Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate GFF3292 HP15_3234 isocitrate lyase
Query= BRENDA::Q9I0K4 (531 letters) >FitnessBrowser__Marino:GFF3292 Length = 530 Score = 858 bits (2217), Expect = 0.0 Identities = 427/528 (80%), Positives = 474/528 (89%), Gaps = 2/528 (0%) Query: 4 YQNEIKAVAALKEKNGSSWSAINPEYAARMRIQNRFKTGLDIAKYTAAIMRKDMAEYDAD 63 Y ++ +A+L +++ +W+AINP++AARMR QN+FKTGLDIAKYTA IMR+DMA YD D Sbjct: 3 YAQDVDQIASLLKQH-PTWNAINPKHAARMRAQNKFKTGLDIAKYTAKIMREDMANYDKD 61 Query: 64 SSVYTQSLGCWHGFIGQQKLISIKKHLKTTNKRYLYLSGWMVAALRSDFGPLPDQSMHEK 123 +S YTQSLGCWHGFIGQQK++SIKKH TT +RYLYLSGWMVAALRS+FGPLPDQSMHEK Sbjct: 62 TSQYTQSLGCWHGFIGQQKMLSIKKHFGTTKRRYLYLSGWMVAALRSEFGPLPDQSMHEK 121 Query: 124 TAVSGLIEELYTFLRQADARELDLLFTGLDAARAAGDKAKEAELLAQIDNFETHVVPIIA 183 TAVSGLIEELYTFLRQADA EL+ LF L+ A AGD AK EL+ QIDN ETHVVPIIA Sbjct: 122 TAVSGLIEELYTFLRQADAWELNHLFRALEEAENAGDNAKAEELIKQIDNHETHVVPIIA 181 Query: 184 DIDAGFGNAEATYLLAKKMIEAGACCIQIENQVSDEKQCGHQDGKVTVPHIDFLAKINAV 243 DIDAGFGNAEATYLLAK+MIEAGACCIQIENQVSDEKQCGHQDGKVTVPH DFL+KINAV Sbjct: 182 DIDAGFGNAEATYLLAKQMIEAGACCIQIENQVSDEKQCGHQDGKVTVPHADFLSKINAV 241 Query: 244 RYAFLELGVDDGVIVARTDSLGAGLTKQIAVTNEPGDLGDLYNSFLDCEEISESE-LGNG 302 R AFLELGVDDGVIVARTDSLGAGLT++IAVTNEPGDLGD YNSF+D E I ++E + NG Sbjct: 242 RLAFLELGVDDGVIVARTDSLGAGLTQKIAVTNEPGDLGDQYNSFIDGEVIEKAEDINNG 301 Query: 303 DVVIKREGKLLRPKRLASNLFQFRKGTGEDRCVLDCITSLQNGADLLWIETEKPHVGQIK 362 DVVIK+ G+L+RPKRLAS LFQF+ GTGEDR VLDCITSLQNGADLLWIETEKPHVGQI Sbjct: 302 DVVIKQNGQLVRPKRLASGLFQFKPGTGEDRVVLDCITSLQNGADLLWIETEKPHVGQIA 361 Query: 363 AMVDRIREVIPNAKLVYNNSPSFNWTLNFRQQVFDAFVAEGKDVSAYDRNKLMSVEYDDT 422 AMV+RI+EV+P+AKLVYNNSPSFNWTLNFRQQVFDA+ EGKDVSAYDR KLMS EYD+T Sbjct: 362 AMVNRIKEVVPDAKLVYNNSPSFNWTLNFRQQVFDAWKEEGKDVSAYDRAKLMSEEYDNT 421 Query: 423 ELAKVADEKIRTFQRDGSAHAGIFHHLITLPTYHTAALSTDNLAKGYFADEGMLAYVKGV 482 EL ++ADE R FQRDGS AGIFHHLITLPTYHTAALSTDNLAKGYF DEGMLAYV GV Sbjct: 422 ELGQLADEWCRNFQRDGSREAGIFHHLITLPTYHTAALSTDNLAKGYFGDEGMLAYVAGV 481 Query: 483 QRQELRQGIACVKHQNMAGSDIGDNHKEYFAGEAALKASGKDNTMNQF 530 QR+E+RQGIA VKHQ+MAGS+IGD+HKE+FAGEAALKA GKDNTMNQF Sbjct: 482 QRKEIRQGIATVKHQDMAGSNIGDDHKEFFAGEAALKAGGKDNTMNQF 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: 911 Number of extensions: 24 Number of successful extensions: 3 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: 530 Length adjustment: 35 Effective length of query: 496 Effective length of database: 495 Effective search space: 245520 Effective search space used: 245520 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