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 CCNA_03774 CCNA_03774 citrate lyase beta chain/citryl-CoA lyase subunit
Query= SwissProt::P0A9I1 (302 letters) >FitnessBrowser__Caulo:CCNA_03774 Length = 295 Score = 140 bits (353), Expect = 4e-38 Identities = 90/290 (31%), Positives = 145/290 (50%), Gaps = 10/290 (3%) Query: 12 RTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYRDI 71 R RRS L++P +NA V + AD ++ DLED+VA K AR A++ + Sbjct: 8 RPRRSALYMPASNAKAVEKARTLDADVIILDLEDAVAPEMKPAAREAAVAAVKAGGFGPR 67 Query: 72 ETIVRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGREPGS 131 E ++RVN LD+ WG +DL A G D V +PK + A DV ++ + P S Sbjct: 68 EVVIRVNGLDTPWGADDLAAAAEAGPDAVLVPKVNDAADVRLYDQHL-------SAAPTS 120 Query: 132 TGLLAAIESPLGITRAVEIAHA--SERLIGIALGAEDYVRNLRTERSPEGTELLFARCSI 189 T L IE+ EIA A S RL +G D+ + +R ++P+ L Sbjct: 121 TRLWTMIETAKAAFHLWEIAEAAHSTRLSAWVMGVNDFAKEMRARQTPDRAPFLPLLTLS 180 Query: 190 LQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLYAPTQK 249 + AAR+ G+ D V++D + A GFDGK+LI+P+ +++ + +++P+ + Sbjct: 181 VAAARAHGLMILDGVHNDIEDLAALEAVCVQGVDFGFDGKTLIHPKHLEICNRVFSPSPE 240 Query: 250 EVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRA-RLVLSRAELSG 298 +V + V+ A A G G + ++GKM + + +A RLV +SG Sbjct: 241 DVAWSHAVIAAFNAPENAGKGALRVDGKMAERLHLAQAERLVAVAQAISG 290 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: 201 Number of extensions: 12 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: 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