Align (S)-citramalyl-CoA lyase (EC 4.1.3.25); (R)-citramalyl-CoA lyase (EC 4.1.3.46) (characterized)
to candidate GFF357 PGA1_c03680 putative citrate lyase subunit beta
Query= BRENDA::A0A172MLA1 (322 letters) >FitnessBrowser__Phaeo:GFF357 Length = 284 Score = 137 bits (346), Expect = 2e-37 Identities = 97/296 (32%), Positives = 149/296 (50%), Gaps = 26/296 (8%) Query: 9 RALLYIPGSSQRFIDKSRTLTADCVAYDLEDSVTPHKKAEARSLVRRALDQPAPAGILER 68 R++LYIPGS R ++K+R+L D + +DLED+V+ +K AR + AL + G + Sbjct: 9 RSVLYIPGSKLRALEKARSLPVDAIIFDLEDAVSAEEKVNARQTLEEAL-RAGGYGARMK 67 Query: 69 AVRINSVDSGLALADLTEVLQSPNLSTIVIPKVNSASDLTFVTDVITHTLSQLPLSQSAS 128 VRIN +D+ AD + + I++PKV+S DL + VIT Sbjct: 68 IVRINGLDTVWGRADAAAAARM-DCDAILLPKVSSPEDLDALA-VIT-----------GD 114 Query: 129 RPPISLLALVESAKSLTNLSQICAASPLLQGLIFAAEDFALDLSLTRTPALTEFLFARSA 188 +P L A++E+ + + N + I AA PLLQG++ D A +L P + Sbjct: 115 KP---LWAMMETPRGMLNAAAI-AAHPLLQGMVMGTNDLAKELQTRFRPDRLPLMAGLGQ 170 Query: 189 IATAARAANLPSTIDLVCTTYKSDKGDGSPPVVLQQECRDGKNLGFNGKQCIHPSQVSTV 248 AA+A + +D V +K +G L+ EC G+++GF+GK IHP+QV Sbjct: 171 CLLAAKAKGI-IIVDGVYNAFKDAEG-------LEAECDQGRDMGFDGKTLIHPAQVDVA 222 Query: 249 QQIFGPELEEVQWAVRVTIADDKASKAGRGAWTLDGKMIDIPVAEKARAIVKKADA 304 F P +E+ A R A D A G+G +DGK+++ AR I+ KADA Sbjct: 223 NSAFAPSEDEIDLARRQIAAFDAAEAEGQGVAVVDGKIVENLHVATAREILAKADA 278 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: 173 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: 322 Length of database: 284 Length adjustment: 27 Effective length of query: 295 Effective length of database: 257 Effective search space: 75815 Effective search space used: 75815 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