Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase
Query= uniprot:D8ITH5 (401 letters) >lcl|FitnessBrowser__Koxy:BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase Length = 400 Score = 617 bits (1590), Expect = 0.0 Identities = 310/399 (77%), Positives = 352/399 (88%), Gaps = 1/399 (0%) Query: 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61 +A ICDA+RTPFGR+GG L +RADDLAA P+++L+ERNPG+D +R++D++YGCANQAGE Sbjct: 3 QAFICDAVRTPFGRFGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQAGE 62 Query: 62 DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121 DNRNVARMA LLAGLP +VPGSTVNRLCGSSLDA+G+AARAIKSGE QLMIAGGVESM+R Sbjct: 63 DNRNVARMALLLAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVESMSR 122 Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181 APFVMGKAESAF+R+ + DTTIGWRF+NP MKA YG+DSMPETAENVA DF I+RADQD Sbjct: 123 APFVMGKAESAFSRTMRMEDTTIGWRFINPQMKALYGVDSMPETAENVADDFAISRADQD 182 Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241 AFALRSQ R AAAQ AG FA E+ +++PQ+KG+PL+ + DEHPR TT LA+L+GVV Sbjct: 183 AFALRSQLRTAAAQEAGRFADELIAVSVPQRKGEPLLFSRDEHPR-TTTAEALARLRGVV 241 Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301 RPDGTVTAGNASGVNDGACALLLAS +A L+P ARV+G+ATAGVAPRIMGFGPAPA Sbjct: 242 RPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVATAGVAPRIMGFGPAPA 301 Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361 VRKVLAQ GLTL QMDVIELNEAFAAQ LAV RDLGLPDDAA+VNPNGGAIA+GHPLGAS Sbjct: 302 VRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNPNGGAIALGHPLGAS 361 Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 G RL TA QL R+GGRYALCTMCIGVGQGIAL+IERV Sbjct: 362 GGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIERV 400 Lambda K H 0.320 0.135 0.394 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: 594 Number of extensions: 16 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 BWI76_RS16135 BWI76_RS16135 (acetyl-CoA acetyltransferase)
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.29641.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-222 724.1 9.8 2.6e-222 723.9 9.8 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 723.9 9.8 2.6e-222 2.6e-222 2 400 .] 3 400 .] 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 723.9 bits; conditional E-value: 2.6e-222 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaal 72 +++i+da+rtp+Gr+gG+l+++raddlaa+plkall+rnp ld a iddvi+GcanqaGednrnvarma+l lcl|FitnessBrowser__Koxy:BWI76_RS16135 3 QAFICDAVRTPFGRFGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQAGEDNRNVARMALL 73 79********************************************************************* PP TIGR02430 73 laGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledtt 143 laGlp+svpg+tvnrlcgs+lda+g+aaraik+Ge++l+iaGGvesmsrapfv+Gka+safsr+ ++edtt lcl|FitnessBrowser__Koxy:BWI76_RS16135 74 LAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVESMSRAPFVMGKAESAFSRTMRMEDTT 144 *********************************************************************** PP TIGR02430 144 iGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkG 214 iGwrf+np++kalyGvdsmpetaenva++f++sr+dqdafalrsq rtaaaq++G fa+e++ v+++q+kG lcl|FitnessBrowser__Koxy:BWI76_RS16135 145 IGWRFINPQMKALYGVDSMPETAENVADDFAISRADQDAFALRSQLRTAAAQEAGRFADELIAVSVPQRKG 215 *********************************************************************** PP TIGR02430 215 eetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaa 285 e+ +++deh+r tt eala+l++vvr+dgtvtaGnasGvndGa+alllase+a+++++l+p ar++++a lcl|FitnessBrowser__Koxy:BWI76_RS16135 216 EPLLFSRDEHPR-TTTAEALARLRGVVRPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVA 285 ************.89******************************************************** PP TIGR02430 286 saGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGh 356 +aGv+pr+mG+gp+pav+k+la++gl+l ++dvielneafaaqalav+r+lgl+dd+a vnpnGGaialGh lcl|FitnessBrowser__Koxy:BWI76_RS16135 286 TAGVAPRIMGFGPAPAVRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNPNGGAIALGH 356 *********************************************************************** PP TIGR02430 357 plGasGarlvltalkqleksggryalatlciGvGqGialvierv 400 plGasG rl++ta +ql+++ggryal+t+ciGvGqGial+ierv lcl|FitnessBrowser__Koxy:BWI76_RS16135 357 PLGASGGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIERV 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: 00:00:00.01 # Mc/sec: 11.42 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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