Align Citrate lyase alpha chain; Citrase alpha chain; Citrate (pro-3S)-lyase alpha chain; Citrate CoA-transferase subunit; EC 4.1.3.6; EC 2.8.3.10 (characterized)
to candidate 14752 b0615 citrate lyase, citrate-ACP transferase (alpha) subunit (NCBI)
Query= SwissProt::P75726 (510 letters) >FitnessBrowser__Keio:14752 Length = 510 Score = 1000 bits (2586), Expect = 0.0 Identities = 510/510 (100%), Positives = 510/510 (100%) Query: 1 MTQKIEQSQRQERVAAWNRRAECDLAAFQNSPKQTYQAEKARDRKLCANLEEAIRRSGLQ 60 MTQKIEQSQRQERVAAWNRRAECDLAAFQNSPKQTYQAEKARDRKLCANLEEAIRRSGLQ Sbjct: 1 MTQKIEQSQRQERVAAWNRRAECDLAAFQNSPKQTYQAEKARDRKLCANLEEAIRRSGLQ 60 Query: 61 DGMTVSFHHAFRGGDLTVNMVMDVIAKMGFKNLTLASSSLSDCHAPLVEHIRQGVVTRIY 120 DGMTVSFHHAFRGGDLTVNMVMDVIAKMGFKNLTLASSSLSDCHAPLVEHIRQGVVTRIY Sbjct: 61 DGMTVSFHHAFRGGDLTVNMVMDVIAKMGFKNLTLASSSLSDCHAPLVEHIRQGVVTRIY 120 Query: 121 TSGLRGPLAEEISRGLLAEPVQIHSHGGRVHLVQSGELNIDVAFLGVPSCDEFGNANGYT 180 TSGLRGPLAEEISRGLLAEPVQIHSHGGRVHLVQSGELNIDVAFLGVPSCDEFGNANGYT Sbjct: 121 TSGLRGPLAEEISRGLLAEPVQIHSHGGRVHLVQSGELNIDVAFLGVPSCDEFGNANGYT 180 Query: 181 GKACCGSLGYAIVDADNAKQVVMLTEELLPYPHNPASIEQDQVDLIVKVDRVGDAAKIGA 240 GKACCGSLGYAIVDADNAKQVVMLTEELLPYPHNPASIEQDQVDLIVKVDRVGDAAKIGA Sbjct: 181 GKACCGSLGYAIVDADNAKQVVMLTEELLPYPHNPASIEQDQVDLIVKVDRVGDAAKIGA 240 Query: 241 GATRMTTNPRELLIARSAADVIVNSGYFKEGFSMQTGTGGASLAVTRFLEDKMRSRDIRA 300 GATRMTTNPRELLIARSAADVIVNSGYFKEGFSMQTGTGGASLAVTRFLEDKMRSRDIRA Sbjct: 241 GATRMTTNPRELLIARSAADVIVNSGYFKEGFSMQTGTGGASLAVTRFLEDKMRSRDIRA 300 Query: 301 DFALGGITATMVDLHEKGLIRKLLDVQSFDSHAAQSLARNPNHIEISANQYANWGSKGAS 360 DFALGGITATMVDLHEKGLIRKLLDVQSFDSHAAQSLARNPNHIEISANQYANWGSKGAS Sbjct: 301 DFALGGITATMVDLHEKGLIRKLLDVQSFDSHAAQSLARNPNHIEISANQYANWGSKGAS 360 Query: 361 VDRLDVVVLSALEIDTQFNVNVLTGSDGVLRGASGGHCDTAIASALSIIVAPLVRGRIPT 420 VDRLDVVVLSALEIDTQFNVNVLTGSDGVLRGASGGHCDTAIASALSIIVAPLVRGRIPT Sbjct: 361 VDRLDVVVLSALEIDTQFNVNVLTGSDGVLRGASGGHCDTAIASALSIIVAPLVRGRIPT 420 Query: 421 LVDNVLTCITPGSSVDILVTDHGIAVNPARPELAERLQEAGIKVVSIEWLRERARLLTGE 480 LVDNVLTCITPGSSVDILVTDHGIAVNPARPELAERLQEAGIKVVSIEWLRERARLLTGE Sbjct: 421 LVDNVLTCITPGSSVDILVTDHGIAVNPARPELAERLQEAGIKVVSIEWLRERARLLTGE 480 Query: 481 PQPIEFTDRVVAVVRYRDGSVIDVVHQVKE 510 PQPIEFTDRVVAVVRYRDGSVIDVVHQVKE Sbjct: 481 PQPIEFTDRVVAVVRYRDGSVIDVVHQVKE 510 Lambda K H 0.319 0.134 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: 978 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: 510 Length of database: 510 Length adjustment: 34 Effective length of query: 476 Effective length of database: 476 Effective search space: 226576 Effective search space used: 226576 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 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