Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF1320 PS417_06710 beta-ketoadipyl CoA thiolase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__WCS417:GFF1320 Length = 400 Score = 243 bits (619), Expect = 9e-69 Identities = 162/407 (39%), Positives = 220/407 (54%), Gaps = 32/407 (7%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59 M + I RTPIG+ + G L+ L I+ ++R +D V++V +G A Q Sbjct: 1 MRDVFICDAIRTPIGR-FGGGLSTVRADDLAALPIKALIERNPSVDWTAVDEVFLGCANQ 59 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G N+AR ALL AGLP + G T++R CASG+ AI A R++ +E+A+ GG ES Sbjct: 60 AGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVES 119 Query: 120 IS----------------LVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGIS 163 +S + D + ++P ++A G AM TA+ VA Y +S Sbjct: 120 MSRAPFVMGKADAAFSRTMKLEDTTIGWRFINPLMKAQYG--VDAMPQTADNVADDYHVS 177 Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223 R QD ++L SQ+RTAAAQ G F +EI P+ A + + QDE PR Sbjct: 178 RADQDAFALRSQQRTAAAQAAGFFAEEIVPVRV----------AHKKGETVVEQDEHPRA 227 Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283 +TT E L LK V G T+TAGNAS ++DGA+A ++ S + GL GM S Sbjct: 228 DTTLEALTKLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARARVLGMASA 287 Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341 G P MGIGPV AV +L++R GL+V D + ELNEAFA Q L +LGI D ++N Sbjct: 288 GVAPRVMGIGPVPAVRKLVERLGLAVTDFDVIELNEAFASQGLAVLRELGIADDAPQVNP 347 Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 NGGAI++GHP GMSGARL AL + + + TMCVG G G A Sbjct: 348 NGGAIALGHPLGMSGARLVLTALHQLEKTGGSKGLATMCVGVGQGLA 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: 414 Number of extensions: 23 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 Apr 09 2024. 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