Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_015446959.1 R2APBS1_RS03900 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000230695.2:WP_015446959.1 Length = 400 Score = 493 bits (1268), Expect = e-144 Identities = 246/399 (61%), Positives = 304/399 (76%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M ++ DA RTP GR GGALAGVRADDLAA+P+ AL+ +P + W +DEV GCANQA Sbjct: 1 MTSAWLVDATRTPFGRLGGALAGVRADDLAALPIAALMARHPTLDWAALDEVILGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARMA LLAGLP+S+P VT+NRLCASG++AIG A RAIA GE EL +AGGVESM Sbjct: 61 GEDNRNVARMATLLAGLPQSVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAP+V+ KA+ Y+R +LEDTT+GWR +NP M++ YG+DSM +TA+N+A ++ + R Sbjct: 121 SRAPYVLAKADVAYARGQQLEDTTLGWRLVNPRMQAGYGIDSMTQTAENLAREHGIDRDS 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240 QDA+ALRSQQ+ A AQA G+ AEEI V H K +V+ DEH R +TT L LKP+ Sbjct: 181 QDAYALRSQQRTAHAQAQGWLAEEITAVHAPHGKESLVVQVDEHPRADTTAAKLAALKPL 240 Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 G ++TAGNASG+NDGAAA++LAS A+ ++GL P AR++GMA+ GVAPRVMGIGPVP Sbjct: 241 LGAGSSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAPRVMGIGPVP 300 Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360 A+ KL R G+ SDFD IE+NEAFA+Q LA R LG+ DDA VN NGGAIALGHPLG Sbjct: 301 AIHKLLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDDAEHVNANGGAIALGHPLGA 360 Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399 SGARL LTA L + + L ++CVGVGQGLALA+ER Sbjct: 361 SGARLALTAAFALRRHRQHRALVSLCVGVGQGLALALER 399 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: 479 Number of extensions: 11 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_015446959.1 R2APBS1_RS03900 (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.2001012.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-134 434.7 8.8 1.6e-134 434.6 8.8 1.0 1 NCBI__GCF_000230695.2:WP_015446959.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000230695.2:WP_015446959.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 434.6 8.8 1.6e-134 1.6e-134 2 385 .] 7 398 .. 6 398 .. 0.93 Alignments for each domain: == domain 1 score: 434.6 bits; conditional E-value: 1.6e-134 TIGR01930 2 vdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglpe 72 vda+Rtp+g+lgg+l+ ++a+dL+a i +l++r ld +++devilG++ qage+ n+aR+a+l aglp+ NCBI__GCF_000230695.2:WP_015446959.1 7 VDATRTPFGRLGGALAGVRADDLAALPIAALMARHpTLDWAALDEVILGCANQAGEDnRNVARMATLLAGLPQ 79 9********************************************************9*************** PP TIGR01930 73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl. 144 svpa+tvnr+CaSgl+A+ +aa++i++Gea++vvaGGvEsmSr+p++l ++ + ++ ++ ++ + NCBI__GCF_000230695.2:WP_015446959.1 80 SVPAVTVNRLCASGLEAIGQAARAIACGEAELVVAGGVESMSRAPYVLAKADV-AYARGQQLEDTTL----Gw 147 **********************************************9999732.2233333333332....12 PP TIGR01930 145 .........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvs 206 + sm++tAenla+++gi R++qD+yalrS+q++a+A+++g +++ei+ v+ ++ + vv+ NCBI__GCF_000230695.2:WP_015446959.1 148 rlvnprmqaGYGIDSMTQTAENLAREHGIDRDSQDAYALRSQQRTAHAQAQGWLAEEITAVHAPHGkeSLVVQ 220 345778776455669**********************************************99877889999* PP TIGR01930 207 kDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdp 279 De++r++tt++kLa Lkp + +gs +tAgN+s+lnDGAaa+ll+se++++++gl+plariv++a agv p NCBI__GCF_000230695.2:WP_015446959.1 221 VDEHPRADTTAAKLAALKPLLG--AGSSITAGNASGLNDGAAAVLLASEAALARYGLQPLARIVGMAAAGVAP 291 *********************8..5778********************************************* PP TIGR01930 280 eemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGar 351 ++mg+gpvpAi+k+L+++gl +sd+d +EinEAFAaqvla+++ lg+ d e vN nGGAiAlGHPlGasGar NCBI__GCF_000230695.2:WP_015446959.1 292 RVMGIGPVPAIHKLLARTGLGASDFDRIEINEAFAAQVLACTRSLGLPDdAEHVNANGGAIALGHPLGASGAR 364 **********************************************85569********************** PP TIGR01930 352 ivltllkeLkergkkyGlatlCvggGqGaAvile 385 + lt + +L++++++++l++lCvg GqG A+ le NCBI__GCF_000230695.2:WP_015446959.1 365 LALTAAFALRRHRQHRALVSLCVGVGQGLALALE 398 ******************************9886 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 29.31 // [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