Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_086508612.1 BZY95_RS03570 3-oxoadipyl-CoA thiolase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_002151265.1:WP_086508612.1 Length = 400 Score = 558 bits (1438), Expect = e-163 Identities = 279/405 (68%), Positives = 328/405 (80%), Gaps = 5/405 (1%) Query: 7 LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66 + D ++ RT IGR+GG L++VR DD A KA+ PDLD + I++V GCANQA Sbjct: 1 MTDVFLCHPRRTAIGRFGGTLASVRPDDFAATIFKAVLAEAPDLDPAAIEEVFMGCANQA 60 Query: 67 GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126 GEDNR+VARMS LLAGLP VPG+T+NRLCGSGMDAVG+A RAI+ GE +L +AGGVESM Sbjct: 61 GEDNRNVARMSSLLAGLPTSVPGTTMNRLCGSGMDAVGTAFRAIKAGEMELALAGGVESM 120 Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186 SRAP+V+GKAD AFSR +I DTTIGWRFVNP++KK YGIDSMPETAENVA F ISRED Sbjct: 121 SRAPYVLGKADGAFSRGQKIEDTTIGWRFVNPLMKKAYGIDSMPETAENVAEQFNISRED 180 Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLPTP 246 QDAFALRSQQ+ AAAQK GR A EITP+ IPRRKQ+PLV DTDEHPRET+LEKLA LPTP Sbjct: 181 QDAFALRSQQKAAAAQKAGRFAIEITPIEIPRRKQEPLVFDTDEHPRETTLEKLAGLPTP 240 Query: 247 FRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAP 306 FRE G++TAGNASGVNDGA A+L+A A++Q+ LKP AR++ MATAGVEPRIMG+GP P Sbjct: 241 FREGGSITAGNASGVNDGAAAMLVASRAAVEQHGLKPMARIIGMATAGVEPRIMGYGPVP 300 Query: 307 ATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGM 366 A RK+L G+ + ++D+ E NEAFAAQALA TRDLGL DD VNPNGGAIALGHPLGM Sbjct: 301 AVRKLLERTGVTMDEIDIFEFNEAFAAQALACTRDLGLADDDPRVNPNGGAIALGHPLGM 360 Query: 367 SGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411 SGARL+ TA +EL+R RYALCTMC+GVGQGIA +IE++ Sbjct: 361 SGARLLLTAAHELQR-----TGKRYALCTMCVGVGQGIATLIEKV 400 Lambda K H 0.318 0.133 0.382 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: 561 Number of extensions: 18 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: 415 Length of database: 400 Length adjustment: 31 Effective length of query: 384 Effective length of database: 369 Effective search space: 141696 Effective search space used: 141696 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_086508612.1 BZY95_RS03570 (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.29992.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-209 679.4 3.4 9.6e-209 679.2 3.4 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508612.1 BZY95_RS03570 3-oxoadipyl-CoA th Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508612.1 BZY95_RS03570 3-oxoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 679.2 3.4 9.6e-209 9.6e-209 2 400 .] 3 400 .] 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 679.2 bits; conditional E-value: 9.6e-209 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarma 70 +v+++ rt iGr+gG+l+svr dd+aa ka+la p+ld aai++v++GcanqaGednrnvarm+ lcl|NCBI__GCF_002151265.1:WP_086508612.1 3 DVFLCHPRRTAIGRFGGTLASVRPDDFAATIFKAVLAEAPDLDPAAIEEVFMGCANQAGEDNRNVARMS 71 79******************************************************************* PP TIGR02430 71 allaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakl 139 llaGlp+svpgtt+nrlcgsg+da+g+a+raikaGe +l +aGGvesmsrap+vlGkad+afsr +k+ lcl|NCBI__GCF_002151265.1:WP_086508612.1 72 SLLAGLPTSVPGTTMNRLCGSGMDAVGTAFRAIKAGEMELALAGGVESMSRAPYVLGKADGAFSRGQKI 140 ********************************************************************* PP TIGR02430 140 edttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpve 208 edttiGwrfvnp +k+ yG+dsmpetaenvae+f++sredqdafalrsqq++aaaq++G fa ei+p+e lcl|NCBI__GCF_002151265.1:WP_086508612.1 141 EDTTIGWRFVNPLMKKAYGIDSMPETAENVAEQFNISREDQDAFALRSQQKAAAAQKAGRFAIEITPIE 209 ********************************************************************* PP TIGR02430 209 ikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltp 277 i+++k e+ v+d+deh+r ettle+la l +++re+g++taGnasGvndGaaa+l+as av++hgl+p lcl|NCBI__GCF_002151265.1:WP_086508612.1 210 IPRRKQEPLVFDTDEHPR-ETTLEKLAGLPTPFREGGSITAGNASGVNDGAAAMLVASRAAVEQHGLKP 277 ******************.************************************************** PP TIGR02430 278 rarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvn 346 ari+++a+aGvepr+mG gpvpav+kll+r+g++++++d+ e+neafaaqala++r+lgladdd rvn lcl|NCBI__GCF_002151265.1:WP_086508612.1 278 MARIIGMATAGVEPRIMGYGPVPAVRKLLERTGVTMDEIDIFEFNEAFAAQALACTRDLGLADDDPRVN 346 ********************************************************************* PP TIGR02430 347 pnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400 pnGGaialGhplG+sGarl lta ++l+++g+ryal+t+c+GvGqGia +ie+v lcl|NCBI__GCF_002151265.1:WP_086508612.1 347 PNGGAIALGHPLGMSGARLLLTAAHELQRTGKRYALCTMCVGVGQGIATLIEKV 400 ****************************************************97 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: 00:00:00.01 # Mc/sec: 10.75 // [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