Align Acetaldehyde dehydrogenase; Acetaldehyde dehydrogenase [acetylating]; EC 1.2.1.10 (characterized)
to candidate GFF4095 HP15_4035 acetaldehyde dehydrogenase
Query= SwissProt::Q52060 (312 letters) >FitnessBrowser__Marino:GFF4095 Length = 311 Score = 498 bits (1282), Expect = e-146 Identities = 250/311 (80%), Positives = 280/311 (90%) Query: 1 MNQKLKVAIIGSGNIGTDLMIKVLRNAKYLEMGAMVGIDAASDGLARAQRMGVTTTYAGV 60 M++K+K AIIGSGNIGTDLMIK+LRN K +EMGAMVGID SDGLARA RMGV TT+ GV Sbjct: 1 MSKKIKAAIIGSGNIGTDLMIKILRNGKNIEMGAMVGIDPESDGLARAARMGVATTHEGV 60 Query: 61 EGLIKLPEFADIDFVFDATSASAHVQNEALLRQAKPGIRLIDLTPAAIGPYCVPVVNLEE 120 +GL+K+PEFADID VFDATSA AH+ NE LR K I++ID+TPAAIGPYCVPVVNLE+ Sbjct: 61 DGLVKMPEFADIDIVFDATSAKAHMHNEVFLRGHKESIKIIDMTPAAIGPYCVPVVNLEQ 120 Query: 121 HLGKLNVNMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTS 180 L + NVNMVTCGGQATIPMVAAVSRVAK HYAEIVASISSKSAGPGTRANIDEFT+TTS Sbjct: 121 QLQEGNVNMVTCGGQATIPMVAAVSRVAKAHYAEIVASISSKSAGPGTRANIDEFTQTTS 180 Query: 181 KAIEVIGGAAKGKAIIIMNPAEPPLIMRDTVYVLSAAADQAAVAASVAEMVQAVQAYVPG 240 +AIEV+GGA KGKAIII+NPAEPPL+MRDTVYVLS AAD+A V ASV EMVQAV +YVPG Sbjct: 181 RAIEVVGGAQKGKAIIILNPAEPPLLMRDTVYVLSDAADKAEVEASVEEMVQAVNSYVPG 240 Query: 241 YRLKQQVQFDVIPESAPLNIPGLGRFSGLKTSVFLEVEGAAHYLPAYAGNLDIMTSAALA 300 YRLKQ+VQFD IPE P+N+PGLGRFSGLKTS+FLEVEGAAHYLPAYAGNLDIMTSAAL Sbjct: 241 YRLKQKVQFDDIPEDQPMNVPGLGRFSGLKTSIFLEVEGAAHYLPAYAGNLDIMTSAALG 300 Query: 301 TAERMAQSMLN 311 TAER+A+S++N Sbjct: 301 TAERIAESLVN 311 Lambda K H 0.317 0.132 0.362 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: 348 Number of extensions: 3 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: 312 Length of database: 311 Length adjustment: 27 Effective length of query: 285 Effective length of database: 284 Effective search space: 80940 Effective search space used: 80940 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: 48 (23.1 bits)
Align candidate GFF4095 HP15_4035 (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.31853.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-145 469.6 5.3 2e-145 469.4 5.3 1.0 1 lcl|FitnessBrowser__Marino:GFF4095 HP15_4035 acetaldehyde dehydroge Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF4095 HP15_4035 acetaldehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 469.4 5.3 2e-145 2e-145 1 283 [. 4 309 .. 4 311 .] 0.98 Alignments for each domain: == domain 1 score: 469.4 bits; conditional E-value: 2e-145 TIGR03215 1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didivfda 71 k+k+aiiGsGnigtdl+ik+lr ++++e+ ++vGidpesdGlara+++gv+t++eGvd+l++++ didivfda lcl|FitnessBrowser__Marino:GFF4095 4 KIKAAIIGSGNIGTDLMIKILRnGKNIEMGAMVGIDPESDGLARAARMGVATTHEGVDGLVKMPefaDIDIVFDA 78 79********************99***************************************99999******* PP TIGR03215 72 tsakahaenaklleel..gkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvkya 144 tsakah++n+ +l+ + +++id+tPaa+Gpy+vP+vnle++l++ nvn+vtCgGqatiP+vaavsrvak++ya lcl|FitnessBrowser__Marino:GFF4095 79 TSAKAHMHNEVFLRGHkeSIKIIDMTPAAIGPYCVPVVNLEQQLQEGNVNMVTCGGQATIPMVAAVSRVAKAHYA 153 *************876437899***************************************************** PP TIGR03215 145 eivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalveeadeeaieasve 219 eivasi+sksaGpgtranideft+tts+a+e vgGa+kgkaiiilnPaePpllmrdtvy+l+++ad++++easve lcl|FitnessBrowser__Marino:GFF4095 154 EIVASISSKSAGPGTRANIDEFTQTTSRAIEVVGGAQKGKAIIILNPAEPPLLMRDTVYVLSDAADKAEVEASVE 228 *************************************************************************** PP TIGR03215 220 emveevqkyvpGyrlkqevvld.................gekvsvlleveGagdylPkyaGnldiltaaalavae 277 emv++v++yvpGyrlkq+v++d g k+s++leveGa++ylP+yaGnldi+t+aal +ae lcl|FitnessBrowser__Marino:GFF4095 229 EMVQAVNSYVPGYRLKQKVQFDdipedqpmnvpglgrfsGLKTSIFLEVEGAAHYLPAYAGNLDIMTSAALGTAE 303 *************************************************************************** PP TIGR03215 278 klaeel 283 ++ae+l lcl|FitnessBrowser__Marino:GFF4095 304 RIAESL 309 ***986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (311 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: 00:00:00.00 # Mc/sec: 11.37 // [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