Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_086509762.1 BZY95_RS09850 acetyl-CoA C-acyltransferase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_002151265.1:WP_086509762.1 Length = 402 Score = 435 bits (1118), Expect = e-126 Identities = 233/400 (58%), Positives = 281/400 (70%), Gaps = 3/400 (0%) Query: 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61 +A I D +RTPFGR+GG+L AVR DDL +++L+ RN G E++L GC NQAGE Sbjct: 3 DAYIFDGLRTPFGRHGGSLAAVRPDDLLGHVLKALVARN-GFAAEAYEEVLAGCTNQAGE 61 Query: 62 DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121 D+RNVAR AGLLAGLP+ V TVNRLCGS L AV AARA + GE +L +AGGVESM+R Sbjct: 62 DSRNVARHAGLLAGLPVEVAAQTVNRLCGSGLAAVIDAARATRLGEGELFLAGGVESMSR 121 Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181 AP+V+GKAES FAR+ ++DT IG RF NP + +YG SMPETA+NVA D I R D Sbjct: 122 APYVLGKAESPFARNQPLYDTVIGSRFPNPWLAREYGSHSMPETADNVAHDLGIGRDASD 181 Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQ-KKGDPLVVTTDEHPRPDTTLATLAKLKGV 240 FA RSQ +A A A GF+ E+ + +PQ +K PL V DEHPRP T LA+L G Sbjct: 182 VFAARSQAHYAEALARGFYDDELLAVEVPQGRKQPPLTVDRDEHPRPGTDADKLARL-GP 240 Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300 + G VTAGNASG+NDGA AL++ S A + + PRAR++ A AGV PR+MG GP P Sbjct: 241 LFEGGVVTAGNASGLNDGAAALIVGSLAAGERAGMAPRARIVASAVAGVPPRVMGLGPVP 300 Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360 A RK L + GL LAQMD IE+NEAFA Q L + LGL D + +N NGGAIAIGHPLGA Sbjct: 301 ASRKALERAGLNLAQMDAIEINEAFAVQVLGCTQQLGLDPDDSRLNANGGAIAIGHPLGA 360 Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 SG RL TA+ QLE GGRYAL TMCIGVGQGIA +IER+ Sbjct: 361 SGTRLALTALRQLEAGGGRYALVTMCIGVGQGIACIIERM 400 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: 517 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: 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 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