Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Pf6N2E2_1851 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1851 Length = 402 Score = 272 bits (695), Expect = 1e-77 Identities = 179/422 (42%), Positives = 238/422 (56%), Gaps = 50/422 (11%) Query: 5 FICDGIRTPIGR--YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGE 62 FI D +RTP G+ GAL SV+ +AA L EL R LD +DDV+LGC GE Sbjct: 6 FIYDAVRTPRGKGKKDGALYSVKPVHMAAGLLTELQQRYD-LDTSRVDDVVLGCGQPVGE 64 Query: 63 DNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSR 122 +VA+ AG +SV G I+R C SGL+A+ AA I +G DL++AGGVESMSR Sbjct: 65 QGGDVAKCVVQYAGWDESVPGVQIDRFCASGLEAVNQAASRIASGWEDLIVAGGVESMSR 124 Query: 123 APFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPET--AENVAELLKISRED 180 P MG A A+ + E+ F S+P+ A+ +A L SRED Sbjct: 125 LP--MGAAGQAWIQDPEI----------------AFKLQSVPQGIGADLLAALDGYSRED 166 Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240 D FAL SQQR A A+ SG +VPV ++ G+V ++ DE ++P TTLE L LK Sbjct: 167 VDRFALVSQQRAAHARDSGYFDRSVVPV--RDLNGLVV-LERDEFIKPATTLEALSQLKP 223 Query: 241 PFRANGVI--------------------TAGNASGVNDGAAALIIASEQMAAAQGLTPRA 280 F A G + TAGN+SG+ DGA+A ++ SE++ GL PR Sbjct: 224 SFAAMGKLGYSDVALRKYPQVARIEPIHTAGNSSGIVDGASATLLGSERIGQQLGLAPRG 283 Query: 281 RIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLP 340 RI+A A EP LM GP PA ++ L +AGLS+ D+D+ E+NEAFA+ L +R+L Sbjct: 284 RIIATAVLSTEPTLMLAGPGPAAKKALAKAGLSVQDIDLFEINEAFASVVLRFMRDL--- 340 Query: 341 DDAPHV-NPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILE 399 D +P + N NGGAIALGHP+G +GA L EL RRN + L +C+G G GIA I+E Sbjct: 341 DISPEITNVNGGAIALGHPIGATGAMLVGTVLDELERRNLKRGLIALCVGGGMGIATIIE 400 Query: 400 RV 401 R+ Sbjct: 401 RL 402 Lambda K H 0.319 0.135 0.384 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: 433 Number of extensions: 20 Number of successful extensions: 5 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: 401 Length of database: 402 Length adjustment: 31 Effective length of query: 370 Effective length of database: 371 Effective search space: 137270 Effective search space used: 137270 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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