Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate BPHYT_RS17345 BPHYT_RS17345 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__BFirm:BPHYT_RS17345 Length = 400 Score = 588 bits (1516), Expect = e-173 Identities = 295/401 (73%), Positives = 343/401 (85%), Gaps = 1/401 (0%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 MN+A I DA+RTPIGRY GAL VRADDLGA+P+KALI R+P +DW VDDVIYGCANQA Sbjct: 1 MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 GEDNRNVARM+ALLAGLPV PG+T+NRLCGSG+DAVG+AARA++ GEA LM+AGGVESM Sbjct: 61 GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180 +RAPFVMGK+ AF R A+I+DTTIGWRF+N LM++ +G+DSMPETAENVAA+F++SRAD Sbjct: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180 Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240 QDAFAL SQ KAA A +G LA+EIV VEIAQ+KG DEHPR +T+LE L KL Sbjct: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPR-ETSLESLGKLKG 239 Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300 R GSVTAGNASGVNDGACALLLA+ +AA ++GL+ RARVVGMATAGVEPRIMGIGP Sbjct: 240 VVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPA 299 Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360 PAT+K+L+ G+ L +DVIELNEAFA+QGLAVLR LGL DDD RVNPNGGAIALGHPLG Sbjct: 300 PATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLG 359 Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 SGARL+TTAL++LE GR+ALCTMCIGVGQGIAL+IER+ Sbjct: 360 ASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400 Lambda K H 0.319 0.134 0.384 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: 572 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 BPHYT_RS17345 BPHYT_RS17345 (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.2065982.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-221 718.9 9.8 9.9e-221 718.7 9.8 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS17345 BPHYT_RS17345 acetyl-CoA acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS17345 BPHYT_RS17345 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 718.7 9.8 9.9e-221 9.9e-221 2 400 .] 3 400 .] 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 718.7 bits; conditional E-value: 9.9e-221 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaa 71 +++i+dairtpiGrygG+l vraddl+avp+kal++rnp +d+ ++ddvi+GcanqaGednrnvarm+a lcl|FitnessBrowser__BFirm:BPHYT_RS17345 3 DAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQAGEDNRNVARMSA 72 79******************************************************************** PP TIGR02430 72 llaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakled 141 llaGlpv+ pg+t+nrlcgsg+da+g+aaraikaGea l+iaGGvesm+rapfv+Gka saf+r+a++ d lcl|FitnessBrowser__BFirm:BPHYT_RS17345 73 LLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESMTRAPFVMGKATSAFARQADIYD 142 ********************************************************************** PP TIGR02430 142 ttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikq 211 ttiGwrf+np +k++yGvdsmpetaenva ef+vsr+dqdafal sqq++a+aq+ G +a+eiv vei+q lcl|FitnessBrowser__BFirm:BPHYT_RS17345 143 TTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRADQDAFALASQQKAARAQQDGTLAQEIVGVEIAQ 212 ********************************************************************** PP TIGR02430 212 kkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprari 281 kkG+++ deh+r et+le+l klk+vvr+dg+vtaGnasGvndGa+allla ++a+ ++gl+ rar+ lcl|FitnessBrowser__BFirm:BPHYT_RS17345 213 KKGDPVRALLDEHPR-ETSLESLGKLKGVVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARV 281 ***************.****************************************************** PP TIGR02430 282 laaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGa 351 +++a+aGvepr+mG+gp+pa++kll+++g++le+ldvielneafa+q+lavlr lgl+ddd rvnpnGGa lcl|FitnessBrowser__BFirm:BPHYT_RS17345 282 VGMATAGVEPRIMGIGPAPATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGA 351 ********************************************************************** PP TIGR02430 352 ialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400 ialGhplGasGarl++tal+qle+++gr+al+t+ciGvGqGialvier+ lcl|FitnessBrowser__BFirm:BPHYT_RS17345 352 IALGHPLGASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400 ***********************************************96 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 20.00 // [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