Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_010626093.1 BZY95_RS06835 3-oxoadipyl-CoA thiolase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_002151265.1:WP_010626093.1 Length = 401 Score = 642 bits (1655), Expect = 0.0 Identities = 325/406 (80%), Positives = 359/406 (88%), Gaps = 6/406 (1%) Query: 7 LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66 +KDA I+DAIRTPIGRYGGAL++VRADDLGA+P++AL R+P LDW ++DD+ YGCANQA Sbjct: 1 MKDALIIDAIRTPIGRYGGALASVRADDLGAVPLRALMARHPSLDWRQVDDIFYGCANQA 60 Query: 67 GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126 GEDNR+VARMS LLAGLPV+VPG+T NRLCGSG+DAVG+AARAI+TGE LMIAGGVESM Sbjct: 61 GEDNRNVARMSALLAGLPVEVPGTTFNRLCGSGLDAVGNAARAIKTGEAGLMIAGGVESM 120 Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186 SRAPFVMGKA+ AFSR AEIFDTTIGWRFVN +K Q+GIDSMPETAENVA F ISRED Sbjct: 121 SRAPFVMGKAEQAFSRSAEIFDTTIGWRFVNRQMKAQFGIDSMPETAENVAEQFAISRED 180 Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPR-ETSLEKLASLPT 245 QD FALRSQQRTAAA + GRLAAEI PV + RRKQ PLVVDTDEHPR T+LE+LA LPT Sbjct: 181 QDLFALRSQQRTAAAMEAGRLAAEIVPVEVARRKQAPLVVDTDEHPRAATTLEQLAGLPT 240 Query: 246 PFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPA 305 PFRE+G+VTAGNASGVNDGACALLLA A+ +++ L+PRARVV MAT GVEPRIMGFGPA Sbjct: 241 PFREDGSVTAGNASGVNDGACALLLASAEQAERFGLEPRARVVGMATVGVEPRIMGFGPA 300 Query: 306 PATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLG 365 PATRKVL GL L MDVIELNEAFAAQALAVTR+LGLPDDAEHVNPNGGAIALGHPLG Sbjct: 301 PATRKVLTQTGLSLEQMDVIELNEAFAAQALAVTRNLGLPDDAEHVNPNGGAIALGHPLG 360 Query: 366 MSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411 MSGARLVTTAL ELERR + RYALCTMCIGVGQGIALIIER+ Sbjct: 361 MSGARLVTTALYELERR-----QGRYALCTMCIGVGQGIALIIERL 401 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: 591 Number of extensions: 13 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: 415 Length of database: 401 Length adjustment: 31 Effective length of query: 384 Effective length of database: 370 Effective search space: 142080 Effective search space used: 142080 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