Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate CCNA_03575 CCNA_03575 3-ketoacyl-CoA thiolase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Caulo:CCNA_03575 Length = 395 Score = 487 bits (1253), Expect = e-142 Identities = 252/394 (63%), Positives = 296/394 (75%), Gaps = 1/394 (0%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M EAVIVS ART + K+ RG N T GA + GHAI+HAV RAG++ EVEDVV+G + Sbjct: 1 MREAVIVSYARTGLAKSVRGGFNNTHGAAMAGHAIQHAVSRAGLEGAEVEDVVLGCGGPE 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 GATG N+AR A + AGLPVTT+G TI+R C+SGLQAIA AA V DG +A+GGG ESI Sbjct: 61 GATGMNVARNAAMWAGLPVTTSGQTINRFCSSGLQAIATAANYVRNDGANVAIGGGVESI 120 Query: 121 SLVQ-NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179 SLV MN FH + L ++MAM+DTA+ VAKRY +SRE QDEY+L SQ+R A Sbjct: 121 SLVNAGGHMNRFHITEEKLMQTHPALWMAMIDTADIVAKRYNVSREYQDEYALRSQQRIA 180 Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239 AAQ G F DEI P++TKM VV+K T SF D + +DE R +TT EGLA LK V GE Sbjct: 181 AAQAAGLFKDEIVPMATKMKVVNKETKEESFVDYVVDKDECNRADTTLEGLASLKPVMGE 240 Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVP 299 G ITAGNASQLSDGA+A V+M K A +GL PLG FRG GCEPDEMGIGPVFAVP Sbjct: 241 GKFITAGNASQLSDGAAAVVVMEAKEAEKRGLTPLGAFRGFAVAGCEPDEMGIGPVFAVP 300 Query: 300 RLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARL 359 RLL+RHGL VDDI +WELNEAFA Q LY RD+LGIDPEK NVNGG+I++GHP+GM+GAR Sbjct: 301 RLLERHGLKVDDIDIWELNEAFASQCLYSRDRLGIDPEKYNVNGGSIAIGHPFGMTGARC 360 Query: 360 AGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEI 393 AGH L+EG+RRKAK VVTMC+GGGMG+AGLFEI Sbjct: 361 AGHLLLEGKRRKAKLGVVTMCIGGGMGAAGLFEI 394 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: 526 Number of extensions: 18 Number of successful extensions: 2 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: 395 Length adjustment: 31 Effective length of query: 364 Effective length of database: 364 Effective search space: 132496 Effective search space used: 132496 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 17 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