVPII 181 Query: 183 ADIDAGFGNAEATYLLAKKMIEAGACCIQIENQVSDEKQCGHQDGKVTVPHIDFLAKINA 242 ADIDAGFGNAEATYLLAKKMIEAGAC +QIENQVSDEKQCGHQDGKVTVPH DFLAK+ A Sbjct: 182 ADIDAGFGNAEATYLLAKKMIEAGACALQIENQVSDEKQCGHQDGKVTVPHEDFLAKVRA 241 Query: 243 VRYAFLELGVDDGVIVARTDSLGAGLTKQIAVTNEPGDLGDLYNSFLDCEEISESELGNG 302 RYAFLELGVDDG+IV RTDSLGAGLTKQIA + E GDLGD YN+FLDCEE+++ G Sbjct: 242 CRYAFLELGVDDGIIVTRTDSLGAGLTKQIAYSKEKGDLGDQYNAFLDCEEVTDPATLRG 301 Query: 303 DVVIKREGKLLRPKRLASNLFQFRKGTGEDRCVLDCITSLQNGADLLWIETEKPHVGQIK 362 DVVI+R+GKL+RPKRL SNLFQFR+GTG DRCVLDCITSLQ+GADLLWIETEKPH+ QI Sbjct: 302 DVVIERDGKLMRPKRLPSNLFQFREGTGADRCVLDCITSLQHGADLLWIETEKPHIEQIA 361 Query: 363 AMVDRIREVIPNAKLVYNNSPSFNWTLNFRQQVFDAFVAEGKDVSAYDRNKLMSVEYDDT 422 +MVDRIREVIPNAKLVYNNSPSFNWTLNFRQQVFDA+ A GKDVSAYDR KLMSV+YD T Sbjct: 362 SMVDRIREVIPNAKLVYNNSPSFNWTLNFRQQVFDAWEAAGKDVSAYDRAKLMSVDYDGT 421 Query: 423 ELAKVADEKIRTFQRDGSAHAGIFHHLITLPTYHTAALSTDNLAKGYFADEGMLAYVKGV 482 +LA ADEKIRTFQ+D +A AGIFHHLITLPTYHTAALSTDNLAK YF DE ML YVKGV Sbjct: 422 DLAVEADEKIRTFQKDAAARAGIFHHLITLPTYHTAALSTDNLAKAYFGDEAMLGYVKGV 481 Query: 483 QRQELRQGIACVKHQNMAGSDIGDNHKEYFAGEAALKASGKDNTMNQF 530 QR+E+RQGIACVKHQNM+GSDIGD+HKEYFAGEAALKA G NTMNQF Sbjct: 482 QREEIRQGIACVKHQNMSGSDIGDDHKEYFAGEAALKAGGVHNTMNQF 529 Lambda K H 0.318 0.134 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: 922 Number of extensions: 21 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: 531 Length of database: 531 Length adjustment: 35 Effective length of query: 496 Effective length of database: 496 Effective search space: 246016 Effective search space used: 246016 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