Align Acetaldehyde dehydrogenase; Acetaldehyde dehydrogenase [acetylating]; EC 1.2.1.10 (characterized)
to candidate BPHYT_RS07245 BPHYT_RS07245 acetaldehyde dehydrogenase
Query= SwissProt::Q9KWS1 (316 letters) >FitnessBrowser__BFirm:BPHYT_RS07245 Length = 314 Score = 426 bits (1094), Expect = e-124 Identities = 218/307 (71%), Positives = 251/307 (81%) Query: 4 DRLSVAIIGSGNIGTDLMIKIMRNSKLLKVGAMVGIDPKSDGLARAQRLGVPTTAEGVDG 63 D+ +VAIIGSGNIGTDLMIK++R++K L++GAMVGIDP SDGLARA+RLGV TTA G++G Sbjct: 6 DKQAVAIIGSGNIGTDLMIKVLRDAKHLEMGAMVGIDPASDGLARAKRLGVATTAHGIEG 65 Query: 64 LLDMPAFRDIKIAFDATSAGAQAIHNQKLQAHGVRVIDLTPAAIGPYVIPVVNFDQHVDA 123 L+ MP F I+IAFDATSAGA H L+ HGV VIDLTPAAIGP+V+PVVN H+DA Sbjct: 66 LVTMPNFGAIRIAFDATSAGAHHRHAAVLREHGVTVIDLTPAAIGPFVVPVVNLFAHLDA 125 Query: 124 PNINMVTCGGQATIPIVHAVSKVSPVHYAEIVASISSKSAGPGTRANIDEFTETTSKAIL 183 PN+NMVTCGGQATIPIVHAVS+V+PV YAEIVASI+S+SAGPGTRANIDEFTETTSKAI Sbjct: 126 PNLNMVTCGGQATIPIVHAVSRVAPVRYAEIVASIASRSAGPGTRANIDEFTETTSKAIE 185 Query: 184 EVGGAAQGRAIIILNPAEPPLIMRDTVYCFVSAEANIDAITDSVEQMVKSVQEYVPGYRL 243 VGGAA+G+AII+LNPAEPPL+MRDTVYC EA+ D I S+ MV +V YVPGYRL Sbjct: 186 TVGGAARGKAIIVLNPAEPPLMMRDTVYCLTEEEADTDEIESSIRAMVSAVASYVPGYRL 245 Query: 244 KQKVQFEKIVAGNEQNIPGLGWSTGLKVSVFLEVEGAGHYLPSYAGNLDIMTSAGLTVAE 303 KQ VQF++ A N + GLKVSVFLEVEGA HYLPSYAGNLDIMTSA L AE Sbjct: 246 KQAVQFDRYTAANPLALHANERRAGLKVSVFLEVEGAAHYLPSYAGNLDIMTSAALAAAE 305 Query: 304 RIAGSGV 310 +IA S V Sbjct: 306 QIAASRV 312 Lambda K H 0.317 0.134 0.380 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: 351 Number of extensions: 8 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: 316 Length of database: 314 Length adjustment: 27 Effective length of query: 289 Effective length of database: 287 Effective search space: 82943 Effective search space used: 82943 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 (21.6 bits) S2: 48 (23.1 bits)
Align candidate BPHYT_RS07245 BPHYT_RS07245 (acetaldehyde dehydrogenase)
to HMM TIGR03215 (acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10))
# 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/TIGR03215.hmm # target sequence database: /tmp/gapView.27015.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03215 [M=285] Accession: TIGR03215 Description: ac_ald_DH_ac: acetaldehyde dehydrogenase (acetylating) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-146 473.5 6.2 1.4e-146 473.2 6.2 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS07245 BPHYT_RS07245 acetaldehyde dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS07245 BPHYT_RS07245 acetaldehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.2 6.2 1.4e-146 1.4e-146 2 284 .. 8 312 .. 7 313 .. 0.98 Alignments for each domain: == domain 1 score: 473.2 bits; conditional E-value: 1.4e-146 TIGR03215 2 vkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didi 67 vaiiGsGnigtdl+ik+lr +++le+ ++vGidp+sdGlara++lgv+t+a+G+++l++++ i+i lcl|FitnessBrowser__BFirm:BPHYT_RS07245 8 QAVAIIGSGNIGTDLMIKVLRdAKHLEMGAMVGIDPASDGLARAKRLGVATTAHGIEGLVTMPnfgAIRI 77 679******************99***************************************988889** PP TIGR03215 68 vfdatsakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsr 137 +fdatsa ah+++a++l+e+g++vidltPaa+Gp+vvP+vnl ++lda+n+n+vtCgGqatiPiv+avsr lcl|FitnessBrowser__BFirm:BPHYT_RS07245 78 AFDATSAGAHHRHAAVLREHGVTVIDLTPAAIGPFVVPVVNLFAHLDAPNLNMVTCGGQATIPIVHAVSR 147 ********************************************************************** PP TIGR03215 138 vakvkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalv. 206 va+v+yaeivasias+saGpgtranideftettska+e+vgGa++gkaii+lnPaePpl+mrdtvy+l+ lcl|FitnessBrowser__BFirm:BPHYT_RS07245 148 VAPVRYAEIVASIASRSAGPGTRANIDEFTETTSKAIETVGGAARGKAIIVLNPAEPPLMMRDTVYCLTe 217 *********************************************************************8 PP TIGR03215 207 eeadeeaieasveemveevqkyvpGyrlkqevvld.................gekvsvlleveGagdylP 259 eead+++ie+s+++mv++v++yvpGyrlkq v++d g kvsv+leveGa++ylP lcl|FitnessBrowser__BFirm:BPHYT_RS07245 218 EEADTDEIESSIRAMVSAVASYVPGYRLKQAVQFDrytaanplalhanerraGLKVSVFLEVEGAAHYLP 287 899******************************************************************* PP TIGR03215 260 kyaGnldiltaaalavaeklaeell 284 +yaGnldi+t+aala+ae++a++++ lcl|FitnessBrowser__BFirm:BPHYT_RS07245 288 SYAGNLDIMTSAALAAAEQIAASRV 312 *********************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (314 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: 00:00:00.00 # Mc/sec: 10.55 // [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