Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate Pf6N2E2_2289 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= BRENDA::P28790 (391 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 Length = 383 Score = 738 bits (1904), Expect = 0.0 Identities = 366/383 (95%), Positives = 377/383 (98%) Query: 9 VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNSKVDPGEVEDVIWGCVNQTLEQ 68 VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISK+LERN KVDP EVEDVIWGCVNQTLEQ Sbjct: 1 VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGCVNQTLEQ 60 Query: 69 GWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV 128 GWNIARMASLMTQIPHT+A QTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV Sbjct: 61 GWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV 120 Query: 129 SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLAHKATVEGK 188 SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGI+REQQDAF VRSHQLAHKATVEGK Sbjct: 121 SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRSHQLAHKATVEGK 180 Query: 189 FKDEIIPMQGYDENGFLKIFDYDETIRPDTTLESLAALKPAFNPKGGTVTAGTSSQITDG 248 FKDEIIPMQGYDENGFLK+FDYDETIRP+TTLESLAALKPAFNPKGGTVTAGTSSQITDG Sbjct: 181 FKDEIIPMQGYDENGFLKLFDYDETIRPETTLESLAALKPAFNPKGGTVTAGTSSQITDG 240 Query: 249 ASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLNMADIDF 308 ASCMIVMSAQRA+DLG++P+AVIRSMAVAGVDPAIMGYGPVPATQKALKRAGL +ADIDF Sbjct: 241 ASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLGIADIDF 300 Query: 309 IELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG 368 ELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG Sbjct: 301 FELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG 360 Query: 369 GTFGLSTMCIGLGQGIATVFERV 391 GTFG+STMCIGLGQGIATVFERV Sbjct: 361 GTFGVSTMCIGLGQGIATVFERV 383 Lambda K H 0.318 0.133 0.386 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: 670 Number of extensions: 13 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: 391 Length of database: 383 Length adjustment: 30 Effective length of query: 361 Effective length of database: 353 Effective search space: 127433 Effective search space used: 127433 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate Pf6N2E2_2289 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9))
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.18026.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-238 775.9 8.5 3.7e-238 775.8 8.5 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 3-ketoacyl-CoA thiolase (EC 2.3. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase ( # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 775.8 8.5 3.7e-238 3.7e-238 3 385 .] 1 383 [] 1 383 [] 1.00 Alignments for each domain: == domain 1 score: 775.8 bits; conditional E-value: 3.7e-238 TIGR02445 3 vivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfni 66 vivd++rtpmgrskgg++rntraed+sahl++kll+rn kv++ eved++wgcv+qtleqg+ni lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 1 VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGCVNQTLEQGWNI 64 8*************************************************************** PP TIGR02445 67 arnaallaevphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdf 130 ar+a+l++++ph+ a +tv+rlcgssm+alh+aa+aimtg+++v+++ggvehmghvsm+hgvd+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 65 ARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVSMMHGVDP 128 **************************************************************** PP TIGR02445 131 hpglskhvakaagmmgltaemlgklhgisreqqdafaarsharahaatlegkfkneiiptegyd 194 +p++s +aka+gmmgltaemlgk+hgi+reqqdaf++rsh++ah+at+egkfk+eiip++gyd lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 129 NPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRSHQLAHKATVEGKFKDEIIPMQGYD 192 **************************************************************** PP TIGR02445 195 adgvlkvldydevirpettvealaalrpafdpkngtvtagtssalsdgasamlvmseeraqelg 258 ++g+lk +dyde+irpett+e+laal+paf+pk+gtvtagtss+++dgas+m+vms++raq+lg lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 193 ENGFLKLFDYDETIRPETTLESLAALKPAFNPKGGTVTAGTSSQITDGASCMIVMSAQRAQDLG 256 **************************************************************** PP TIGR02445 259 vkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelneafaaqalpvlkdlgl 322 ++p+a+irsmavagvdp+imgygpvpat+kalkragl i did++elneafaaqalpvlkdl++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 257 IQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLGIADIDFFELNEAFAAQALPVLKDLKV 320 **************************************************************** PP TIGR02445 323 ldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvferv 385 ldk++ekvnl+ggaialghp+gcsgaris+tlln+m++++++fg++tmciglgqgiatvferv lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 321 LDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNGGTFGVSTMCIGLGQGIATVFERV 383 **************************************************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (383 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: 11.88 // [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