Align 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate BWI76_RS20460 BWI76_RS20460 acetyl-CoA C-acyltransferase FadI
Query= SwissProt::P76503 (436 letters) >lcl|FitnessBrowser__Koxy:BWI76_RS20460 BWI76_RS20460 acetyl-CoA C-acyltransferase FadI Length = 436 Score = 758 bits (1958), Expect = 0.0 Identities = 385/436 (88%), Positives = 413/436 (94%) Query: 1 MGQVLPLVTRQGDRIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIE 60 M Q LPLVTRQGDRIAIVSGLRTPFARQATAFHG+PAVDLGK+VVGE+LARS IPA++IE Sbjct: 1 MSQALPLVTRQGDRIAIVSGLRTPFARQATAFHGVPAVDLGKLVVGEMLARSTIPADIIE 60 Query: 61 QLVFGQVVQMPEAPNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRA 120 QLVFGQVVQMPEAPNIAREIVLGTGM+VHTDAYSVSRACATSFQAVANVAESLMAGTIRA Sbjct: 61 QLVFGQVVQMPEAPNIAREIVLGTGMSVHTDAYSVSRACATSFQAVANVAESLMAGTIRA 120 Query: 121 GIAGGADSSSVLPIGVSKKLARVLVDVNKARTMSQRLKLFSRLRLRDLMPVPPAVAEYST 180 GIAGGADSSSVLPIGVSKKLAR LVD NKART+ QRLKLFSRLR RDL+PVPPAVAEYST Sbjct: 121 GIAGGADSSSVLPIGVSKKLARTLVDANKARTLGQRLKLFSRLRFRDLLPVPPAVAEYST 180 Query: 181 GLRMGDTAEQMAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVE 240 GLRMGDTAEQMAKT+GITRE+QDALA RSHQ AA+AW +GKL EVMTA+ PP+++PL + Sbjct: 181 GLRMGDTAEQMAKTWGITRERQDALALRSHQLAAKAWEEGKLSAEVMTAYTPPFREPLEQ 240 Query: 241 DNNIRGNSSLADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGY 300 DNNIR NS+LADY KLRPAFDR+HG+VTAANSTPLTDGAAAVILMTESRAKELGLVPLGY Sbjct: 241 DNNIRKNSTLADYQKLRPAFDRQHGSVTAANSTPLTDGAAAVILMTESRAKELGLVPLGY 300 Query: 301 LRSYAFTAIDVWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSE 360 LRSYAFTAIDV QDMLLGPAWSTPLALERAGLT++DLTLIDMHEAFAAQTLAN+ + S+ Sbjct: 301 LRSYAFTAIDVRQDMLLGPAWSTPLALERAGLTLADLTLIDMHEAFAAQTLANLHCMASD 360 Query: 361 RFAREALGRAHATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVT 420 RFARE LGR+ A GEVD+SKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVT Sbjct: 361 RFAREVLGRSQAIGEVDESKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVT 420 Query: 421 ACAAGGLGAAMVLEAE 436 ACAAGGLG+AMVLEAE Sbjct: 421 ACAAGGLGSAMVLEAE 436 Lambda K H 0.319 0.133 0.377 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: 702 Number of extensions: 7 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: 436 Length of database: 436 Length adjustment: 32 Effective length of query: 404 Effective length of database: 404 Effective search space: 163216 Effective search space used: 163216 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: 51 (24.3 bits)
Align candidate BWI76_RS20460 BWI76_RS20460 (acetyl-CoA C-acyltransferase FadI)
to HMM TIGR02446 (fadI: acetyl-CoA C-acyltransferase FadI (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/TIGR02446.hmm # target sequence database: /tmp/gapView.8879.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02446 [M=430] Accession: TIGR02446 Description: FadI: acetyl-CoA C-acyltransferase FadI 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-262 854.5 3.4 9.7e-262 854.3 3.4 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS20460 BWI76_RS20460 acetyl-CoA C-acylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS20460 BWI76_RS20460 acetyl-CoA C-acyltransferase FadI # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 854.3 3.4 9.7e-262 9.7e-262 1 430 [] 7 436 .] 7 436 .] 1.00 Alignments for each domain: == domain 1 score: 854.3 bits; conditional E-value: 9.7e-262 TIGR02446 1 vktrqgeriaivaglrtpfarqatafhgipavdlgkmvvsellarseidaklieqlvfgqvvqmpeapnia 71 ++trqg+riaiv+glrtpfarqatafhg+pavdlgk+vv+e+lars i+a++ieqlvfgqvvqmpeapnia lcl|FitnessBrowser__Koxy:BWI76_RS20460 7 LVTRQGDRIAIVSGLRTPFARQATAFHGVPAVDLGKLVVGEMLARSTIPADIIEQLVFGQVVQMPEAPNIA 77 589******************************************************************** PP TIGR02446 72 reivlgtgmnvhtdaysvtracatsfqsavnvaesimagaieigiaggadsssvlpigvskklaralvdln 142 reivlgtgm vhtdaysv+racatsfq+++nvaes+mag+i++giaggadsssvlpigvskklar+lvd n lcl|FitnessBrowser__Koxy:BWI76_RS20460 78 REIVLGTGMSVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSSVLPIGVSKKLARTLVDAN 148 *********************************************************************** PP TIGR02446 143 kartlgqklkvlsrlglkdllpvppavaeystglsmgqtaeqmaktygitraeqdalahrshtlaaqawad 213 kartlgq+lk++srl+++dllpvppavaeystgl+mg+taeqmakt+gitr+ qdala rsh+laa+aw++ lcl|FitnessBrowser__Koxy:BWI76_RS20460 149 KARTLGQRLKLFSRLRFRDLLPVPPAVAEYSTGLRMGDTAEQMAKTWGITRERQDALALRSHQLAAKAWEE 219 *********************************************************************** PP TIGR02446 214 gklkeevmtafvepykkfiaednnirenssladyaklrpafdrkygsvtaanstpltdgaaavilmsegra 284 gkl evmta+++p+++++++dnnir+ns+lady klrpafdr++gsvtaanstpltdgaaavilm+e+ra lcl|FitnessBrowser__Koxy:BWI76_RS20460 220 GKLSAEVMTAYTPPFREPLEQDNNIRKNSTLADYQKLRPAFDRQHGSVTAANSTPLTDGAAAVILMTESRA 290 *********************************************************************** PP TIGR02446 285 kelgleilgyirsyaftaidveqdmllgpsyatplalkraglelsdltlidmheafaaqtlanvkllasek 355 kelgl++lgy+rsyaftaidv qdmllgp+++tplal+ragl+l dltlidmheafaaqtlan++ +as++ lcl|FitnessBrowser__Koxy:BWI76_RS20460 291 KELGLVPLGYLRSYAFTAIDVRQDMLLGPAWSTPLALERAGLTLADLTLIDMHEAFAAQTLANLHCMASDR 361 *********************************************************************** PP TIGR02446 356 faeeklgrakaigeidmskfnvlggsiayghpfaatgarlitqtlrelkrrggglglatacaagglgaami 426 fa+e lgr++aige+d+skfnvlggsiayghpfaatgar+itqtl+el+rrggg+gl+tacaagglg+am+ lcl|FitnessBrowser__Koxy:BWI76_RS20460 362 FAREVLGRSQAIGEVDESKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVTACAAGGLGSAMV 432 *********************************************************************** PP TIGR02446 427 leve 430 le+e lcl|FitnessBrowser__Koxy:BWI76_RS20460 433 LEAE 436 **97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (430 nodes) Target sequences: 1 (436 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: 11.78 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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