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_005812973.1 DHAF_RS15385 CoA ester lyase
Query= SwissProt::P0A9I1 (302 letters) >NCBI__GCF_000021925.1:WP_005812973.1 Length = 295 Score = 165 bits (418), Expect = 1e-45 Identities = 103/284 (36%), Positives = 159/284 (55%), Gaps = 2/284 (0%) Query: 15 RSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYRDIETI 74 RS++++PG N MV+ + PAD + FDLED+V EK+TAR++V L++ + Sbjct: 5 RSVMYIPGNNPKMVAKAPEIPADIITFDLEDAVPPAEKETARQIVRENLEYGAKGGAQVF 64 Query: 75 VRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGREPGSTGL 134 VR+N ++ +DLEA+V G + V L KT A DV +E ++ +E G G+ + Sbjct: 65 VRINNWETGLTNDDLEAIVWPGLNGVTLAKTGCAADVQRLEWKLEELEMRRGIPVGTVKI 124 Query: 135 LAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRTERSPEGTELLFARCSILQAAR 194 +E+ GI A E AS+R + GA DY R++R + + E E + R + A R Sbjct: 125 SMLLETAKGIAHAEECCLASKRNVNAIFGAVDYCRDMRVKITNEAVEQQYGRAKVGVACR 184 Query: 195 SAGIQAFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLYAPTQKEVDHA 254 +AGI A D + D N F + A KQ+G++G+ +I+P Q++ + +YAP +V A Sbjct: 185 AAGIVAIDAPFVDYANIPAFEKNVAEGKQMGYEGRMIIHPGQVEPSNRMYAPDPADVKWA 244 Query: 255 RRVVEA-AEAAAREGLGVVSLNGKMVDGPVIDRARLVL-SRAEL 296 VV+ E +G VSLNGKMVD PV A+ +L S+AE+ Sbjct: 245 NDVVKVFEEEGLAKGKAAVSLNGKMVDTPVYLNAKDILASQAEI 288 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: 197 Number of extensions: 9 Number of successful extensions: 2 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: 295 Length adjustment: 27 Effective length of query: 275 Effective length of database: 268 Effective search space: 73700 Effective search space used: 73700 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 24 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