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 WP_017598633.1 D471_RS0110795 CoA ester lyase
Query= SwissProt::P0A9I1 (302 letters) >NCBI__GCF_000341125.1:WP_017598633.1 Length = 315 Score = 155 bits (391), Expect = 1e-42 Identities = 106/302 (35%), Positives = 154/302 (50%), Gaps = 13/302 (4%) Query: 12 RTRRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYRDI 71 R+RRS+L VPG+N V + DA DLED+VA EK AR V AL + Sbjct: 5 RSRRSVLAVPGSNPRFVEKARGLDVDAFFLDLEDAVAPLEKAAARENVVRALNDGGWDGK 64 Query: 72 ETIVRVNALDSEWGVNDLEAVVRGGA---DVVRLPKTDTAQDVLDIEKEILRIEKACGRE 128 VRVN + +EW D+ VV G D + LPK + +DV ++ + +IE+A G E Sbjct: 65 LRSVRVNDVSTEWAYRDVITVVEGAGAELDCLVLPKVTSPRDVHWLDTLLTQIERAVGLE 124 Query: 129 PGSTGLLAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRT------ERSP---EG 179 G G+ A IE G+T IA AS RL + G D++ +L E+ P G Sbjct: 125 VGRIGIEAQIEDARGLTEVDAIAAASPRLESLVYGPADFMASLNMKSLVVGEQPPGYDTG 184 Query: 180 TELLFARCSILQAARSAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDL 239 + IL AAR+ G+QA D Y + F + AA LGFDGK +++P Q++ Sbjct: 185 DAYHYVLMRILTAARAHGLQAVDGPYLQIRDVDAFRRSAARTAALGFDGKWVLHPLQVEA 244 Query: 240 LHNLYAPTQKEVDHARRVVEA-AEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRAELSG 298 + +YAPTQ++ DHA +++A A A + G V L +M+D A +V + +G Sbjct: 245 ANEVYAPTQEDYDHAELILDAYAHATTVDRRGAVMLGDEMLDEASRKMALVVAGKGRAAG 304 Query: 299 IR 300 +R Sbjct: 305 LR 306 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: 224 Number of extensions: 15 Number of successful extensions: 5 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: 315 Length adjustment: 27 Effective length of query: 275 Effective length of database: 288 Effective search space: 79200 Effective search space used: 79200 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 Apr 09 2024. 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