Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_011879665.1 acetyl-CoA acetyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982 (397 letters) >NCBI__GCF_000016205.1:WP_011879665.1 Length = 396 Score = 562 bits (1449), Expect = e-165 Identities = 280/391 (71%), Positives = 330/391 (84%) Query: 4 SNDPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVLPA 63 + DPIVIV RTPMGGFQG L + +A +LGA AI+AA+ERA V ++ +DE++FGCVLPA Sbjct: 3 TQDPIVIVGTARTPMGGFQGALAAASASELGAVAIRAALERANVPAERIDEIVFGCVLPA 62 Query: 64 GLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMS 123 G GQAPARQAAL AGL TT+NKMCGSGM+AA+ AHD+L AGSADV VAGGMESM+ Sbjct: 63 GQGQAPARQAALKAGLPLGAGATTVNKMCGSGMKAAMFAHDLLFAGSADVAVAGGMESMT 122 Query: 124 NAPYLLDRARAGYRMGHGRVQDSMFLDGLEDAYDKGRLMGTFAEDCAETNGFSREAQDAF 183 NAPYLL +ARAG RMGHG+V D MFLDGLEDAYDKGRLMGTFAEDCA+ FSREAQD F Sbjct: 123 NAPYLLPKARAGMRMGHGQVLDHMFLDGLEDAYDKGRLMGTFAEDCAQAYAFSREAQDDF 182 Query: 184 AIASTTRAQQAIKDGSFKAEIVPLTVTVGKEQVVISNDEQPPKARLDKIASLKPAFREGG 243 AIAS TRAQ+AI +G F +EI P+TV GK + V+S DEQP A+LDKI +LKPAFREGG Sbjct: 183 AIASLTRAQRAIAEGRFTSEIAPVTVKAGKTEAVVSIDEQPGNAKLDKIPTLKPAFREGG 242 Query: 244 TVTAANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIKKL 303 TVTAANSSSISDGAAALV+MR+SQA++ G+ P AVI GH+ +A+ PGLF APIGAI+KL Sbjct: 243 TVTAANSSSISDGAAALVMMRRSQAERLGVTPKAVIVGHSTYANKPGLFATAPIGAIRKL 302 Query: 304 MKKTGWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARILV 363 +KTGW+L DVDL E+NEAFAVV MAAM L++PH+K+NVHGGACALGHPIGASGAR++V Sbjct: 303 SEKTGWNLRDVDLFEINEAFAVVAMAAMRVLDLPHDKVNVHGGACALGHPIGASGARVVV 362 Query: 364 TLLSALRQKGLKRGVAAICIGGGEATAMAVE 394 TLL+AL GLKRGVA++CIGGGEATA+A+E Sbjct: 363 TLLAALETYGLKRGVASLCIGGGEATALAIE 393 Lambda K H 0.318 0.132 0.376 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: 551 Number of extensions: 15 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: 397 Length of database: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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