Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_027458119.1 K420_RS0111065 acetyl-CoA C-acyltransferase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_000519045.1:WP_027458119.1 Length = 398 Score = 322 bits (825), Expect = 1e-92 Identities = 192/409 (46%), Positives = 243/409 (59%), Gaps = 27/409 (6%) Query: 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61 EA I A R P + GG VR DD+ A I+S++ + PG+D +R+ D++ GCA E Sbjct: 7 EAYIVAATRLPVAKKGGMFRNVRPDDMLAHAIKSVVAQVPGIDPARIGDVIVGCAMPEAE 66 Query: 62 DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121 NVAR+ LLAGLPI VPG T+NR C S L AV AA I+ G +MIA G ESMT Sbjct: 67 QGMNVARIGALLAGLPITVPGITINRFCSSGLQAVADAANQIRLGLADVMIAAGTESMTI 126 Query: 122 APFVMGKAESAFARSAAIF-DTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180 P +MG + A + AIF D IG YG M TAE VA +QI+R +Q Sbjct: 127 MPQIMG---NKMAMNPAIFTDENIG---------IAYG---MGLTAEKVANQWQISREEQ 171 Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGD---------PLVVTTDEHPRPDTTL 231 DAFAL S Q+ AA AAG F E +P I + D V DE PRPD +L Sbjct: 172 DAFALASNQKACAAIAAGHFKAETSPYLIRESLPDLKTGQIKVRERTVEFDEGPRPDASL 231 Query: 232 ATLAKLKGVVRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAP 291 L KL+ V G+VTAGN+S ++DGA A++L S K + L P AR A GVAP Sbjct: 232 EKLGKLRPVFHARGSVTAGNSSQMSDGAAAVMLVSEKVLKEHNLTPLARFASFAVGGVAP 291 Query: 292 RIMGFGPAPAVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGA 351 IMG GP A+ K LAQ G+ +D IELNEAFAAQ LAV+++LGL D + +NP GGA Sbjct: 292 EIMGIGPIAAIPKALAQAGIRQEDLDWIELNEAFAAQSLAVVKELGL--DPSKINPLGGA 349 Query: 352 IAIGHPLGASGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 IA+GHPLGA+GA T ++ L+R+GG+Y + +MCIG G G A + ERV Sbjct: 350 IALGHPLGATGAIRTATIVHGLQRTGGKYGMVSMCIGTGMGAAGIFERV 398 Lambda K H 0.320 0.135 0.394 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: 448 Number of extensions: 21 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: 401 Length of database: 398 Length adjustment: 31 Effective length of query: 370 Effective length of database: 367 Effective search space: 135790 Effective search space used: 135790 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 24 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