Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10); propanal dehydrogenase (CoA-propanoylating) (EC 1.2.1.87) (characterized)
to candidate PfGW456L13_2505 Acetaldehyde dehydrogenase, acetylating, (EC 1.2.1.10) in gene cluster for degradation of phenols, cresols, catechol
Query= BRENDA::Q79AF6 (304 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2505 Length = 302 Score = 465 bits (1197), Expect = e-136 Identities = 223/299 (74%), Positives = 262/299 (87%) Query: 1 MTKKIKCALIGPGNIGTDLLAKLQRSPVLEPIWMVGIDPESDGLKRAREMGIKTTADGVD 60 M+KK++ A+IGPGNIGTDLL K+ RS +EP+WMVG+DP+S+GLKRAREMGIKTTA GVD Sbjct: 1 MSKKLRAAIIGPGNIGTDLLMKMCRSQWIEPVWMVGVDPDSEGLKRAREMGIKTTAGGVD 60 Query: 61 GLIPHMQADGVQIVFDATSAYVHADNSRKVNALGALMIDLTPAAIGPFCVPTVNLKEHVG 120 GL+PH+ D ++I FDATSAYVHA+NSRK+N LG +MIDLTPAAIGP+CVP VNLKEH Sbjct: 61 GLLPHVLDDDIRIAFDATSAYVHAENSRKLNELGVIMIDLTPAAIGPYCVPPVNLKEHAS 120 Query: 121 KGEMNVNMVTCGGQATIPMVAAVSRVQPVAYGEIVATVSSKSAGPGTRKNIDEFTRTTAG 180 MNVNMVTCGGQATIPMVAAVSRVQPV+YGEIVATVSS S GPGTR+NIDEFTRTTAG Sbjct: 121 SLAMNVNMVTCGGQATIPMVAAVSRVQPVSYGEIVATVSSGSVGPGTRQNIDEFTRTTAG 180 Query: 181 AVEKVGGAKKGKAIIILNPAEPPLIMRDTVHCLLESEPDQAKITESIHAMIKEVQKYVPG 240 AVEK+GGA++GKAII++NPAEPPL+MRDT+HCL + EP+Q I S+ M++EVQ+YVPG Sbjct: 181 AVEKIGGARRGKAIIVINPAEPPLMMRDTIHCLTDDEPNQDAIRTSVLEMVREVQRYVPG 240 Query: 241 YKLVNGPVFDGLRVSVYLEVEGLGDYLPKYAGNLDIMTAAAARTAEMFAEEILAGQLTL 299 YKL+NGPVFDG +VS+++EVEGLGD+LPK AGNLDIMTAA RTAEMFAEE G L L Sbjct: 241 YKLINGPVFDGRKVSIFIEVEGLGDFLPKSAGNLDIMTAAGLRTAEMFAEEAHKGTLQL 299 Lambda K H 0.317 0.135 0.388 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: 347 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: 304 Length of database: 302 Length adjustment: 27 Effective length of query: 277 Effective length of database: 275 Effective search space: 76175 Effective search space used: 76175 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 PfGW456L13_2505 (Acetaldehyde dehydrogenase, acetylating, (EC 1.2.1.10) in gene cluster for degradation of phenols, cresols, catechol)
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.26214.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-143 463.2 0.2 1.8e-143 463.0 0.2 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2505 Acetaldehyde dehydrogenase, acet Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2505 Acetaldehyde dehydrogenase, acetylating, (EC 1.2.1.10) in gen # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 463.0 0.2 1.8e-143 1.8e-143 1 283 [. 4 292 .. 4 294 .. 0.98 Alignments for each domain: == domain 1 score: 463.0 bits; conditional E-value: 1.8e-143 TIGR03215 1 kvkvaiiGsGnigtdllikllrsevlelallvGidpesdGlararelgvetsaeG 55 k+++aiiG+Gnigtdll+k+ rs+ +e++++vG+dp+s+Gl+rare+g++t+a G lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2505 4 KLRAAIIGPGNIGTDLLMKMCRSQWIEPVWMVGVDPDSEGLKRAREMGIKTTAGG 58 789**************************************************** PP TIGR03215 56 vdalleee...didivfdatsakahaenaklleelgkividltPaavGpyvvPav 107 vd+ll + di+i+fdatsa++haen+++l+elg+i+idltPaa+Gpy+vP+v lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2505 59 VDGLLPHVlddDIRIAFDATSAYVHAENSRKLNELGVIMIDLTPAAIGPYCVPPV 113 ******98888******************************************** PP TIGR03215 108 nleevldak..nvnlvtCgGqatiPivaavsrvakvkyaeivasiasksaGpgtr 160 nl+e+ + nvn+vtCgGqatiP+vaavsrv++v+y+eiva+++s s+Gpgtr lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2505 114 NLKEHASSLamNVNMVTCGGQATIPMVAAVSRVQPVSYGEIVATVSSGSVGPGTR 168 *****987667******************************************** PP TIGR03215 161 anideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalv.eeadeeai 214 +nideft+tt+ a+e++gGa++gkaii++nPaePpl+mrdt+++l+ +e++++ai lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2505 169 QNIDEFTRTTAGAVEKIGGARRGKAIIVINPAEPPLMMRDTIHCLTdDEPNQDAI 223 **********************************************899****** PP TIGR03215 215 easveemveevqkyvpGyrlkqevvldgekvsvlleveGagdylPkyaGnldilt 269 ++sv emv+evq+yvpGy+l + +v+dg+kvs+++eveG gd+lPk aGnldi+t lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2505 224 RTSVLEMVREVQRYVPGYKLINGPVFDGRKVSIFIEVEGLGDFLPKSAGNLDIMT 278 ******************************************************* PP TIGR03215 270 aaalavaeklaeel 283 aa l++ae++aee lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2505 279 AAGLRTAEMFAEEA 292 ***********975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (302 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: 7.28 // [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