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 Pf6N2E2_1831 Citrate lyase beta chain (EC 4.1.3.6)
Query= SwissProt::P0A9I1 (302 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1831 Length = 299 Score = 144 bits (363), Expect = 2e-39 Identities = 99/281 (35%), Positives = 149/281 (53%), Gaps = 5/281 (1%) Query: 15 RSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYRDIETI 74 RS+LFVP + ADA + DLEDSVA +K AR A Q+ R ++ + Sbjct: 9 RSLLFVPAHIGKFTEKAHERNADACILDLEDSVAPGQKTQARDAASSAAQNISNRGLDVL 68 Query: 75 VRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGREPGSTGL 134 VR+N LDS G+ DL+A+V V LPK +A+ V + ++ R+E G + G T + Sbjct: 69 VRINTLDSG-GLLDLQAIVSPAVCAVVLPKVASAEVVRHVALQLDRLETERGMDAGQTLI 127 Query: 135 LAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRTERSPEGTELLFARCSILQAAR 194 LA IE + EIA AS RL+G++LG ED+ + E PE LL+ + A R Sbjct: 128 LAQIEDVAALPLLDEIATASPRLMGMSLGPEDFSVSAGMEPVPE--TLLWPNQQVAFACR 185 Query: 195 SAGIQ--AFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLYAPTQKEVD 252 AGI F +D ++ F Q +QLG G I+P Q+ +L+ +++P EV+ Sbjct: 186 RAGILPFGFPGSIADFSDIPRFRQALVLGRQLGMIGAFCIHPEQVAVLNEVFSPGDAEVE 245 Query: 253 HARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSR 293 ++ ++ A EG G + GKM+D P++ RAR +L+R Sbjct: 246 YSVALLAEYACAEAEGRGAFAFRGKMIDAPIVARARELLTR 286 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: 180 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: 299 Length adjustment: 27 Effective length of query: 275 Effective length of database: 272 Effective search space: 74800 Effective search space used: 74800 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