Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_015446959.1 R2APBS1_RS03900 3-oxoadipyl-CoA thiolase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_000230695.2:WP_015446959.1 Length = 400 Score = 479 bits (1233), Expect = e-140 Identities = 249/405 (61%), Positives = 304/405 (75%), Gaps = 7/405 (1%) Query: 7 LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66 + A++VDA RTP GR GGAL+ VRADDL A+PI AL R+P LDW+ +D+V+ GCANQA Sbjct: 1 MTSAWLVDATRTPFGRLGGALAGVRADDLAALPIAALMARHPTLDWAALDEVILGCANQA 60 Query: 67 GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126 GEDNR+VARM+ LLAGLP VP T+NRLC SG++A+G AARAI GE +L++AGGVESM Sbjct: 61 GEDNRNVARMATLLAGLPQSVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESM 120 Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186 SRAP+V+ KAD A++R ++ DTT+GWR VNP ++ YGIDSM +TAEN+A + GI R+ Sbjct: 121 SRAPYVLAKADVAYARGQQLEDTTLGWRLVNPRMQAGYGIDSMTQTAENLAREHGIDRDS 180 Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPR-ETSLEKLASLPT 245 QDA+ALRSQQRTA AQ +G LA EIT V P K+ LVV DEHPR +T+ KLA+L Sbjct: 181 QDAYALRSQQRTAHAQAQGWLAEEITAVHAPHGKES-LVVQVDEHPRADTTAAKLAALKP 239 Query: 246 PFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPA 305 ++TAGNASG+NDGA A+LLA AL +Y L+P AR+V MA AGV PR+MG GP Sbjct: 240 LLGAGSSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAPRVMGIGPV 299 Query: 306 PATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLG 365 PA K+LA GL +D D IE+NEAFAAQ LA TR LGLPDDAEHVN NGGAIALGHPLG Sbjct: 300 PAIHKLLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDDAEHVNANGGAIALGHPLG 359 Query: 366 MSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIER 410 SGARL TA L RRH + AL ++C+GVGQG+AL +ER Sbjct: 360 ASGARLALTAAFAL-RRH----RQHRALVSLCVGVGQGLALALER 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: 514 Number of extensions: 25 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: 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