Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate H281DRAFT_01504 H281DRAFT_01504 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Burk376:H281DRAFT_01504 Length = 400 Score = 570 bits (1470), Expect = e-167 Identities = 287/401 (71%), Positives = 336/401 (83%), Gaps = 1/401 (0%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M EA + DA+RTPIGRYAG+L+SVRADDLGA+PLKAL+ R+ +DWS +DDVIYGCANQA Sbjct: 1 MTEAFLCDAIRTPIGRYAGSLSSVRADDLGAVPLKALMERNKNVDWSVIDDVIYGCANQA 60 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 GEDNRNVARM+ LLAGLP VPG+T+NRLCGSG+DAVG AARA++ GEA LM+AGGVESM Sbjct: 61 GEDNRNVARMSLLLAGLPKDVPGSTVNRLCGSGMDAVGIAARAIKSGEAALMVAGGVESM 120 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 SRAPFVMGK+ AF R A+I+DTTIGWRFVN LM+Q +G+DSMPET ENVA +NISRAD Sbjct: 121 SRAPFVMGKATSAFSRQADIYDTTIGWRFVNPLMKQMYGVDSMPETGENVATDYNISRAD 180 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240 QDAFALRSQ KAA A +G LA+EIV V IAQ+KG V DEHPR +T+LE LAKL Sbjct: 181 QDAFALRSQQKAARAQKDGTLAQEIVGVTIAQKKGDPITVSQDEHPR-ETSLETLAKLKG 239 Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300 R G+VTAGNASGVNDGA ALLLA+ E A+R GL RARV+G+ATAGV PRIMG+GP Sbjct: 240 VVRPDGTVTAGNASGVNDGAAALLLANEETAKRFGLTPRARVLGIATAGVAPRIMGMGPA 299 Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360 PA +K++ + + DVIELNEAFA+QG+AVLR LG+ADDD RVNPNGGAIALGHPLG Sbjct: 300 PAAQKLMARLNMTIDQFDVIELNEAFASQGIAVLRTLGVADDDARVNPNGGAIALGHPLG 359 Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 MSGARLVTTA+++L+ QGR+ALCTMCIGVGQGIA+ IER+ Sbjct: 360 MSGARLVTTAMYQLQRTQGRFALCTMCIGVGQGIAIAIERV 400 Lambda K H 0.319 0.134 0.384 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: 549 Number of extensions: 12 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: 401 Length of database: 400 Length adjustment: 31 Effective length of query: 370 Effective length of database: 369 Effective search space: 136530 Effective search space used: 136530 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 H281DRAFT_01504 H281DRAFT_01504 (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.22348.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-226 736.5 11.7 4.4e-226 736.3 11.7 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_01504 H281DRAFT_01504 3-oxoadipyl-CoA Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_01504 H281DRAFT_01504 3-oxoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 736.3 11.7 4.4e-226 4.4e-226 2 400 .] 3 400 .] 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 736.3 bits; conditional E-value: 4.4e-226 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnva 67 e++++dairtpiGry+Gslssvraddl+avplkal++rn+++d++ iddvi+GcanqaGednrnva lcl|FitnessBrowser__Burk376:H281DRAFT_01504 3 EAFLCDAIRTPIGRYAGSLSSVRADDLGAVPLKALMERNKNVDWSVIDDVIYGCANQAGEDNRNVA 68 89**************************************************************** PP TIGR02430 68 rmaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsaf 133 rm++llaGlp++vpg+tvnrlcgsg+da+g+aaraik+Gea l++aGGvesmsrapfv+Gka saf lcl|FitnessBrowser__Burk376:H281DRAFT_01504 69 RMSLLLAGLPKDVPGSTVNRLCGSGMDAVGIAARAIKSGEAALMVAGGVESMSRAPFVMGKATSAF 134 ****************************************************************** PP TIGR02430 134 srsakledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGf 199 sr+a++ dttiGwrfvnp +k++yGvdsmpet enva+++++sr+dqdafalrsqq++a+aq+ G lcl|FitnessBrowser__Burk376:H281DRAFT_01504 135 SRQADIYDTTIGWRFVNPLMKQMYGVDSMPETGENVATDYNISRADQDAFALRSQQKAARAQKDGT 200 ****************************************************************** PP TIGR02430 200 faeeivpveikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaallla 265 +a+eiv v+i+qkkG++ +v++deh+r et+le+laklk+vvr+dgtvtaGnasGvndGaaallla lcl|FitnessBrowser__Burk376:H281DRAFT_01504 201 LAQEIVGVTIAQKKGDPITVSQDEHPR-ETSLETLAKLKGVVRPDGTVTAGNASGVNDGAAALLLA 265 ***************************.************************************** PP TIGR02430 266 seeavkrhgltprarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqala 331 ee++kr+gltprar+l++a+aGv+pr+mG+gp+pa++kl+ar++++++++dvielneafa+q++a lcl|FitnessBrowser__Burk376:H281DRAFT_01504 266 NEETAKRFGLTPRARVLGIATAGVAPRIMGMGPAPAAQKLMARLNMTIDQFDVIELNEAFASQGIA 331 ****************************************************************** PP TIGR02430 332 vlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvi 397 vlr lg+adddarvnpnGGaialGhplG+sGarlv+ta++ql++++gr+al+t+ciGvGqGia++i lcl|FitnessBrowser__Burk376:H281DRAFT_01504 332 VLRTLGVADDDARVNPNGGAIALGHPLGMSGARLVTTAMYQLQRTQGRFALCTMCIGVGQGIAIAI 397 ****************************************************************** PP TIGR02430 398 erv 400 erv lcl|FitnessBrowser__Burk376:H281DRAFT_01504 398 ERV 400 **8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 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: 6.88 // [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