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_011427687.1 RHE_RS23145 CoA ester lyase
Query= SwissProt::P0A9I1 (302 letters) >NCBI__GCF_000092045.1:WP_011427687.1 Length = 278 Score = 102 bits (254), Expect = 1e-26 Identities = 90/289 (31%), Positives = 133/289 (46%), Gaps = 25/289 (8%) Query: 15 RSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYRDIET- 73 RS+LFVPG + + ADA++ DLEDSVA K AR V+ +Q R ET Sbjct: 4 RSLLFVPGDRPERFAKALASGADAVILDLEDSVAPPNKPKARDSVHEFVQR---RPGETK 60 Query: 74 -IVRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGREPGST 132 ++R+N L S DL A+ + LPK + A VL + + +T Sbjct: 61 LLIRINPLASPEFEGDLAALSGLQPFGLMLPKAEGAASVLKLASAL-----------AAT 109 Query: 133 GLLAAI--ESPLGITRAVEIAHASERLIGIALGAEDYVRNL--RTERSPEGT---ELLFA 185 L+ I E+P I S+ L G+ GAED + T R +G A Sbjct: 110 ILILPIATETPSAIFEIGSYREVSDNLCGLTWGAEDLPAAIGATTARRTDGRYTPPYELA 169 Query: 186 RCSILQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLYA 245 R L AA +A + A DTVY D + G ++ GF G I+P Q++ +++ + Sbjct: 170 RSLTLFAAHAAAVPAIDTVYPDFRDLNGLRAYVGRARRDGFSGMMAIHPSQVETINHAFT 229 Query: 246 PTQKEVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRA 294 P E+ A +V A AA GV+ L+G+M+D P + A +L+ A Sbjct: 230 PDAFEIAWAEKV--TAAFAASPDAGVIQLDGRMLDLPHLKLAHRILASA 276 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: 183 Number of extensions: 14 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: 278 Length adjustment: 26 Effective length of query: 276 Effective length of database: 252 Effective search space: 69552 Effective search space used: 69552 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