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 RR42_RS24350 RR42_RS24350 malyl-CoA thiolesterase
Query= SwissProt::P0A9I1 (302 letters) >FitnessBrowser__Cup4G11:RR42_RS24350 Length = 292 Score = 162 bits (410), Expect = 9e-45 Identities = 89/282 (31%), Positives = 157/282 (55%), Gaps = 5/282 (1%) Query: 10 KTRTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYR 69 + R RRS+L+ PGAN + + + AD + DLED+VA K+ AR V A++ Y Sbjct: 3 RNRHRRSVLYTPGANVRALEKAKLLNADGFILDLEDAVAPDAKEDARENVARAIESGGYG 62 Query: 70 DIETIVRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGREP 129 E +VR+N+LD++WG DLE V R AD + +PK ++A++V ++ ++ + P Sbjct: 63 GKEVLVRINSLDTKWGKGDLEIVARSAADGIVIPKVESAENVREVRAIMIEVGA-----P 117 Query: 130 GSTGLLAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRTERSPEGTELLFARCSI 189 S + IE+P G+ RA EIA + +L G+ +G D + L + +L + Sbjct: 118 ESMRIWCMIETPRGVLRAEEIAGSDAQLGGLIMGTSDLAKELGCAHTRMRLPMLASLGRC 177 Query: 190 LQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLYAPTQK 249 + AR+ G+ D V+ D ++ GF ++ GF+GK+LI+P+ ID + +++P Q Sbjct: 178 VLVARAYGLSILDGVHLDLDDAKGFQLSCEQGREFGFNGKTLIHPKTIDKANEIFSPNQD 237 Query: 250 EVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVL 291 E++ A++++ A EG GVV ++G +++ + A+ +L Sbjct: 238 ELNWAKKIIAAYRQGVAEGKGVVVVDGHLIENLHVAAAQELL 279 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: 181 Number of extensions: 10 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: 292 Length adjustment: 26 Effective length of query: 276 Effective length of database: 266 Effective search space: 73416 Effective search space used: 73416 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