Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_086511957.1 BZY95_RS21635 3-oxoadipyl-CoA thiolase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_002151265.1:WP_086511957.1 Length = 400 Score = 535 bits (1379), Expect = e-157 Identities = 268/404 (66%), Positives = 324/404 (80%), Gaps = 5/404 (1%) Query: 7 LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66 + Y+ R+ +GR+GG L++VR DDL A +KA+ + PDLD S I++V GCANQA Sbjct: 1 MNSVYLCHPQRSAVGRFGGTLASVRPDDLAAAIVKAVLAQAPDLDPSAIEEVFMGCANQA 60 Query: 67 GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126 GEDNR+VARM+ LLAGLPV +PG+T+NRLCGSGMDAVG+A RAI+ GE +L +AGGVESM Sbjct: 61 GEDNRNVARMASLLAGLPVSIPGTTLNRLCGSGMDAVGTAFRAIKAGEMELALAGGVESM 120 Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186 SRAP+VMGKADSAFSR +I DTTIGWRF+NP++KK YG++SMPETAENVA F ISRED Sbjct: 121 SRAPYVMGKADSAFSRGQKIEDTTIGWRFINPLMKKAYGVESMPETAENVAEQFAISRED 180 Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLPTP 246 QDAFALRSQQ+ AAAQ+ GR A EIT + IPRRKQ+PL D DEH R T+LEKLA LP P Sbjct: 181 QDAFALRSQQKAAAAQEAGRFACEITAIEIPRRKQEPLRFDQDEHLRATTLEKLAGLPAP 240 Query: 247 FRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAP 306 FRE G+VTAGNASGVNDGA A+L+A A++++ L P A+++ MATAGVEPRIMG GP P Sbjct: 241 FREGGSVTAGNASGVNDGAAAMLVASRQAVEKHGLTPMAKILGMATAGVEPRIMGIGPVP 300 Query: 307 ATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGM 366 A RK+LA G+ L ++DVIELNEAFAAQALA R+LG+ D VNPNGGAIALGHPLGM Sbjct: 301 AVRKLLARTGVSLDEIDVIELNEAFAAQALAGMRELGIADGDPRVNPNGGAIALGHPLGM 360 Query: 367 SGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIER 410 SGARL+ TA +EL++ RYALCTMC+GVGQGIA ++ER Sbjct: 361 SGARLLLTAAHELQK-----SGKRYALCTMCVGVGQGIATLLER 399 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: 534 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_086511957.1 BZY95_RS21635 (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.10521.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-208 677.6 7.9 3.4e-208 677.4 7.9 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511957.1 BZY95_RS21635 3-oxoadipyl-CoA th Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511957.1 BZY95_RS21635 3-oxoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 677.4 7.9 3.4e-208 3.4e-208 2 399 .. 3 399 .. 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 677.4 bits; conditional E-value: 3.4e-208 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarma 70 +vy++ r+ +Gr+gG+l+svr ddlaa +ka+la+ p+ld +ai++v++GcanqaGednrnvarma lcl|NCBI__GCF_002151265.1:WP_086511957.1 3 SVYLCHPQRSAVGRFGGTLASVRPDDLAAAIVKAVLAQAPDLDPSAIEEVFMGCANQAGEDNRNVARMA 71 69******************************************************************* PP TIGR02430 71 allaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakl 139 llaGlpvs+pgtt+nrlcgsg+da+g+a+raikaGe +l +aGGvesmsrap+v+Gkadsafsr +k+ lcl|NCBI__GCF_002151265.1:WP_086511957.1 72 SLLAGLPVSIPGTTLNRLCGSGMDAVGTAFRAIKAGEMELALAGGVESMSRAPYVMGKADSAFSRGQKI 140 ********************************************************************* PP TIGR02430 140 edttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpve 208 edttiGwrf+np +k+ yGv+smpetaenvae+f++sredqdafalrsqq++aaaq++G fa ei+ +e lcl|NCBI__GCF_002151265.1:WP_086511957.1 141 EDTTIGWRFINPLMKKAYGVESMPETAENVAEQFAISREDQDAFALRSQQKAAAAQEAGRFACEITAIE 209 ********************************************************************* PP TIGR02430 209 ikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltp 277 i+++k e+ +d+dehlr ttle+la l a++re+g+vtaGnasGvndGaaa+l+as +av++hgltp lcl|NCBI__GCF_002151265.1:WP_086511957.1 210 IPRRKQEPLRFDQDEHLR-ATTLEKLAGLPAPFREGGSVTAGNASGVNDGAAAMLVASRQAVEKHGLTP 277 ******************.89************************************************ PP TIGR02430 278 rarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvn 346 a+il++a+aGvepr+mG+gpvpav+kllar+g+sl+++dvielneafaaqala +relg+ad d rvn lcl|NCBI__GCF_002151265.1:WP_086511957.1 278 MAKILGMATAGVEPRIMGIGPVPAVRKLLARTGVSLDEIDVIELNEAFAAQALAGMRELGIADGDPRVN 346 ********************************************************************* PP TIGR02430 347 pnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvier 399 pnGGaialGhplG+sGarl lta ++l+ksg+ryal+t+c+GvGqGia ++er lcl|NCBI__GCF_002151265.1:WP_086511957.1 347 PNGGAIALGHPLGMSGARLLLTAAHELQKSGKRYALCTMCVGVGQGIATLLER 399 ****************************************************9 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: 10.98 // [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