Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate RR42_RS25095 RR42_RS25095 citryl-CoA lyase
Query= BRENDA::Q037K5 (292 letters) >FitnessBrowser__Cup4G11:RR42_RS25095 Length = 296 Score = 119 bits (298), Expect = 8e-32 Identities = 87/287 (30%), Positives = 147/287 (51%), Gaps = 3/287 (1%) Query: 3 KLRRTMMFVPGANPGMLRDAPIYGADAIMFDLEDAVSLKEKDTARMLVYSALKTFDYSSV 62 K R+MMFVPG P + + ADA++ DLED+V +K AR +V S L Sbjct: 7 KPMRSMMFVPGNKPDWIEKSVAAKADALILDLEDSVPPAQKVEAREIVKSKLDWLAGQKP 66 Query: 63 ETVVRVNALDAGGD-QDIEAMVLGGINVVRLPKTETAQDIIDVDAVITAVEEKYGIQNGT 121 VR+N D +DI A+V + + + K +DI V +++ E + G+ G Sbjct: 67 RIWVRINRSAHLYDYEDILAIVNPVVEGIVISKPCGPEDIHTVSSMLAEAEYRAGVPVGH 126 Query: 122 THMMAAIESAEGVLNAREIAQASS--RMIGIALGAEDYLTSQHTHRSTDGAELSFARNYI 179 T ++ +E+A + A EIAQ ++G D + T S +G E + ++ I Sbjct: 127 TRVIPLLETARSLQYAYEIAQHERVPAIVGATAKNADVARALKTVWSLEGRETLYLKSRI 186 Query: 180 LHAAREAGIAAIDTVYTQVDNEEGLRHETALIKQLGFDGKSVINPRQIPVINGVFAPALA 239 + AAR AG I V+ QV + EGL+ +A +QLG G+ V++P + ++N ++P Sbjct: 187 VMAARAAGKLPIGGVWQQVHDLEGLKVSSANDRQLGMSGELVLHPSNVEIVNKTYSPTEE 246 Query: 240 EVQKAREIVAGLKEAEAKGAGVVSVNGQMVDKPVVERAQYTIALAKA 286 EV + ++ L++A+A+G +G+ +D V+ A+ I LA++ Sbjct: 247 EVAFYQGMIDALEKAQAEGRASCIYDGEHIDIAHVKTAREIIELAQS 293 Lambda K H 0.316 0.132 0.355 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: 169 Number of extensions: 7 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: 292 Length of database: 296 Length adjustment: 26 Effective length of query: 266 Effective length of database: 270 Effective search space: 71820 Effective search space used: 71820 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 (21.6 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