Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_011951599.1 SWIT_RS03835 3-oxoadipyl-CoA thiolase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_000016765.1:WP_011951599.1 Length = 399 Score = 555 bits (1430), Expect = e-163 Identities = 279/399 (69%), Positives = 329/399 (82%), Gaps = 2/399 (0%) Query: 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61 +A ICDA RTP GRYGG+L AVRADDLAA P+R L ERNPG+ ++DIL+GCANQAGE Sbjct: 3 DAYICDAARTPIGRYGGSLAAVRADDLAAIPMRVLRERNPGIV-GHIDDILFGCANQAGE 61 Query: 62 DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121 DNRNVARMA LL+GL PG+T+NRLCGS +DAV AARAIK+GE L++AGGVESM+R Sbjct: 62 DNRNVARMAALLSGLGEDAPGTTINRLCGSGMDAVAYAARAIKAGEADLIVAGGVESMSR 121 Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181 APFVM KA+ AF+RS A++DTTIGWRFVN LMK ++GIDSMPETAENVA DFQ++R DQD Sbjct: 122 APFVMPKADGAFSRSNAVYDTTIGWRFVNKLMKERFGIDSMPETAENVAQDFQVSREDQD 181 Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241 FA+ SQ+R AAAQA G A EI P+TIPQ+KGDP+VV DEHPR +T++ L KLK +V Sbjct: 182 RFAVESQRRAAAAQANGRLAAEIVPVTIPQRKGDPIVVDRDEHPR-ETSMEALGKLKPIV 240 Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301 R DGT+TAGNASGVNDGA A+++AS A + Y L PRA+VLG A AGV PRIMG GPAPA Sbjct: 241 RADGTITAGNASGVNDGAAAIIVASKAAVEAYGLTPRAKVLGGAVAGVPPRIMGIGPAPA 300 Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361 +K+L ++G+ + +DV+ELNEAFA+QGLAV+R LGLPDDAAHVNPNGGAIA+GHPLG S Sbjct: 301 SKKLLERLGIGIGAIDVVELNEAFASQGLAVLRQLGLPDDAAHVNPNGGAIALGHPLGMS 360 Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 GARLV TA +L RSG ALCTMCIGVGQGIAL IERV Sbjct: 361 GARLVLTATEELVRSGAGKALCTMCIGVGQGIALAIERV 399 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: 531 Number of extensions: 14 Number of successful extensions: 3 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: 399 Length adjustment: 31 Effective length of query: 370 Effective length of database: 368 Effective search space: 136160 Effective search space used: 136160 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)
Align candidate WP_011951599.1 SWIT_RS03835 (3-oxoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02430.hmm # target sequence database: /tmp/gapView.21873.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02430 [M=400] Accession: TIGR02430 Description: pcaF: 3-oxoadipyl-CoA thiolase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-207 674.5 12.9 2.9e-207 674.4 12.9 1.0 1 lcl|NCBI__GCF_000016765.1:WP_011951599.1 SWIT_RS03835 3-oxoadipyl-CoA thi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016765.1:WP_011951599.1 SWIT_RS03835 3-oxoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 674.4 12.9 2.9e-207 2.9e-207 2 400 .] 3 399 .] 2 399 .] 0.99 Alignments for each domain: == domain 1 score: 674.4 bits; conditional E-value: 2.9e-207 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarma 70 ++yi+da rtpiGrygGsl++vraddlaa+p++ l +rnp + + idd+++GcanqaGednrnvarma lcl|NCBI__GCF_000016765.1:WP_011951599.1 3 DAYICDAARTPIGRYGGSLAAVRADDLAAIPMRVLRERNPGI-VGHIDDILFGCANQAGEDNRNVARMA 70 69**************************************99.679*********************** PP TIGR02430 71 allaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakl 139 all+Gl ++ pgtt+nrlcgsg+da+++aaraikaGeadl++aGGvesmsrapfv+ kad+afsrs+ + lcl|NCBI__GCF_000016765.1:WP_011951599.1 71 ALLSGLGEDAPGTTINRLCGSGMDAVAYAARAIKAGEADLIVAGGVESMSRAPFVMPKADGAFSRSNAV 139 ********************************************************************* PP TIGR02430 140 edttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpve 208 dttiGwrfvn +k+ +G+dsmpetaenva++f+vsredqd fa+ sq+r+aaaqa+G +a+eivpv+ lcl|NCBI__GCF_000016765.1:WP_011951599.1 140 YDTTIGWRFVNKLMKERFGIDSMPETAENVAQDFQVSREDQDRFAVESQRRAAAAQANGRLAAEIVPVT 208 ********************************************************************* PP TIGR02430 209 ikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltp 277 i+q+kG++ vvd+deh+r et++eal klk++vr+dgt+taGnasGvndGaaa+++as+ av+++gltp lcl|NCBI__GCF_000016765.1:WP_011951599.1 209 IPQRKGDPIVVDRDEHPR-ETSMEALGKLKPIVRADGTITAGNASGVNDGAAAIIVASKAAVEAYGLTP 276 ******************.************************************************** PP TIGR02430 278 rarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvn 346 ra++l+ a aGv pr+mG+gp+pa kkll+r+g+ + +dv+elneafa+q+lavlr+lgl+dd+a+vn lcl|NCBI__GCF_000016765.1:WP_011951599.1 277 RAKVLGGAVAGVPPRIMGIGPAPASKKLLERLGIGIGAIDVVELNEAFASQGLAVLRQLGLPDDAAHVN 345 ********************************************************************* PP TIGR02430 347 pnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400 pnGGaialGhplG+sGarlvlta ++l +sg al+t+ciGvGqGial+ierv lcl|NCBI__GCF_000016765.1:WP_011951599.1 346 PNGGAIALGHPLGMSGARLVLTATEELVRSGAGKALCTMCIGVGQGIALAIERV 399 *****************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (399 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.92 // [ok]
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