Align acetaldehyde dehydrogenase; EC 1.2.1.10 (characterized)
to candidate 14489 b0351 acetaldehyde dehydrogenase (NCBI)
Query= CharProtDB::CH_002283 (316 letters) >FitnessBrowser__Keio:14489 Length = 316 Score = 612 bits (1579), Expect = e-180 Identities = 316/316 (100%), Positives = 316/316 (100%) Query: 1 MSKRKVAIIGSGNIGTDLMIKILRHGQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVI 60 MSKRKVAIIGSGNIGTDLMIKILRHGQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVI Sbjct: 1 MSKRKVAIIGSGNIGTDLMIKILRHGQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVI 60 Query: 61 GLMNMPEFADIDIVFDATSAGAHVKNDAALREAKPDIRLIDLTPAAIGPYCVPVVNLEAN 120 GLMNMPEFADIDIVFDATSAGAHVKNDAALREAKPDIRLIDLTPAAIGPYCVPVVNLEAN Sbjct: 61 GLMNMPEFADIDIVFDATSAGAHVKNDAALREAKPDIRLIDLTPAAIGPYCVPVVNLEAN 120 Query: 121 VDQLNVNMVTCGGQATIPMVAAVSRVARVHYAEIIASIASKSAGPGTRANIDEFTETTSR 180 VDQLNVNMVTCGGQATIPMVAAVSRVARVHYAEIIASIASKSAGPGTRANIDEFTETTSR Sbjct: 121 VDQLNVNMVTCGGQATIPMVAAVSRVARVHYAEIIASIASKSAGPGTRANIDEFTETTSR 180 Query: 181 AIEVVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSDEASQDDIEASINEMAEAVQAYVPGY 240 AIEVVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSDEASQDDIEASINEMAEAVQAYVPGY Sbjct: 181 AIEVVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSDEASQDDIEASINEMAEAVQAYVPGY 240 Query: 241 RLKQRVQFEVIPQDKPVNLPGVGQFSGLKTAVWLEVEGAAHYLPAYAGNLDIMTSSALAT 300 RLKQRVQFEVIPQDKPVNLPGVGQFSGLKTAVWLEVEGAAHYLPAYAGNLDIMTSSALAT Sbjct: 241 RLKQRVQFEVIPQDKPVNLPGVGQFSGLKTAVWLEVEGAAHYLPAYAGNLDIMTSSALAT 300 Query: 301 AEKMAQSLARKAGEAA 316 AEKMAQSLARKAGEAA Sbjct: 301 AEKMAQSLARKAGEAA 316 Lambda K H 0.317 0.132 0.368 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: 451 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: 316 Length of database: 316 Length adjustment: 27 Effective length of query: 289 Effective length of database: 289 Effective search space: 83521 Effective search space used: 83521 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 14489 b0351 (acetaldehyde dehydrogenase (NCBI))
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.8316.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-146 471.5 5.4 5.2e-146 471.3 5.4 1.0 1 lcl|FitnessBrowser__Keio:14489 b0351 acetaldehyde dehydrogenase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:14489 b0351 acetaldehyde dehydrogenase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 471.3 5.4 5.2e-146 5.2e-146 1 283 [. 3 308 .. 3 310 .. 0.98 Alignments for each domain: == domain 1 score: 471.3 bits; conditional E-value: 5.2e-146 TIGR03215 1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...didivfdatsak 75 k kvaiiGsGnigtdl+ik+lr +++le+a++vGidp+sdGlarar++gv+t++eGv +l++++ didivfdatsa lcl|FitnessBrowser__Keio:14489 3 KRKVAIIGSGNIGTDLMIKILRhGQHLEMAVMVGIDPQSDGLARARRMGVATTHEGVIGLMNMPefaDIDIVFDATSAG 81 679*******************99***************************************99999*********** PP TIGR03215 76 ahaenaklleel..gkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvkyaeivasias 152 ah++n+++l+e+ ++++idltPaa+Gpy+vP+vnle+++d+ nvn+vtCgGqatiP+vaavsrva+v+yaei+asias lcl|FitnessBrowser__Keio:14489 82 AHVKNDAALREAkpDIRLIDLTPAAIGPYCVPVVNLEANVDQLNVNMVTCGGQATIPMVAAVSRVARVHYAEIIASIAS 160 *********9987789*************************************************************** PP TIGR03215 153 ksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalveeadeeaieasveemveevqkyvpG 231 ksaGpgtranideftetts+a+e vgGa+kgkaii+lnPaePpl+mrdtvy+l++ea++++ieas++em e+vq+yvpG lcl|FitnessBrowser__Keio:14489 161 KSAGPGTRANIDEFTETTSRAIEVVGGAAKGKAIIVLNPAEPPLMMRDTVYVLSDEASQDDIEASINEMAEAVQAYVPG 239 ******************************************************************************* PP TIGR03215 232 yrlkqevvld.................gekvsvlleveGagdylPkyaGnldiltaaalavaeklaeel 283 yrlkq+v+++ g k++v+leveGa++ylP+yaGnldi+t++ala+aek+a++l lcl|FitnessBrowser__Keio:14489 240 YRLKQRVQFEvipqdkpvnlpgvgqfsGLKTAVWLEVEGAAHYLPAYAGNLDIMTSSALATAEKMAQSL 308 ******************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (316 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.23 // [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