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 WP_011427269.1 RHE_RS20895 CoA ester lyase
Query= SwissProt::P0A9I1 (302 letters) >NCBI__GCF_000092045.1:WP_011427269.1 Length = 301 Score = 139 bits (351), Expect = 6e-38 Identities = 93/297 (31%), Positives = 148/297 (49%), Gaps = 9/297 (3%) Query: 9 RKTRTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLY 68 R + RRS+L VP N + S DA++FDLEDSVA +K+ AR + P Sbjct: 8 RSSSLRRSVLSVPAINLRALEKSRSLDCDAVIFDLEDSVAPEKKEEARENLRRFFAGPPL 67 Query: 69 RDIETIVRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGRE 128 E I+R+N+L SE+G DL+ V D V LPK D QDV D+ + +A +E Sbjct: 68 EGKERIIRINSLSSEFGPADLDLVKEVSPDAVLLPKVDEPQDVTDVGD---LLTEADAQE 124 Query: 129 PGSTGLLAAIESPLGITRAVEIAH----ASERLIGIALGAEDYVRNLRTERSPEGTELLF 184 + A IE+P G+ IA RL + +G D + P T L+ Sbjct: 125 --EVRIWAMIETPRGVLNVGAIAEFGHTPGSRLDCLVVGLNDLRKETGVLPQPGRTYLVP 182 Query: 185 ARCSILQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLY 244 ++ A ++ G+ A D+V++D + GF E + +GF GK LI+P QI + + Sbjct: 183 WLMQVILAVKAYGLDALDSVFNDFRDGEGFEAECGQGRAMGFAGKMLIHPTQIAAANRHF 242 Query: 245 APTQKEVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRAELSGIRE 301 P+ +E+ A+ ++ A A GL V++ NG+M++ + +A ++ +A L R+ Sbjct: 243 GPSAEEIAEAQAIISAFADPAARGLNVINANGRMIERLHLVQAEALVHKARLISARK 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: 189 Number of extensions: 7 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: 302 Length of database: 301 Length adjustment: 27 Effective length of query: 275 Effective length of database: 274 Effective search space: 75350 Effective search space used: 75350 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 Apr 09 2024. 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