Align 3-ketoacyl-CoA thiolase FadA; Acetyl-CoA acyltransferase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate 1937156 b3845 acetyl-CoA acetyltransferase (NCBI)
Query= SwissProt::P21151 (387 letters) >FitnessBrowser__Keio:1937156 Length = 387 Score = 761 bits (1964), Expect = 0.0 Identities = 387/387 (100%), Positives = 387/387 (100%) Query: 1 MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ 60 MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ Sbjct: 1 MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ 60 Query: 61 TLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH 120 TLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH Sbjct: 61 TLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH 120 Query: 121 MGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLARMHGISREMQDAFAARSHARAWAAT 180 MGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLARMHGISREMQDAFAARSHARAWAAT Sbjct: 121 MGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLARMHGISREMQDAFAARSHARAWAAT 180 Query: 181 QSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPAFDPVNGMVTAGTSSA 240 QSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPAFDPVNGMVTAGTSSA Sbjct: 181 QSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPAFDPVNGMVTAGTSSA 240 Query: 241 LSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS 300 LSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS Sbjct: 241 LSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS 300 Query: 301 DIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIALGHPLGCSGARISTTLLNLM 360 DIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIALGHPLGCSGARISTTLLNLM Sbjct: 301 DIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIALGHPLGCSGARISTTLLNLM 360 Query: 361 ERKDVQFGLATMCIGLGQGIATVFERV 387 ERKDVQFGLATMCIGLGQGIATVFERV Sbjct: 361 ERKDVQFGLATMCIGLGQGIATVFERV 387 Lambda K H 0.320 0.133 0.387 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: 651 Number of extensions: 17 Number of successful extensions: 1 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: 387 Length of database: 387 Length adjustment: 30 Effective length of query: 357 Effective length of database: 357 Effective search space: 127449 Effective search space used: 127449 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate 1937156 b3845 (acetyl-CoA acetyltransferase (NCBI))
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16))
# 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/TIGR02445.hmm # target sequence database: /tmp/gapView.2426451.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02445 [M=385] Accession: TIGR02445 Description: fadA: acetyl-CoA C-acyltransferase FadA 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-247 806.9 8.7 1.5e-247 806.7 8.7 1.0 1 FitnessBrowser__Keio:1937156 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Keio:1937156 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 806.7 8.7 1.5e-247 1.5e-247 1 385 [] 3 387 .] 3 387 .] 1.00 Alignments for each domain: == domain 1 score: 806.7 bits; conditional E-value: 1.5e-247 TIGR02445 1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaallaevpheva 81 +vvivda+rtpmgrskggafrn+raedlsahl+++llarnp++eaa+++diywgcvqqtleqgfniarnaallaevph+v+ FitnessBrowser__Keio:1937156 3 QVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQTLEQGFNIARNAALLAEVPHSVP 83 79******************************************************************************* PP TIGR02445 82 avtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmgltaemlgklhgisreq 162 avtvnrlcgssmqalhdaar+imtgda++cl+ggvehmghv+mshgvdfhpgls++vakaagmmgltaeml+++hgisre+ FitnessBrowser__Keio:1937156 84 AVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEHMGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLARMHGISREM 164 ********************************************************************************* PP TIGR02445 163 qdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaalrpafdpkngtvtagtssalsdga 243 qdafaarshara+aat++++fkneiipt+g+dadgvlk+++ydevirpettveala+lrpafdp+ng+vtagtssalsdga FitnessBrowser__Keio:1937156 165 QDAFAARSHARAWAATQSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPAFDPVNGMVTAGTSSALSDGA 245 ********************************************************************************* PP TIGR02445 244 samlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelneafaaqalpvlkdlglld 324 +amlvmse+ra+elg+kprar+rsmav+g+dpsimgygpvpa+k+alk+agls+sdi+v+e+neafaaq+lp++kdlgl++ FitnessBrowser__Keio:1937156 246 AAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSASDIGVFEMNEAFAAQILPCIKDLGLIE 326 ********************************************************************************* PP TIGR02445 325 kldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvferv 385 ++dek+nlnggaialghplgcsgaristtllnlmerkd++fglatmciglgqgiatvferv FitnessBrowser__Keio:1937156 327 QIDEKINLNGGAIALGHPLGCSGARISTTLLNLMERKDVQFGLATMCIGLGQGIATVFERV 387 ************************************************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (387 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: 11.59 // [ok]
This GapMind analysis is from Apr 09 2024. 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