Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A (characterized)
to candidate WP_140162538.1 BZY95_RS18560 CoA-transferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2111 (232 letters) >NCBI__GCF_002151265.1:WP_140162538.1 Length = 118 Score = 204 bits (518), Expect = 8e-58 Identities = 94/118 (79%), Positives = 113/118 (95%) Query: 1 MAGFDKRVSSYEEALEGLKDGMTVIAGGFGLCGIPENLIAEIKRKGIRDLTVVSNNCGVD 60 M+GFDKRV SYEEA++G++ GMT++AGGFGLCGIPENLIAE+KR+G++DLTV+SNNCGVD Sbjct: 1 MSGFDKRVYSYEEAMDGIESGMTLVAGGFGLCGIPENLIAEVKRRGVKDLTVISNNCGVD 60 Query: 61 GFGLGVLLEDRQIRKVVASYVGENALFEQQLLSGEIEVVLTPQGTLAEKMRAGGAGIP 118 GFGLG+LLED+QI++ ASYVGENALFEQQ+L+ EIEV+LTPQGTLAEKMRAGGAGIP Sbjct: 61 GFGLGLLLEDKQIKRFYASYVGENALFEQQMLNEEIEVILTPQGTLAEKMRAGGAGIP 118 Lambda K H 0.319 0.139 0.403 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: 166 Number of extensions: 5 Number of successful extensions: 1 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: 232 Length of database: 118 Length adjustment: 18 Effective length of query: 214 Effective length of database: 100 Effective search space: 21400 Effective search space used: 21400 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: 43 (21.2 bits)
Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A (characterized)
to candidate WP_140162537.1 BZY95_RS18555 CoA-transferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2111 (232 letters) >NCBI__GCF_002151265.1:WP_140162537.1 Length = 112 Score = 187 bits (476), Expect = 5e-53 Identities = 89/111 (80%), Positives = 99/111 (89%) Query: 122 TATGVGTPVAEGKEVREFHGRQYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPLA 181 TATG GTP+ EGKEVREF+GR Y++EE+ DFAIVKGWKAD +GNV+YR TAQNFNPLA Sbjct: 1 TATGYGTPIGEGKEVREFNGRHYILEEAFHADFAIVKGWKADRYGNVVYRDTAQNFNPLA 60 Query: 182 ATAGKITVVEVEEIVEPGELDPTQIHTPGIYVDRVICGTFEKRIEQRTVRK 232 AT GKITVVEVEEIVEPGEL P QIHTPGIYVDR+I GTFEKRIE+RTVR+ Sbjct: 61 ATCGKITVVEVEEIVEPGELRPDQIHTPGIYVDRIIQGTFEKRIEKRTVRE 111 Lambda K H 0.319 0.139 0.403 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: 120 Number of extensions: 2 Number of successful extensions: 1 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: 232 Length of database: 112 Length adjustment: 17 Effective length of query: 215 Effective length of database: 95 Effective search space: 20425 Effective search space used: 20425 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: 43 (21.2 bits)
This GapMind analysis is from Apr 09 2024. 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