Align (S)-citramalyl-CoA lyase (EC 4.1.3.25); (R)-citramalyl-CoA lyase (EC 4.1.3.46) (characterized)
to candidate BWI76_RS04445 BWI76_RS04445 citrate (pro-3S)-lyase subunit beta
Query= BRENDA::A0A172MLA1 (322 letters) >FitnessBrowser__Koxy:BWI76_RS04445 Length = 289 Score = 148 bits (373), Expect = 2e-40 Identities = 95/292 (32%), Positives = 158/292 (54%), Gaps = 15/292 (5%) Query: 8 RRALLYIPGSSQRFIDKSRTLTADCVAYDLEDSVTPHKKAEARSLVRRALDQPAPAGILE 67 RR++L+IPG++ + S AD V +DLED+V+ +K AR LV AL P + E Sbjct: 4 RRSMLFIPGANAAMLSTSFVYGADAVMFDLEDAVSLREKDTARLLVHHALQHPLYRDV-E 62 Query: 68 RAVRINSVDSGLALADLTEVLQSPNLSTIVIPKVNSASDLTFVTDVITHTLSQLPLSQSA 127 VRIN +++ LADL V+++ + + +PK +S D+ + + + + Sbjct: 63 TVVRINPLNTPFGLADLEAVVRA-GVDMVRLPKTDSKEDIHELEAHVERIERECGREVGS 121 Query: 128 SRPPISLLALVESAKSLTNLSQICAASPLLQGLIFAAEDFALDLSLTRTPALTEFLFARS 187 ++ L+A +ESA + N +I +SP L + AA D+ +D+ R TE +AR Sbjct: 122 TK----LMAAIESALGVVNAVEIARSSPRLSAIALAAFDYVMDMGTCRGDG-TELFYARC 176 Query: 188 AIATAARAANLPSTIDLVCTTYKSDKGDGSPPVVLQQECRDGKNLGFNGKQCIHPSQVST 247 A+ AAR A + + D+V + +++G E KNLGFNGK ++P Q+ Sbjct: 177 AVLHAARVAGI-AAYDVVWSDINNEEG-------FLAEANLAKNLGFNGKSLVNPRQIEL 228 Query: 248 VQQIFGPELEEVQWAVRVTIADDKASKAGRGAWTLDGKMIDIPVAEKARAIV 299 + Q++ P L++V+ A V A ++A + G G +L+GKMID P+ + AR +V Sbjct: 229 LHQVYAPTLKDVEHARDVIAAAEEAEERGLGVVSLNGKMIDGPIIDHARKVV 280 Lambda K H 0.316 0.130 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: 186 Number of extensions: 11 Number of successful extensions: 4 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: 322 Length of database: 289 Length adjustment: 27 Effective length of query: 295 Effective length of database: 262 Effective search space: 77290 Effective search space used: 77290 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