Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_013054067.1 V474_RS21625 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_001046635.1:WP_013054067.1 Length = 403 Score = 288 bits (737), Expect = 2e-82 Identities = 173/404 (42%), Positives = 245/404 (60%), Gaps = 8/404 (1%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 + A I+ +RT +G++ G L+++ A LGA +KAL+ R +D VDDV++G + Sbjct: 3 LRRAAIVSPLRTAVGKFGGGLSALTAGQLGATIIKALVERSG-IDPERVDDVVFGHGYPS 61 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 GE ++ R + L AG+P +VPG L+R CGSGL A+ AA ++ G A +++AGG ESM Sbjct: 62 GEAP-SIGRWSWLAAGMPQNVPGFQLDRRCGSGLQAIIEAAMMVQTGAADVVVAGGAESM 120 Query: 121 SRAP-FVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRA 179 S + + A S E+ D R +++ +++ I M ETAEN+A + I+R Sbjct: 121 SNVEHYSTALRKGARMGSLELHDRLTRARLMSQPIERYGVITGMIETAENLARDYGITRE 180 Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLG 239 DA+A+RS +AAAA G+ A EIV V + Q++G I + DE R D +LE L L Sbjct: 181 QSDAYAVRSHQRAAAAWREGKFADEIVPVAVPQKRGEPVIFDRDEGFREDASLETLGGL- 239 Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299 P +GG VTAGNAS ND A A L+ + + + GL+ VG A AG +P MGIGP Sbjct: 240 KPI-EGGVVTAGNASQQNDAAAACLVVAEDQLAKLGLEPSGWFVGWAAAGCDPSRMGIGP 298 Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDER---VNPNGGAIALG 356 V A +++ TGL DMD+IE+NEAFAAQ LA+L+ +DD R +N NG I+LG Sbjct: 299 VGAVQRLFARTGLGWDDMDLIEINEAFAAQVLALLKAWEWGEDDSRLDKLNVNGSGISLG 358 Query: 357 HPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 HP+G++GAR+ T L+E+ R RY L TMCIG GQG+A I ER Sbjct: 359 HPIGVTGARIAATMLNEMRRRDARYGLETMCIGGGQGLAAIFER 402 Lambda K H 0.319 0.134 0.384 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: 459 Number of extensions: 33 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: 401 Length of database: 403 Length adjustment: 31 Effective length of query: 370 Effective length of database: 372 Effective search space: 137640 Effective search space used: 137640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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