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 SMc03793 SMc03793 citrate lyase subunit beta
Query= SwissProt::P0A9I1 (302 letters) >FitnessBrowser__Smeli:SMc03793 Length = 300 Score = 133 bits (335), Expect = 4e-36 Identities = 92/296 (31%), Positives = 145/296 (48%), Gaps = 10/296 (3%) Query: 5 SLQQRKTRTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQ 64 ++ R RRS+L VP N ++ + ADA++FDLEDSV+ K AR + L Sbjct: 3 AIDHHPVRLRRSVLSVPADNQRALAKACELAADAVIFDLEDSVSPDRKAAARDALVRHLA 62 Query: 65 HPLYRDIETIVRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKA 124 + ET++RVNA S +G DL A + D + LPK ++ D+ + + Sbjct: 63 GNRPQG-ETVIRVNAAGSGFGEADLAAALAARPDAILLPKVESPADIQGALDWLSERDA- 120 Query: 125 CGREPGSTGLLAAIESPLGITRAVEIAHASE----RLIGIALGAEDYVRNLRTERSPEGT 180 P L A IE+P G+ IA RL +G D + T Sbjct: 121 ----PDELRLWAMIETPRGVVNGPAIAETGRTSGGRLDCFVVGLNDLRKETGVPALSGRT 176 Query: 181 ELLFARCSILQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLL 240 L+ IL AAR +G+ A D V++D + GF E + +GFDGK LI+P QID Sbjct: 177 YLVPWLMQILLAARGSGLDAIDAVFNDFRDPEGFEAECRQGRDMGFDGKMLIHPAQIDAA 236 Query: 241 HNLYAPTQKEVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRAEL 296 + +A + V+ AR ++EA G GV++L+G+MV+ +++A + ++A++ Sbjct: 237 NRHFAADEAAVEEARAIIEAFALPDNSGKGVINLHGRMVERLHLEQAMKIAAKADI 292 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: 194 Number of extensions: 11 Number of successful extensions: 3 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: 300 Length adjustment: 27 Effective length of query: 275 Effective length of database: 273 Effective search space: 75075 Effective search space used: 75075 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