Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate Ga0059261_3671 Ga0059261_3671 Citrate lyase beta subunit
Query= BRENDA::Q037K5 (292 letters) >FitnessBrowser__Korea:Ga0059261_3671 Length = 278 Score = 134 bits (336), Expect = 3e-36 Identities = 99/290 (34%), Positives = 144/290 (49%), Gaps = 20/290 (6%) Query: 6 RTMMFVPGANPGMLRDAPIYGADAIMFDLEDAVSLKEKDTARMLVYSALKTFDYSSVETV 65 R+M+FVPG P + A GADA++ DLED+V+ K AR+ V L S V Sbjct: 4 RSMLFVPGDRPDRMEKALASGADALILDLEDSVTPANKGAARLAVAKFLAE-TRSEVSHW 62 Query: 66 VRVNALDAGGDQDIEAMVLGGINVVRLPKTETAQDIIDVDAVITAVEEKYGIQNGTTHMM 125 VR+N LD+G QD A G +V LPK E D+ +DA++ + + + Sbjct: 63 VRINPLDSGMTQDDLAAAHGADGIV-LPKAENGADVASLDAMLGGIAARI--------LP 113 Query: 126 AAIESAEGVLNAREIAQASSRMIGIALGAEDYLTS--QHTHRSTDGAELS---FARNYIL 180 A E+ V A S R+ GI GAED + + R DG+ S R L Sbjct: 114 IATETPAAVFGLGSYAGCSPRLAGITWGAEDLPAAIGAVSSREKDGSYTSPYEIVRALTL 173 Query: 181 HAAREAGIAAIDTVYTQVDNEEGLRHETALIKQLGFDGKSVINPRQIPVINGVFAPALAE 240 A AG+ AI+TVY N +GL+ A + GF G I+P QI +IN F P+ Sbjct: 174 FGAHAAGVRAIETVYPDFRNLDGLKAYCARAMRDGFTGMMAIHPAQIEIINAAFTPSEEA 233 Query: 241 VQKAREIVAGLKEAEAKGAGVVSVNGQMVDKPVVERAQYTIALAKASGME 290 V A+ +VA + AG + ++G+M+D P +++A+ AL K +G+E Sbjct: 234 VAHAQRVVAAF--SANPEAGALQLDGKMIDAPHLKQAE---ALLKRAGVE 278 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: 207 Number of extensions: 12 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: 292 Length of database: 278 Length adjustment: 26 Effective length of query: 266 Effective length of database: 252 Effective search space: 67032 Effective search space used: 67032 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: 47 (22.7 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