Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_086511957.1 BZY95_RS21635 3-oxoadipyl-CoA thiolase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_002151265.1:WP_086511957.1 Length = 400 Score = 535 bits (1379), Expect = e-157 Identities = 268/404 (66%), Positives = 324/404 (80%), Gaps = 5/404 (1%) Query: 7 LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66 + Y+ R+ +GR+GG L++VR DDL A +KA+ + PDLD S I++V GCANQA Sbjct: 1 MNSVYLCHPQRSAVGRFGGTLASVRPDDLAAAIVKAVLAQAPDLDPSAIEEVFMGCANQA 60 Query: 67 GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126 GEDNR+VARM+ LLAGLPV +PG+T+NRLCGSGMDAVG+A RAI+ GE +L +AGGVESM Sbjct: 61 GEDNRNVARMASLLAGLPVSIPGTTLNRLCGSGMDAVGTAFRAIKAGEMELALAGGVESM 120 Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186 SRAP+VMGKADSAFSR +I DTTIGWRF+NP++KK YG++SMPETAENVA F ISRED Sbjct: 121 SRAPYVMGKADSAFSRGQKIEDTTIGWRFINPLMKKAYGVESMPETAENVAEQFAISRED 180 Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLPTP 246 QDAFALRSQQ+ AAAQ+ GR A EIT + IPRRKQ+PL D DEH R T+LEKLA LP P Sbjct: 181 QDAFALRSQQKAAAAQEAGRFACEITAIEIPRRKQEPLRFDQDEHLRATTLEKLAGLPAP 240 Query: 247 FRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAP 306 FRE G+VTAGNASGVNDGA A+L+A A++++ L P A+++ MATAGVEPRIMG GP P Sbjct: 241 FREGGSVTAGNASGVNDGAAAMLVASRQAVEKHGLTPMAKILGMATAGVEPRIMGIGPVP 300 Query: 307 ATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGM 366 A RK+LA G+ L ++DVIELNEAFAAQALA R+LG+ D VNPNGGAIALGHPLGM Sbjct: 301 AVRKLLARTGVSLDEIDVIELNEAFAAQALAGMRELGIADGDPRVNPNGGAIALGHPLGM 360 Query: 367 SGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIER 410 SGARL+ TA +EL++ RYALCTMC+GVGQGIA ++ER Sbjct: 361 SGARLLLTAAHELQK-----SGKRYALCTMCVGVGQGIATLLER 399 Lambda K H 0.318 0.133 0.382 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: 534 Number of extensions: 18 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: 415 Length of database: 400 Length adjustment: 31 Effective length of query: 384 Effective length of database: 369 Effective search space: 141696 Effective search space used: 141696 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: 50 (23.9 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