Align Acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 6935813 Sama_0031 3-ketoacyl-CoA thiolase (RefSeq)
Query= reanno::SB2B:6935813 (387 letters) >FitnessBrowser__SB2B:6935813 Length = 387 Score = 758 bits (1958), Expect = 0.0 Identities = 387/387 (100%), Positives = 387/387 (100%) Query: 1 MKQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQ 60 MKQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQ Sbjct: 1 MKQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQ 60 Query: 61 TLEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEH 120 TLEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEH Sbjct: 61 TLEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEH 120 Query: 121 MGHVPMNHGVDFHPGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAHAAS 180 MGHVPMNHGVDFHPGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAHAAS Sbjct: 121 MGHVPMNHGVDFHPGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAHAAS 180 Query: 181 IEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVTAGTSSA 240 IEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVTAGTSSA Sbjct: 181 IEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVTAGTSSA 240 Query: 241 LSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQ 300 LSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQ Sbjct: 241 LSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQ 300 Query: 301 DMDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLM 360 DMDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLM Sbjct: 301 DMDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLM 360 Query: 361 EHKDATLGLATMCIGLGQGIATVFERV 387 EHKDATLGLATMCIGLGQGIATVFERV Sbjct: 361 EHKDATLGLATMCIGLGQGIATVFERV 387 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: 723 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate 6935813 Sama_0031 (3-ketoacyl-CoA thiolase (RefSeq))
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.17997.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-224 730.3 11.4 2.6e-224 730.2 11.4 1.0 1 lcl|FitnessBrowser__SB2B:6935813 Sama_0031 3-ketoacyl-CoA thiolas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6935813 Sama_0031 3-ketoacyl-CoA thiolase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 730.2 11.4 2.6e-224 2.6e-224 2 385 .] 4 387 .] 3 387 .] 1.00 Alignments for each domain: == domain 1 score: 730.2 bits; conditional E-value: 2.6e-224 TIGR02445 2 vvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaallaevph 78 vivd++rtpmgrskgg+frn+rae lsa l+k+ll rnp v++ +ed++wgcvqqtleqgfniarna+lla+vp+ lcl|FitnessBrowser__SB2B:6935813 4 AVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQTLEQGFNIARNASLLAGVPK 80 79*************************************************************************** PP TIGR02445 79 evaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmgltaemlgkl 155 + +avtvnrlcgssm+alh+a+raimtg ++ ++iggvehmghv+m+hgvdfhpgl+ +vaka+gmmgltaemlgkl lcl|FitnessBrowser__SB2B:6935813 81 TAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEHMGHVPMNHGVDFHPGLAANVAKASGMMGLTAEMLGKL 157 ***************************************************************************** PP TIGR02445 156 hgisreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaalrpafdpkngtvt 232 hgisre+qd+fa+rsh+rahaa++eg+f nei +eg+da+g l ++dydevirpett+e+la lrp+fdp+ngtvt lcl|FitnessBrowser__SB2B:6935813 158 HGISREMQDQFAVRSHQRAHAASIEGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVT 234 ***************************************************************************** PP TIGR02445 233 agtssalsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelneaf 309 agtssalsdga+amlvm ee+a+ lg+++rar+rsmavag+d +imgygpvpat+kal raglsi+d+dv+elneaf lcl|FitnessBrowser__SB2B:6935813 235 AGTSSALSDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQDMDVIELNEAF 311 ***************************************************************************** PP TIGR02445 310 aaqalpvlkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvferv 385 aaq+lp++kdlgl+d++++kvnlnggaialghplgcsgaristtl+nlme+kda+ glatmciglgqgiatvferv lcl|FitnessBrowser__SB2B:6935813 312 AAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLMEHKDATLGLATMCIGLGQGIATVFERV 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: 9.17 // [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