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 AZOBR_RS14115 AZOBR_RS14115 (3S)-malyl-CoA thiolesterase
Query= SwissProt::P0A9I1 (302 letters) >FitnessBrowser__azobra:AZOBR_RS14115 Length = 291 Score = 171 bits (434), Expect = 1e-47 Identities = 98/284 (34%), Positives = 162/284 (57%), Gaps = 5/284 (1%) Query: 12 RTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYRDI 71 R RRS+L++PG+N + PAD L+ DLED+VA K AR + ++ Y Sbjct: 6 RPRRSVLYMPGSNTRALEKGRSLPADGLILDLEDAVAPDAKAEARATIKASIAAGGYGGR 65 Query: 72 ETIVRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGREPGS 131 E +VR N L++ WG +DL GAD V LPK ++ D+ ++ + +A G G Sbjct: 66 ELVVRTNGLNTPWGYDDLVMAASSGADAVLLPKVESP----DMVRQAEAVLRANGSPDGQ 121 Query: 132 TGLLAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRTERSPEGTELLFARCSILQ 191 T + +E+PLG+ EIA AS +L G+ +G D ++L + + +L + L Sbjct: 122 T-IWCMMETPLGMLNTKEIAGASPKLGGLVMGTSDLAKDLHAAHTRDRLPMLTSLGLCLL 180 Query: 192 AARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLYAPTQKEV 251 AAR+ G+ D V+ D N++AGF + ++LGFDGK+LI+P+ I + +AP+++EV Sbjct: 181 AARAYGLAILDGVHLDLNDDAGFGESCVQGRELGFDGKTLIHPKTIAACNAAFAPSEEEV 240 Query: 252 DHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRAE 295 A R+++A A +G GVV ++G++V+ ++ AR +++ AE Sbjct: 241 AQAHRIIQAHAEAVAQGKGVVLVDGRLVENLHVENARRLVAMAE 284 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: 205 Number of extensions: 9 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: 291 Length adjustment: 26 Effective length of query: 276 Effective length of database: 265 Effective search space: 73140 Effective search space used: 73140 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