Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_008498764.1 B481_RS14465 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_000342445.1:WP_008498764.1 Length = 318 Score = 147 bits (372), Expect = 3e-40 Identities = 95/278 (34%), Positives = 133/278 (47%), Gaps = 20/278 (7%) Query: 3 ALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTE 62 AL +R+LD++ L GP+A L DLGA+VIK+E P GD R + A Sbjct: 4 ALKGVRILDVTYYLPGPYASMRLVDLGAEVIKIEPP-EGDPARYMSGGHVHQAN------ 56 Query: 63 AAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAIN 122 NR K + ID EG + EL +D LIE F+ G + GLDYDSLK++ Sbjct: 57 -------NRGKNIIRIDLKTTEGHMEMLELVKSADALIETFRPGVMKKLGLDYDSLKSLK 109 Query: 123 PQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILT 182 P L+YCS++G+GQ+G A+ +D L G + D P+ D Sbjct: 110 PDLVYCSLSGYGQSGEMARLGSHDLNYMALSGALDQL----KDASGRPIHPTNTFADFTG 165 Query: 183 GLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNI 242 GL +T ILAAL + G GQ++D+AL++V L N Y G + + Sbjct: 166 GLMATEQILAALLKKFRTGHGQYLDIALVEVMAEFLGNHD-RYHAVGISENGIPEIGGTR 224 Query: 243 VPYQDFPTADGDFILTVGNDGQF-RKFAEVAGQPQWAD 279 V Y + T DG +I + +F R F E G PQW + Sbjct: 225 VSYAIYETKDGRYITLGALEEKFWRNFCEFVGNPQWLE 262 Lambda K H 0.319 0.137 0.408 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: 334 Number of extensions: 17 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: 406 Length of database: 318 Length adjustment: 29 Effective length of query: 377 Effective length of database: 289 Effective search space: 108953 Effective search space used: 108953 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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