Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate PP_2051 PP_2051 3-ketoacyl-CoA thiolase (thiolase I)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Putida:PP_2051 Length = 394 Score = 456 bits (1173), Expect = e-133 Identities = 236/395 (59%), Positives = 290/395 (73%), Gaps = 2/395 (0%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M +AVIV+TARTPIGKA RGA N + ++ AI AV+RAGI+P +V+D+V+G AMQ Sbjct: 1 MKDAVIVATARTPIGKAMRGAFNDLKTPSMTAVAIRAAVERAGIEPAQVDDLVLGTAMQS 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G N R + L AGLP + +G T+DRQCASGL AIA AA+ ++ DG+++ +G G E I Sbjct: 61 GTAAINPGRLSALAAGLPQSVSGQTVDRQCASGLMAIATAAKQIMVDGMQVTIGAGQEQI 120 Query: 121 SLVQN-DKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179 SLVQ A DPA+ + YM ML TAE VA+RYGISRE QD Y+L+SQ+RTA Sbjct: 121 SLVQQVHNQLASEAYDPAVLRMSEHAYMPMLQTAERVARRYGISREAQDVYALQSQQRTA 180 Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239 AAQ G F EI P+ + VVDK TG VS +++ L+QDEG RP TT L GLK V E Sbjct: 181 AAQAAGLFAAEIVPVIARKKVVDKLTGVVSHEEVRLTQDEGNRPATTLADLQGLKPVV-E 239 Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVP 299 G +TAGNASQLSDGASA V+M AA G+ LG++RG+ G P+EMGIGPV AVP Sbjct: 240 GGCVTAGNASQLSDGASACVLMEGALAARSGIAALGLYRGIAVAGLAPEEMGIGPVLAVP 299 Query: 300 RLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARL 359 +LL++ GL+VDDIGLWELNEAFA QVLYC +L IDP KLNVNGGAI++GHPYGMSGAR+ Sbjct: 300 KLLRQQGLTVDDIGLWELNEAFACQVLYCAQQLQIDPAKLNVNGGAIAIGHPYGMSGARM 359 Query: 360 AGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 GHAL+EG+RRK KY VVTMCVGGGMG+AGLFE++ Sbjct: 360 VGHALLEGKRRKVKYVVVTMCVGGGMGAAGLFEVL 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: 480 Number of extensions: 17 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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