Align citrate lyase β subunit (EC 4.1.3.34) (characterized)
to candidate H281DRAFT_05549 H281DRAFT_05549 citrate lyase subunit beta / citryl-CoA lyase
Query= metacyc::MONOMER-16999 (289 letters) >FitnessBrowser__Burk376:H281DRAFT_05549 Length = 297 Score = 155 bits (391), Expect = 1e-42 Identities = 90/279 (32%), Positives = 153/279 (54%), Gaps = 4/279 (1%) Query: 5 RSMLFIPGANAAMLSTSFVYGADAVMFDLEDAVSLREKDTARLLVYQALQHPLYQDIETV 64 RS+L++P N + + GADA + DLEDAV++ +K AR + + L P + Sbjct: 7 RSLLYVPADNPRRVEKALNSGADAAILDLEDAVAISKKPEARANLRELLSGP--RPTLAY 64 Query: 65 VRINPLNTPFGLADLEAVVRAGVDMVRLPKTDSKEDIHELEAHVERIERECGREVGSTKL 124 VR+N + T F L D+EA + AG D + LPK ++ D+ ++ + ++ER G +V L Sbjct: 65 VRVNSMATEFCLDDIEAAIAAGADGISLPKVENARDLFAIDWLMSQLERRFGVDVDKVDL 124 Query: 125 MAAIESALGVVNAVEIARASPRLAAIALAAFDYVMDMGTSRG-DGTELFYARCAVLHAAR 183 + +ES LGV+NA E + R+ L D +++ D E R ++ A+ Sbjct: 125 LPVVESGLGVINAPESLKGVRRVKRAGLGVGDLALELNLILSPDQNEARPYRAQLVVASN 184 Query: 184 VAGI-AAYDVVWSDINNEEGFLAEANLAKNLGFNGKSLVNPRQIELLHQVYAPTRKEVDH 242 AG+ A D V+ D+NN +G A + +GF G+ +++P Q+E++++VY+P+ +E+ Sbjct: 185 AAGLDAPLDTVYLDLNNLDGLRASCIESCRIGFQGRRIIHPSQVEIVNEVYSPSPEEIAR 244 Query: 243 ALEVIAAAEEAETRGLGVVSLNGKMIDGPIIDHARKVVA 281 A +I EAE GL + + +D PI + ARK++A Sbjct: 245 AERIINEFTEAEKGGLASMRVGEVFVDYPIAEKARKILA 283 Lambda K H 0.319 0.134 0.375 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: 185 Number of extensions: 8 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: 289 Length of database: 297 Length adjustment: 26 Effective length of query: 263 Effective length of database: 271 Effective search space: 71273 Effective search space used: 71273 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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