Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate 5211293 Shew_3709 2-amino-3-ketobutyrate coenzyme A ligase (RefSeq)
Query= reanno::ANA3:7026975 (397 letters) >FitnessBrowser__PV4:5211293 Length = 397 Score = 726 bits (1873), Expect = 0.0 Identities = 367/397 (92%), Positives = 383/397 (96%) Query: 1 MASTSFYAQINQQLADVKAEGLYKSERVIASPQQTAIQVNHQEVVNFCANNYLGLANHPE 60 MA+TSFY QINQQLA+VKAEGLYKSERVIASPQ+T I+VN EV+NFCANNYLGLANHPE Sbjct: 1 MATTSFYDQINQQLAEVKAEGLYKSERVIASPQKTEIEVNGHEVMNFCANNYLGLANHPE 60 Query: 61 LIKAAQQGLDSHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE 120 LI AAQQGL HGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE Sbjct: 61 LITAAQQGLSDHGFGMASVRFICGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFE 120 Query: 121 TLLDAEDAIISDALNHASIIDGVRLCKAKRFRYANNDMADLETQLIAAKAAGARNILIAT 180 TLLDAEDAI+SDALNHASIIDGVRLCKAKRFRYANNDMADLETQL AAKAAGAR+ILIAT Sbjct: 121 TLLDAEDAIVSDALNHASIIDGVRLCKAKRFRYANNDMADLETQLQAAKAAGARHILIAT 180 Query: 181 DGVFSMDGVIANLQGVCDLADKYGALVMVDDSHAVGFVGLNGRGSHEHCGVMGRVDIITG 240 DGVFSMDGVIANL+GVCDLADKYGALVMVDDSHAVGF+G NGRG+HE+C VM RVDIITG Sbjct: 181 DGVFSMDGVIANLKGVCDLADKYGALVMVDDSHAVGFIGQNGRGTHEYCDVMDRVDIITG 240 Query: 241 TLGKALGGASGGFTSGKKEVIDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRE 300 TLGKALGGASGGFTS KKEV+DWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRE Sbjct: 241 TLGKALGGASGGFTSAKKEVVDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALRE 300 Query: 301 AVWENSRYFREKMSAAGFTLGGADHAIIPVMIGDAKLASDFANRLLAEHIYVIGFSFPVV 360 AVWENSRYFREKM+AAGFTLGGADHAIIPVMIGDAKLASDFANRLL E+IYVIGFSFPVV Sbjct: 301 AVWENSRYFREKMTAAGFTLGGADHAIIPVMIGDAKLASDFANRLLEENIYVIGFSFPVV 360 Query: 361 PKGQARIRTQMSAAHTREQLDKAIEAFTRIAKEMAII 397 PKGQARIRTQMSAAHTREQLD+AI+AFTRIAKEM II Sbjct: 361 PKGQARIRTQMSAAHTREQLDRAIDAFTRIAKEMGII 397 Lambda K H 0.321 0.134 0.385 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: 602 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: 397 Length of database: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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 5211293 Shew_3709 (2-amino-3-ketobutyrate coenzyme A ligase (RefSeq))
to HMM TIGR01822 (kbl: glycine C-acetyltransferase (EC 2.3.1.29))
# 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/TIGR01822.hmm # target sequence database: /tmp/gapView.31497.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01822 [M=393] Accession: TIGR01822 Description: 2am3keto_CoA: glycine C-acetyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-215 699.9 3.2 5e-215 699.7 3.2 1.0 1 lcl|FitnessBrowser__PV4:5211293 Shew_3709 2-amino-3-ketobutyrate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5211293 Shew_3709 2-amino-3-ketobutyrate coenzyme A ligase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 699.7 3.2 5e-215 5e-215 1 393 [] 6 397 .] 6 397 .] 1.00 Alignments for each domain: == domain 1 score: 699.7 bits; conditional E-value: 5e-215 TIGR01822 1 lkailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGlssvrfi 78 ++++++++l ++++Gl+k+er+i+spqk++i v +G+ev+nfcannylGl++hpe+i aa+++l +hGfG++svrfi lcl|FitnessBrowser__PV4:5211293 6 FYDQINQQLAEVKAEGLYKSERVIASPQKTEIEV-NGHEVMNFCANNYLGLANHPELITAAQQGLSDHGFGMASVRFI 82 68999*****************************.9****************************************** PP TIGR01822 79 cGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlckakryryenadled 156 cGtqd+hk+le+ l+eflg+ed+ily+scfdan+Glfe+ll +edai+sdalnhasiidGvrlckakr+ry+n+d++d lcl|FitnessBrowser__PV4:5211293 83 CGTQDIHKQLEASLSEFLGMEDTILYSSCFDANAGLFETLLDAEDAIVSDALNHASIIDGVRLCKAKRFRYANNDMAD 160 ****************************************************************************** PP TIGR01822 157 leaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatGflGatGrGsaelldvldkvdii 234 le++l++a+aagar+ liatdGvfsmdG+ia+l+ +c+la+ky+alv+vd++ha+Gf+G++GrG++e++dv+d+vdii lcl|FitnessBrowser__PV4:5211293 161 LETQLQAAKAAGARHILIATDGVFSMDGVIANLKGVCDLADKYGALVMVDDSHAVGFIGQNGRGTHEYCDVMDRVDII 238 ****************************************************************************** PP TIGR01822 235 tgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasikvlelleasnelrdklventryfrekleaa 312 tgtlGkalGGasGGft+akkevv++lrqrsrpylfsnslap++v+asi+vle+l++++ lr+ ++en+ryfrek++aa lcl|FitnessBrowser__PV4:5211293 239 TGTLGKALGGASGGFTSAKKEVVDWLRQRSRPYLFSNSLAPSIVTASIHVLEMLKSGQALREAVWENSRYFREKMTAA 316 ****************************************************************************** PP TIGR01822 313 GfdvkpaehaiipvmlydaklaqklaerlleeGiyviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrel 390 Gf++ +a+haiipvm++dakla+++a+rllee iyviGf++pvvpkGqarir+q+saah++eqld+a++af+++ +e+ lcl|FitnessBrowser__PV4:5211293 317 GFTLGGADHAIIPVMIGDAKLASDFANRLLEENIYVIGFSFPVVPKGQARIRTQMSAAHTREQLDRAIDAFTRIAKEM 394 ****************************************************************************** PP TIGR01822 391 gvi 393 g+i lcl|FitnessBrowser__PV4:5211293 395 GII 397 997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (393 nodes) Target sequences: 1 (397 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.51 // [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