Align 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16) (characterized)
to candidate WP_099619082.1 CLH62_RS15420 acetyl-CoA C-acyltransferase
Query= reanno::MR1:200842 (396 letters) >NCBI__GCF_002744735.1:WP_099619082.1 Length = 393 Score = 510 bits (1314), Expect = e-149 Identities = 254/390 (65%), Positives = 314/390 (80%) Query: 7 NQEIVIVAAKRTPMGSFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAG 66 + +VI + RTPMG GSLS + S L A AIKA + + + P V EV+MGCVLPAG Sbjct: 3 DNSVVIAGSARTPMGGMMGSLSSVRSPDLGAAAIKAAIERSGLQPADVQEVIMGCVLPAG 62 Query: 67 LGQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQ 126 LGQAPARQA+ +G+P S G TT+NK+CGSGM+ V++AHD IKAG+ ++IAGGME+MSQ Sbjct: 63 LGQAPARQASRASGIPDSSGCTTINKMCGSGMQAVIMAHDQIKAGTNNIMIAGGMENMSQ 122 Query: 127 APYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGGAMGTFAQKTADEFGITREQMDAFAL 186 APYLL KARAG+RMGHG+V+D MFLDGLEDAY GG MG FAQ+TAD++ I+R+ MD FA+ Sbjct: 123 APYLLPKARAGMRMGHGQVMDSMFLDGLEDAYEGGLMGVFAQRTADKYDISRQAMDEFAI 182 Query: 187 SSLEKANAAINSGAFKTEIVPVTVSDRRGDVTIDTDEQPGNARPEKIPTLRPAFAKDGTI 246 SL+K+ AAI +G F+ EIVPVTVS R GD +DTDEQPGNA+PEKIP L+PAFAKDG++ Sbjct: 183 GSLQKSLAAIENGWFRDEIVPVTVSGRGGDTEVDTDEQPGNAKPEKIPHLKPAFAKDGSV 242 Query: 247 TAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKLLS 306 TAANSSSISDGA+AL+L + A A+ GLT A I H THA+ P+ FT AP+GA+ K+L Sbjct: 243 TAANSSSISDGASALVLASAAEADARGLTPQARIVAHATHARLPSEFTLAPIGAIEKVLK 302 Query: 307 NVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALGHPIGCSGARLLVTL 366 GWS D+VDLFEINEAFA+VT+ A++EL L KVNV+GGACALGHPIG SG+R++VTL Sbjct: 303 KAGWSVDDVDLFEINEAFAVVTLAAINELKLPAEKVNVHGGACALGHPIGSSGSRIIVTL 362 Query: 367 IHALKARGLKRGVASLCIGGGEATAMAIEV 396 ++ALK RGLKRGVASLCIGGGE TA+AIE+ Sbjct: 363 MNALKQRGLKRGVASLCIGGGEGTAVAIEL 392 Lambda K H 0.316 0.131 0.364 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: 521 Number of extensions: 17 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: 396 Length of database: 393 Length adjustment: 31 Effective length of query: 365 Effective length of database: 362 Effective search space: 132130 Effective search space used: 132130 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 (21.6 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