Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_035240374.1 Q366_RS14810 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000745975.1:WP_035240374.1 Length = 416 Score = 270 bits (690), Expect = 6e-77 Identities = 166/425 (39%), Positives = 239/425 (56%), Gaps = 38/425 (8%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEP---NPAVQWDQVDEVFFGCA 57 M+DV I A RT IG FGG L + LA++ ++ ++ +PAV +D+V +G Sbjct: 1 MKDVVIVSACRTAIGAFGGTLKDLNGAHLASITMREAVKRANIDPAV----IDDVRYGTC 56 Query: 58 NQAGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGV 117 + D N R+A L+AG+P+++P T+NR+C SGM+A+ + I +G ++ +AGG Sbjct: 57 VEH-HDTLNTTRVAALMAGIPDTVPAATINRVCISGMEAVLSGMAMIQAGMADVILAGGT 115 Query: 118 ESMSRAPFVMGKAESGYSRNMKLEDTTIGWRFINPL--------MKSQYGVDS------- 162 E MS P+ + A G +L+DT I+ L + VD+ Sbjct: 116 EHMSGVPYAVPNARWG----CRLQDTGFVDAMIHALHCGSFLLPLDETSPVDTSQAPAAD 171 Query: 163 -------MPETADNVADDYQVSRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKG 215 M TA+ VA +SRA+ D ALRS A A G FAEEIVPV + +K Sbjct: 172 FLGQPYIMGHTAEFVAQLLDISRAEMDEVALRSHNNAERATNDGSFAEEIVPVEVPQRKK 231 Query: 216 ETIV-ERDEHLRPETTLEALTKLKPVNGPDK-TVTAGNASGVNDGAAALILASAEAVKKH 273 + I+ ++DEH RP TLE L L P P VTAGNASG+NDG+ +++ SAE K+ Sbjct: 232 DPIIFDKDEHFRPGMTLEKLAALPPAFVPKTGKVTAGNASGINDGSTGMVIMSAEKAKEL 291 Query: 274 GLTPRARVLGMASGGVAPRVMGIGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVL 333 GLTP A++ G P VMG+ PVPAV+ L + G+ ++DF +IE+NEAFA+Q L Sbjct: 292 GLTPIAKIKATGMGACHPSVMGLSPVPAVKDLMAKSGITINDFHLIEVNEAFAAQYLGCE 351 Query: 334 RELGVADDAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGL 393 RELG+ + N NG I LGHP+G +GAR++ T ++ ++ G GLAT+C G G + Sbjct: 352 RELGLNREI--TNVNGSGIGLGHPVGSTGARVMTTLMYAMKNKGKSLGLATLCGGGGVSM 409 Query: 394 ALAIE 398 A AIE Sbjct: 410 ACAIE 414 Lambda K H 0.318 0.134 0.383 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: 431 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 416 Length adjustment: 31 Effective length of query: 369 Effective length of database: 385 Effective search space: 142065 Effective search space used: 142065 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