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 3609490 Dshi_2874 Citrate (pro-3S)-lyase (RefSeq)
Query= SwissProt::P0A9I1 (302 letters) >FitnessBrowser__Dino:3609490 Length = 295 Score = 167 bits (423), Expect = 3e-46 Identities = 98/286 (34%), Positives = 156/286 (54%), Gaps = 6/286 (2%) Query: 10 KTRTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYR 69 + R RS+L++PG+ + + P DA++FDLED+VA+ EK AR ++ L Y Sbjct: 8 RARPYRSVLYIPGSKERALHKAQSLPVDAIIFDLEDAVAVEEKANARHLLARTLAETDYG 67 Query: 70 DIETIVRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGREP 129 IVR+N D++WG DL+ + + + LPK +TA DV E L E Sbjct: 68 PRAKIVRINGFDTDWGQADLDVIAAARPEAILLPKVNTAADV-----ETLADRLDARPET 122 Query: 130 GSTGLLAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRTERSPEGTELLFARCSI 189 T + +E+PLG+ A +IA A+ R+ G +G D + L + P+ +L Sbjct: 123 AETTIWTMMETPLGMLNAAQIA-AAPRMAGFVMGTNDLAKELDSRFRPDRLPMLTGLGLC 181 Query: 190 LQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLYAPTQK 249 L AAR+ G+ A D VY+ ++ G E A + +GFDGK+LI+P Q+ + + ++AP+ Sbjct: 182 LLAARAHGLVAVDGVYNAFKDDEGLEAECAQGRDMGFDGKTLIHPAQVAIANAVFAPSDS 241 Query: 250 EVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRAE 295 E+ A R + A E AA G GV ++GK+V+ + AR +L++AE Sbjct: 242 ELALASRQILAFEQAAARGQGVAVVDGKIVENLHVATARQLLAKAE 287 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: 197 Number of extensions: 10 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: 295 Length adjustment: 27 Effective length of query: 275 Effective length of database: 268 Effective search space: 73700 Effective search space used: 73700 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