Align citrate lyase β subunit (EC 4.1.3.34) (characterized)
to candidate WP_015943083.1 DHAF_RS04530 CoA ester lyase
Query= metacyc::MONOMER-16999 (289 letters) >NCBI__GCF_000021925.1:WP_015943083.1 Length = 298 Score = 162 bits (410), Expect = 8e-45 Identities = 100/282 (35%), Positives = 150/282 (53%), Gaps = 2/282 (0%) Query: 5 RSMLFIPGANAAMLSTSFVYGADAVMFDLEDAVSLREKDTARLLVYQALQHPLYQDIETV 64 RS+LF+ G + L + YGADA++ DLED V EK AR +V ++H Q E Sbjct: 5 RSVLFVAGNDKEALDEALTYGADALILDLEDLVPPLEKSRARRMVRVNIKHAGSQGAEVW 64 Query: 65 VRINPLNTPFGLADLEAVVRAGVDMVRLPKTDSKEDIHELEAHVERIERECGREVGSTKL 124 VR+N T DLEA V G+ + L K D+ L +E +ER+ G VGS K+ Sbjct: 65 VRVNAWETNMTDDDLEAAVCEGLTGINLTKVAGAGDVQRLAWRLEELERKNGLAVGSIKI 124 Query: 125 MAAIESALGVVNAVEIARASPRLAAIALAAFDYVMDMGTS-RGDGTELFYARCAVLHAAR 183 IE+A+GV+NA E ASPR+AA A DY DM + E +AR V AAR Sbjct: 125 CLLIETAIGVINAYESCAASPRVAAAIFGAVDYTRDMQVKLTPEAKEQQFARGYVAVAAR 184 Query: 184 VAGIAAYDVVWSDINNEEGFLAEANLAKNLGFNGKSLVNPRQIELLHQVYAPTRKEVDHA 243 AG+ A D + + ++EG++ + LG+ G+ +V+P +E +++YAP ++V A Sbjct: 185 AAGVIALDAPFLNYTDKEGYVHNIAEGRQLGYKGRMIVHPSLVEAANRLYAPDPEDVQWA 244 Query: 244 LEVIAA-AEEAETRGLGVVSLNGKMIDGPIIDHARKVVALSA 284 E+ EEA +G + K++D P+ +A ++A A Sbjct: 245 GEIKKVFEEEAIAKGKAAIVYKDKLVDTPVYSNALDILANQA 286 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: 175 Number of extensions: 6 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: 289 Length of database: 298 Length adjustment: 26 Effective length of query: 263 Effective length of database: 272 Effective search space: 71536 Effective search space used: 71536 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 24 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