Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_004300924.1 C665_RS04210 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000310185.1:WP_004300924.1 Length = 427 Score = 210 bits (534), Expect = 7e-59 Identities = 151/437 (34%), Positives = 220/437 (50%), Gaps = 65/437 (14%) Query: 6 IVSTARTPIGKAYR--GALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGAT 63 IV ARTP KA G A++ AT G A+ + R P ++++V++G A A Sbjct: 7 IVDGARTPFLKAKNAPGPFTASDLATAAGSAL---LMRQPFAPDQLDEVILGCA-SPSAD 62 Query: 64 GGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS-- 121 NI R LR G G T+ R CASG+QAI A ++ ++ + GG +++S Sbjct: 63 EVNIGRVVALRLGCGNKVPGWTVMRNCASGMQAIDSAIANLQCGRSQLVLAGGVDALSHA 122 Query: 122 -LVQNDKM--------------------NTFHA--VDPALEAIKG----DVYMAMLDTAE 154 L+ ++KM TF + P + +KG V M T E Sbjct: 123 PLLFSEKMVRWLAGWYAARSTGDRLAMLRTFRLGHLAPVIGIMKGLTDPIVGQLMGQTGE 182 Query: 155 TVAKRYGISRERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDIT 214 +A ++GI+RE D +++ES RR A Q G + +EI P+ + G V A Sbjct: 183 NLAWKFGITREDMDAFAVESHRRVCAGQDAGHYAEEIVPLIDRDGQVYAA---------- 232 Query: 215 LSQDEGPRPETTAEGLAGLKAVRGEGF-TITAGNASQLSDGASATVIMSDKTAAAKGLKP 273 D+G R +++ LA LK + +T GN+SQ++DGA+ V+ S + GL+P Sbjct: 233 ---DDGVRRDSSMANLAKLKPFFDRKYGRVTPGNSSQITDGAAWLVLASQEAVERHGLQP 289 Query: 274 LGIFRGMVSYGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVL------- 326 LG G PD+MG+GPV A +L+RHGL+ DD+ WELNEAFA QV+ Sbjct: 290 LGRIVDSQWAGLAPDQMGLGPVHATMPILQRHGLAPDDLDAWELNEAFAAQVIACLRAFA 349 Query: 327 ---YCRDKLGI------DPEKLNVNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVV 377 YCR G+ D +LNV+GGA+++GHP G SGAR+ H L RR+ + Sbjct: 350 DDDYCRTHFGVDAPGAPDAARLNVDGGAVALGHPVGASGARIVLHLLEVLRRKGGGRGLA 409 Query: 378 TMCVGGGMGSAGLFEIV 394 ++C+GGG G A L E V Sbjct: 410 SICIGGGQGGAMLVETV 426 Lambda K H 0.316 0.134 0.378 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: 419 Number of extensions: 20 Number of successful extensions: 4 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: 395 Length of database: 427 Length adjustment: 31 Effective length of query: 364 Effective length of database: 396 Effective search space: 144144 Effective search space used: 144144 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