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) >FitnessBrowser__Koxy:BWI76_RS16135 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.3560.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: 9.18 // [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