Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate PfGW456L13_4590 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4590 Length = 400 Score = 244 bits (623), Expect = 3e-69 Identities = 168/415 (40%), Positives = 227/415 (54%), Gaps = 36/415 (8%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59 M + I RTPIG+ + G L+ L I+ ++R +D V++V +G A Q Sbjct: 1 MRDVYICDAIRTPIGR-FGGGLSTVRADDLAAVPIKALMERNPSVDWNAVDEVFLGCANQ 59 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G N+AR ALL AGLP T G T++R CASG+ AI A R++ +E+A+ GG ES Sbjct: 60 AGEDNRNVARMALLLAGLPETIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVES 119 Query: 120 ISLV------------QNDKMNT----FHAVDPALEAIKGDVYMAMLDTAETVAKRYGIS 163 +S +N K+ + ++P ++A G AM TA+ VA Y +S Sbjct: 120 MSRAPFVMGKADAAFSRNMKLEDTTIGWRFINPLMKAQYG--VDAMPQTADNVADDYKVS 177 Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAP--ISTKMGVVDKATGAVSFKDITLSQDEGP 221 R QD ++L SQ+RTAAAQ G F +EI I+ K G + +SQDE P Sbjct: 178 RADQDAFALRSQQRTAAAQAAGFFAEEIVEVRIAHKKG------------ETVVSQDEHP 225 Query: 222 RPETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMV 281 R +TT E L LK V G T+TAGNAS ++DGA+A ++ S + GL GM Sbjct: 226 RADTTLEALTKLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARAKVLGMA 285 Query: 282 SYGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKL 339 S G P MGIGPV AV +L++R G++V D + ELNEAFA Q L +LGI D ++ Sbjct: 286 SAGVAPRVMGIGPVPAVRKLIERLGVAVSDFDVIELNEAFASQGLAVLRELGIADDAAQV 345 Query: 340 NVNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 N NGGAI++GHP GMSGARL AL + + K + TMCVG G G A E V Sbjct: 346 NPNGGAIALGHPLGMSGARLVLTALHQLEKTGGKKGLATMCVGVGQGLALAIERV 400 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: 416 Number of extensions: 26 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: 400 Length adjustment: 31 Effective length of query: 364 Effective length of database: 369 Effective search space: 134316 Effective search space used: 134316 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