Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_012169527.1 AZC_RS05105 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000010525.1:WP_012169527.1 Length = 401 Score = 540 bits (1391), Expect = e-158 Identities = 282/402 (70%), Positives = 322/402 (80%), Gaps = 3/402 (0%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M + +ICD IRTPIGRFGGAL+ VRADDL A+PLKAL+ N + W++VD+V FGCANQA Sbjct: 1 MTEAYICDYIRTPIGRFGGALSAVRADDLGAIPLKALVARNAGLDWEKVDDVIFGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARM+LLLAGLP SI G T+NRLC SGMDA+ TA RAI +GE +L IAGGVESM Sbjct: 61 GEDNRNVARMSLLLAGLPLSIGGTTMNRLCGSGMDAVATAARAIKAGEADLIIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAP VM KA++ +SR ++ DTTIGWRF+NPLMK YGVDSMPET DNVA DY+VSR D Sbjct: 121 SRAPLVMPKADAAFSRRAEIYDTTIGWRFVNPLMKEMYGVDSMPETGDNVAIDYKVSRED 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLRPETTLEALTKLKP 239 QDAFA+RSQ+KA+AAQA G A EI PV + KKG+ +VERDEH R T+LEAL KLKP Sbjct: 181 QDAFAVRSQEKASAAQANGRLAREITPVTLPQKKGDPVVVERDEHPR-ATSLEALAKLKP 239 Query: 240 VNG-PDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGP 298 VN TVTAGNASGVNDGAAALI+AS A K HGLTP ARVLG A GV PRVMGIGP Sbjct: 240 VNRMAGATVTAGNASGVNDGAAALIIASEAAAKAHGLTPIARVLGGAVAGVPPRVMGIGP 299 Query: 299 VPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPL 358 PA +KL RLG+ FDVIELNEAFASQGLA LR LG+ADD +VN NGGAIALGHPL Sbjct: 300 APASQKLMARLGLTQDQFDVIELNEAFASQGLATLRLLGIADDDARVNCNGGAIALGHPL 359 Query: 359 GMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 GMSGAR+ TA +L GGR+ LATMC+GVGQG+A+A+ERV Sbjct: 360 GMSGARITGTAALELTVGGGRRALATMCIGVGQGIAVALERV 401 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: 544 Number of extensions: 20 Number of successful extensions: 2 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: 401 Length adjustment: 31 Effective length of query: 369 Effective length of database: 370 Effective search space: 136530 Effective search space used: 136530 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_012169527.1 AZC_RS05105 (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.17221.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-135 438.1 5.0 1.6e-135 437.9 5.0 1.0 1 lcl|NCBI__GCF_000010525.1:WP_012169527.1 AZC_RS05105 3-oxoadipyl-CoA thio Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_012169527.1 AZC_RS05105 3-oxoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 437.9 5.0 1.6e-135 1.6e-135 1 385 [] 6 399 .. 6 399 .. 0.95 Alignments for each domain: == domain 1 score: 437.9 bits; conditional E-value: 1.6e-135 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaala 67 i d++Rtpig++gg+l+ ++a+dL+a +k+l++r+ gld ek+d+vi+G++ qage+ n+aR+ +l lcl|NCBI__GCF_000010525.1:WP_012169527.1 6 ICDYIRTPIGRFGGALSAVRADDLGAIPLKALVARNaGLDWEKVDDVIFGCANQAGEDnRNVARMSLLL 74 7899******************************************************9********** PP TIGR01930 68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136 aglp s+ ++t+nr+C+Sg++Ava+aa++ikaGead+++aGGvEsmSr+p++++++ + + ++a+ lcl|NCBI__GCF_000010525.1:WP_012169527.1 75 AGLPLSIGGTTMNRLCGSGMDAVATAARAIKAGEADLIIAGGVESMSRAPLVMPKA---DAAFSRRAEI 140 ***************************************************99997...4555566777 PP TIGR01930 137 edqllkdl........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpve 197 +d+++ + sm et +n+a +y++sRe+qD++a+rS++ka++A+++g++++ei+pv+ lcl|NCBI__GCF_000010525.1:WP_012169527.1 141 YDTTIGWRfvnplmkeMYGVDSMPETGDNVAIDYKVSREDQDAFAVRSQEKASAAQANGRLAREITPVT 209 7744433378999998777889*********************************************** PP TIGR01930 198 vkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgl 263 +++k ++vv++De++r t+le+LakLkp+ + +g tvtAgN+s++nDGAaal+++se++ak++gl lcl|NCBI__GCF_000010525.1:WP_012169527.1 210 LPQKkgdPVVVERDEHPR-ATSLEALAKLKPVNRM-AGATVTAGNASGVNDGAAALIIASEAAAKAHGL 276 **999*99**********.899***********95.899****************************** PP TIGR01930 264 tplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lek 331 tp+ar+ + avagv+p++mg+gp+pA++k++++ gl+ +++d++E+nEAFA+q la + lg d +++ lcl|NCBI__GCF_000010525.1:WP_012169527.1 277 TPIARVLGGAVAGVPPRVMGIGPAPASQKLMARLGLTQDQFDVIELNEAFASQGLATLRLLGIADdDAR 345 **************************************************************86679** PP TIGR01930 332 vNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 vN+nGGAiAlGHPlG+sGari+ t + eL g++++lat+C+g GqG+Av le lcl|NCBI__GCF_000010525.1:WP_012169527.1 346 VNCNGGAIALGHPLGMSGARITGTAALELTVGGGRRALATMCIGVGQGIAVALE 399 ***************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (401 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