Align acylating aldehyde dehydrogenase (EC 1.2.1.10) (characterized)
to candidate RR42_RS27895 RR42_RS27895 acetaldehyde dehydrogenase
Query= metacyc::MONOMER-11388 (316 letters) >FitnessBrowser__Cup4G11:RR42_RS27895 Length = 316 Score = 496 bits (1278), Expect = e-145 Identities = 255/316 (80%), Positives = 276/316 (87%), Gaps = 1/316 (0%) Query: 1 MTRKVKAAIIGSGNIGTDLMIKILRHGQHIEMGAMVGIDPASDGLARGERMGVAITHEGV 60 MTRK+KAAIIGSGNIGTDLMIKILRHG H+EMGAMVGIDPASDGLAR R+GVA THEGV Sbjct: 1 MTRKLKAAIIGSGNIGTDLMIKILRHGAHVEMGAMVGIDPASDGLARAARLGVATTHEGV 60 Query: 61 EGLTRLPVFNEIDVVFDATSAGAHVKNEALLRERKPGLRMIDLTPAAIAPYCIPVVNGDD 120 +GLTRLPVF EIDVVFDATSAGAHVKN+A LR +P LRMIDLTPAAI PYCIPVVNGD Sbjct: 61 QGLTRLPVFGEIDVVFDATSAGAHVKNDAFLRGLRPSLRMIDLTPAAIGPYCIPVVNGDA 120 Query: 121 HLDATNVNMVTCGGQATIPMVAAVSRVAKVHYAEIIASISSKSAGPGTRANIDEFTETTS 180 HLDA NVNMVTCGGQATIPMVAAVSRVA V YAEI+ASISSKSAGPGTRANIDEFTETTS Sbjct: 121 HLDAHNVNMVTCGGQATIPMVAAVSRVAPVLYAEIVASISSKSAGPGTRANIDEFTETTS 180 Query: 181 KAIEVVGGAAKGKAIIVLNPAEPPLMMRDAVYTLSDFADIDQIEESVQRMADAVQAYVPG 240 KAIE +GGA KGKAIIVLNPAEPPL+MRD VY LS+ AD I S+ MA V+ YVPG Sbjct: 181 KAIEAIGGAGKGKAIIVLNPAEPPLIMRDTVYCLSEMADEAAIAASIDAMAAEVRQYVPG 240 Query: 241 YRLKQRVQFDRIEADCPIRIPGVGDRMNGLKTSIFLEVEGAAHYLPAYAGNLDIMTSAAL 300 YRLKQ+VQFDRI AD P+ +PGVG R++GLKTS+FLEVEGAAHYLPAYAGNLDIMTSAAL Sbjct: 241 YRLKQKVQFDRIPADAPLVVPGVG-RVSGLKTSVFLEVEGAAHYLPAYAGNLDIMTSAAL 299 Query: 301 RTAEKLAERLLASLVA 316 AE++A +LA A Sbjct: 300 TIAERMASAMLAQRAA 315 Lambda K H 0.319 0.135 0.379 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: 397 Number of extensions: 5 Number of successful extensions: 2 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate RR42_RS27895 RR42_RS27895 (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.8642.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-144 465.3 4.8 4.2e-144 465.1 4.8 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS27895 RR42_RS27895 acetaldehyde dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS27895 RR42_RS27895 acetaldehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 465.1 4.8 4.2e-144 4.2e-144 1 284 [. 4 310 .. 4 311 .. 0.98 Alignments for each domain: == domain 1 score: 465.1 bits; conditional E-value: 4.2e-144 TIGR03215 1 kvkvaiiGsGnigtdllikllr.sevlelallvGidpesdGlararelgvetsaeGvdalleee...di 65 k+k+aiiGsGnigtdl+ik+lr + ++e+ ++vGidp+sdGlara++lgv+t++eGv++l++ + +i lcl|FitnessBrowser__Cup4G11:RR42_RS27895 4 KLKAAIIGSGNIGTDLMIKILRhGAHVEMGAMVGIDPASDGLARAARLGVATTHEGVQGLTRLPvfgEI 72 789*******************999**************************************999*** PP TIGR03215 66 divfdatsakahaenaklleel..gkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPiv 132 d+vfdatsa ah++n+++l+ l ++idltPaa+Gpy++P+vn +++lda+nvn+vtCgGqatiP+v lcl|FitnessBrowser__Cup4G11:RR42_RS27895 73 DVVFDATSAGAHVKNDAFLRGLrpSLRMIDLTPAAIGPYCIPVVNGDAHLDAHNVNMVTCGGQATIPMV 141 ********************9866789****************************************** PP TIGR03215 133 aavsrvakvkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdt 201 aavsrva+v yaeivasi+sksaGpgtranideftettska+e++gGa kgkaii+lnPaePpl+mrdt lcl|FitnessBrowser__Cup4G11:RR42_RS27895 142 AAVSRVAPVLYAEIVASISSKSAGPGTRANIDEFTETTSKAIEAIGGAGKGKAIIVLNPAEPPLIMRDT 210 ********************************************************************* PP TIGR03215 202 vyalveeadeeaieasveemveevqkyvpGyrlkqevvld.................gekvsvlleveG 253 vy+l+e ade+ai+as+ +m +ev++yvpGyrlkq+v++d g k+sv+leveG lcl|FitnessBrowser__Cup4G11:RR42_RS27895 211 VYCLSEMADEAAIAASIDAMAAEVRQYVPGYRLKQKVQFDripadaplvvpgvgrvsGLKTSVFLEVEG 279 ********************************************************************* PP TIGR03215 254 agdylPkyaGnldiltaaalavaeklaeell 284 a++ylP+yaGnldi+t+aal++ae++a+++l lcl|FitnessBrowser__Cup4G11:RR42_RS27895 280 AAHYLPAYAGNLDIMTSAALTIAERMASAML 310 ***************************9876 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: 00:00:00.01 # Mc/sec: 7.33 // [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