Align Citrate lyase subunit beta; Citrase beta chain; Citrate (pro-3S)-lyase subunit beta; Citryl-CoA lyase subunit; EC 4.1.3.6; EC 4.1.3.34 (characterized)
to candidate 3609102 Dshi_2490 Citryl-CoA lyase (RefSeq)
Query= SwissProt::P0A9I1 (302 letters) >FitnessBrowser__Dino:3609102 Length = 310 Score = 132 bits (332), Expect = 1e-35 Identities = 93/299 (31%), Positives = 147/299 (49%), Gaps = 14/299 (4%) Query: 9 RKTRTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLY 68 RK R +RS L VP +N M+ + AD + DLED+VA EK AR+ AL + Sbjct: 2 RKQRLQRSELAVPASNPTMIDKAAESAADFVFLDLEDAVAPPEKVQARKNAIQALNDIDW 61 Query: 69 --RDIETIVRVNALDSEWGVNDLEAVVRGGADVVR---LPKTDTAQDVLDIEKEILRIEK 123 + VR+N LD+ + D+ ++ D V +PK D+ +E + + E Sbjct: 62 AAKGKTVSVRINGLDTHYMYRDVVDIMEQAGDRVHTLLVPKVGVTADLYMVEAMVNQAEM 121 Query: 124 ACGREPGSTGLLAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRTER------SP 177 ACG E GL A IE+ LG+ IA RL + G DY ++R +P Sbjct: 122 ACGLET-RVGLEALIETALGMANVEAIAQFGGRLEALHFGVADYAASMRARTVNIGGLNP 180 Query: 178 E--GTELLFARCSILQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPR 235 + G + + ++ A R+ G++A D + D ++ G++ A LG +GK I+P Sbjct: 181 DYPGDQWHASITRMVIACRAYGLRAIDGPFGDFSDPDGYMAGARRAAALGCEGKWAIHPS 240 Query: 236 QIDLLHNLYAPTQKEVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRA 294 QI++ +++++P + EV A R++E A G G SL+GKM+D AR V+ A Sbjct: 241 QIEMANDVFSPPEAEVSKAHRIIEELRNAEAAGKGAASLDGKMIDAASEKMARNVIDTA 299 Lambda K H 0.318 0.134 0.369 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: 214 Number of extensions: 12 Number of successful extensions: 4 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: 302 Length of database: 310 Length adjustment: 27 Effective length of query: 275 Effective length of database: 283 Effective search space: 77825 Effective search space used: 77825 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: 48 (23.1 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