Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_011385133.1 AMB_RS13850 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000009985.1:WP_011385133.1 Length = 400 Score = 525 bits (1351), Expect = e-153 Identities = 267/401 (66%), Positives = 320/401 (79%), Gaps = 2/401 (0%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M + ICD RTPIGR+ G+LAGVR DDLAA P+KAL+ + + W +VDEV +GCANQA Sbjct: 1 MTEALICDYTRTPIGRYAGSLAGVRTDDLAAHPIKALMARHAGLDWSRVDEVAYGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARMALLLAGLP SI G TLNRLC SGMDA+G A RA+ +GE EL IAGGVESM Sbjct: 61 GEDNRNVARMALLLAGLPHSIGGTTLNRLCGSGMDAVGYAARAVMTGEAELMIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAPFVM KA+S +SR+ +L DTTIGWRF+N LM+ YG DSMPETA+NVA+ + +SR D Sbjct: 121 SRAPFVMNKADSAFSRDARLYDTTIGWRFVNALMEKAYGTDSMPETAENVAEQFNISRED 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLRPETTLEALTKLKP 239 QDAFA RSQ KA+AAQ G FA+EI PV + +KG+ +V DEH R ETT+EAL KLK Sbjct: 181 QDAFAARSQAKASAAQKNGRFAQEISPVTLPARKGDPVVVSHDEHPR-ETTVEALAKLKA 239 Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299 ++TAGNASGVNDGAAAL++AS A K HGLTP AR+LGMA+ GV PR+MGIGPV Sbjct: 240 PFRAGGSITAGNASGVNDGAAALLIASPAAAKAHGLTPIARILGMATAGVEPRIMGIGPV 299 Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359 PA +KL RLG+ ++D DV+E NEAFA+Q LA R+LG+ADD +VNPNGGAIALGHPLG Sbjct: 300 PATQKLLARLGLTMADLDVMEFNEAFAAQALACTRQLGLADDDQRVNPNGGAIALGHPLG 359 Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 MSGAR+V TA QL ++GGR+ L+TMC+GVGQG+A+AIERV Sbjct: 360 MSGARIVGTAALQLAQTGGRRALSTMCIGVGQGIAMAIERV 400 Lambda K H 0.318 0.134 0.383 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: 501 Number of extensions: 15 Number of successful extensions: 1 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: 400 Length of database: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_011385133.1 AMB_RS13850 (3-oxoadipyl-CoA thiolase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))
# 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/TIGR01930.hmm # target sequence database: /tmp/gapView.923.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01930 [M=385] Accession: TIGR01930 Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-139 451.0 7.9 1.9e-139 450.8 7.9 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011385133.1 AMB_RS13850 3-oxoadipyl-CoA thio Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011385133.1 AMB_RS13850 3-oxoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 450.8 7.9 1.9e-139 1.9e-139 1 385 [] 6 398 .. 6 398 .. 0.95 Alignments for each domain: == domain 1 score: 450.8 bits; conditional E-value: 1.9e-139 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaala 67 i d++Rtpig++ gsl+ ++ +dL+a+ ik+l++r gld +++dev++G++ qage+ n+aR+a+l lcl|NCBI__GCF_000009985.1:WP_011385133.1 6 ICDYTRTPIGRYAGSLAGVRTDDLAAHPIKALMARHaGLDWSRVDEVAYGCANQAGEDnRNVARMALLL 74 7899******99**********************************************9********** PP TIGR01930 68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136 aglp+s+ ++t+nr+C+Sg++Av aa+++++Gea++++aGGvEsmSr+p++++++ +s+ ++a+l lcl|NCBI__GCF_000009985.1:WP_011385133.1 75 AGLPHSIGGTTLNRLCGSGMDAVGYAARAVMTGEAELMIAGGVESMSRAPFVMNKA---DSAFSRDARL 140 ***************************************************99997...4555556666 PP TIGR01930 137 edqllkdl........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpve 197 +d+++ ++ sm etAen+a++++isRe+qD++a+rS+ ka++A+++g+f++ei pv+ lcl|NCBI__GCF_000009985.1:WP_011385133.1 141 YDTTIGWRfvnalmekAYGTDSMPETAENVAEQFNISREDQDAFAARSQAKASAAQKNGRFAQEISPVT 209 664433336778899888899************************************************ PP TIGR01930 198 vkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgl 263 ++ + ++vvs+De++r +tt+e+LakLk+ f+ gs +tAgN+s++nDGAaall++s ++ak++gl lcl|NCBI__GCF_000009985.1:WP_011385133.1 210 LPARkgdPVVVSHDEHPR-ETTVEALAKLKAPFRA-GGS-ITAGNASGVNDGAAALLIASPAAAKAHGL 275 *9999999**********.89************96.796.***************************** PP TIGR01930 264 tplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lek 331 tp+ari ++a+agv+p++mg+gpvpA++k+L++ gl++ d+d++E+nEAFAaq+la++++lg+ d +++ lcl|NCBI__GCF_000009985.1:WP_011385133.1 276 TPIARILGMATAGVEPRIMGIGPVPATQKLLARLGLTMADLDVMEFNEAFAAQALACTRQLGLADdDQR 344 **************************************************************8667*** PP TIGR01930 332 vNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 vN nGGAiAlGHPlG+sGariv t + +L++ g++++l t+C+g GqG+A+ +e lcl|NCBI__GCF_000009985.1:WP_011385133.1 345 VNPNGGAIALGHPLGMSGARIVGTAALQLAQTGGRRALSTMCIGVGQGIAMAIE 398 ***************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (400 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: 00:00:00.02 # Mc/sec: 7.70 // [ok]
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