Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_028584037.1 G494_RS0107490 acetyl-CoA C-acyltransferase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_000429965.1:WP_028584037.1 Length = 395 Score = 273 bits (698), Expect = 7e-78 Identities = 179/405 (44%), Positives = 236/405 (58%), Gaps = 16/405 (3%) Query: 8 KDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAG 67 +D +IV+A+RTP G + G+L+ V A +L A I L R L + +D+V+ G Q G Sbjct: 6 QDIFIVEALRTPFGSFLGSLAEVPAPELAAAVIPELLGR-SGLGGTLVDEVIIGQVLQGG 64 Query: 68 EDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMS 127 + AR ++ LAGLP V TIN++CGSG+ A+ AA IR GE L+IAGG+E+MS Sbjct: 65 -CGQAPARQAMRLAGLPDQVHALTINKVCGSGLVAMMLAANTIRAGEASLVIAGGMENMS 123 Query: 128 RAPFVMGKADSAFS-RKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186 AP V+ +A EI D + L+ SM E E ISR + Sbjct: 124 LAPHVLARARKGQRFGHGEILDLLL-----LDGLEDAASGRSMGEITEEWLRGHRISRRE 178 Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLPTP 246 QDA+ALRS A KE A E+ V K LVV DE P EK ASLPT Sbjct: 179 QDAYALRSYGLAQQALKEQIFAPELVEVRFNSGK-GWLVVAEDEEPWRCDPEKFASLPTV 237 Query: 247 FRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAP 306 FRE G++TAGNAS +NDGA L+AG A+++Y L+PRAR+VA ATA P++ Sbjct: 238 FREQGSITAGNASTINDGAALALVAGGAAVERYGLRPRARLVAAATASTGPQLFPEADVE 297 Query: 307 ATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGM 366 A R +A AGL L D+D+ E+NEAFAA AL +T +L L D VN NGGA+A+GHP+G Sbjct: 298 AIRLAVARAGLSLEDIDLFEINEAFAAVAL-LTMEL-LAIDPARVNVNGGAVAIGHPIGA 355 Query: 367 SGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411 SG RLV T + ELER Q+ RY + T+CIG G+ +A + ER+ Sbjct: 356 SGGRLVATLIRELER-----QEKRYGVVTLCIGGGEAVAAVFERI 395 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: 443 Number of extensions: 27 Number of successful extensions: 6 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: 395 Length adjustment: 31 Effective length of query: 384 Effective length of database: 364 Effective search space: 139776 Effective search space used: 139776 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