Align succinyl-CoA:acetoacetate CoA-transferase subunit B (EC 2.8.3.5) (characterized)
to candidate WP_009821792.1 V473_RS08610 CoA transferase subunit B
Query= metacyc::HP0692-MONOMER (207 letters) >NCBI__GCF_001046645.1:WP_009821792.1 Length = 213 Score = 258 bits (658), Expect = 7e-74 Identities = 127/209 (60%), Positives = 164/209 (78%), Gaps = 3/209 (1%) Query: 2 REAIIKRAAKELKEGMYVNLGIGLPTLVANEVS-GMNIVFQSENGLLGIGAYPLEGSVDA 60 R+ + RAAKEL++G YVNLGIG+PTLVAN + G+ + QSENG+LGIG +PL+G DA Sbjct: 5 RDEMAARAAKELEDGFYVNLGIGIPTLVANHIPVGVQVTLQSENGMLGIGPFPLDGEEDA 64 Query: 61 DLINAGKETITVVPGASFFNSADSFAMIRGGHIDLAILGGMEVSQNGDLANWMIPKKLIK 120 DLINAGK+TI+ +P ++F+S+DSFAMIRGGHIDL +LG ME+++NGD+ANWMIP K+IK Sbjct: 65 DLINAGKQTISELPQTAYFSSSDSFAMIRGGHIDLTVLGAMEIAENGDIANWMIPGKMIK 124 Query: 121 GMGGAMDLVHGAKKVIVIMEHCNKYGESKVKKECSLPLTGKGVVHQLITDLAVFEFS--N 178 GMGGAMDLV G KK+IV+MEH +K G K EC+LPLTGK VV +ITDLAVF+ + + Sbjct: 125 GMGGAMDLVAGVKKIIVVMEHTSKDGSPKFIPECTLPLTGKNVVDMIITDLAVFQRADHD 184 Query: 179 NAMKLVELQEGVSLDQVKEKTEAEFEVRL 207 + +L+EL GV+ V+ KT A FEV L Sbjct: 185 SPFRLIELAPGVTRQDVEAKTSASFEVAL 213 Lambda K H 0.317 0.136 0.380 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: 194 Number of extensions: 6 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: 207 Length of database: 213 Length adjustment: 21 Effective length of query: 186 Effective length of database: 192 Effective search space: 35712 Effective search space used: 35712 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: 45 (21.9 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