Align Acetaldehyde dehydrogenase 2; EC 1.2.1.10; Acetaldehyde dehydrogenase [acetylating] 2 (uncharacterized)
to candidate WP_012277178.1 SHAL_RS10915 acetaldehyde dehydrogenase (acetylating)
Query= curated2:Q396N9 (299 letters) >NCBI__GCF_000019185.1:WP_012277178.1 Length = 307 Score = 459 bits (1182), Expect = e-134 Identities = 230/290 (79%), Positives = 253/290 (87%), Gaps = 1/290 (0%) Query: 3 KIKCALIGPGNIGTDLLYKLRRSTVLEPVWMVGVDPASDGLARAREFGLKTTDKGVDGLL 62 KIKCALIG GNIGTDLLYKL RS VLEPVWMVG+DP SDGLARA+ GLK T G++GLL Sbjct: 4 KIKCALIGSGNIGTDLLYKLMRSDVLEPVWMVGIDPESDGLARAKAAGLKVTADGINGLL 63 Query: 63 PHVAADEIRIAFDATSAYVHRDNSDKLTALGVKMIDLTPAAIGPYCVPPVNLDAHLDSAQ 122 P V ADEI+IAFDATSAYVH +NS KL LGV MIDLTPAAIGP+CVPPVNL + LD Sbjct: 64 PFVEADEIKIAFDATSAYVHAENSRKLNELGVVMIDLTPAAIGPFCVPPVNL-SQLDENV 122 Query: 123 TNVNMVTCGGQATIPMVYAVSRVQPVAYGEIVATVSSRSVGPGTRKNIDEFTRTTSGAIE 182 N+NMVTCGGQATIPMV AVSRVQ V YGEIVATVSSRSVGPGTR+NIDEFTRTT+GA+E Sbjct: 123 KNINMVTCGGQATIPMVAAVSRVQAVEYGEIVATVSSRSVGPGTRQNIDEFTRTTAGAVE 182 Query: 183 QVGGARKGKAIIVINPAEPPLIMRDTIHCLTDGPPDVDAITASVHAMVKEVQRYVPGYTL 242 Q+GGA KGKAIIVINPAEPPL+MRDTIHCLT PD AITASVH M+++VQ+YVPGYTL Sbjct: 183 QIGGAEKGKAIIVINPAEPPLLMRDTIHCLTKEQPDEQAITASVHEMIEQVQQYVPGYTL 242 Query: 243 KNGPVFDGNRVSVFMEVEGLGDYLPKYAGNLDIMTAAAAATAERFAEQML 292 KNGPVFDG +V++F+EVEGLGDYLPKYAGNLDIMTAAAA TAE A +ML Sbjct: 243 KNGPVFDGRKVTIFLEVEGLGDYLPKYAGNLDIMTAAAARTAEMLASKML 292 Lambda K H 0.318 0.134 0.391 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: 349 Number of extensions: 11 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: 299 Length of database: 307 Length adjustment: 27 Effective length of query: 272 Effective length of database: 280 Effective search space: 76160 Effective search space used: 76160 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 WP_012277178.1 SHAL_RS10915 (acetaldehyde dehydrogenase (acetylating))
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.2310518.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-148 478.8 1.4 3.1e-148 478.7 1.4 1.0 1 NCBI__GCF_000019185.1:WP_012277178.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000019185.1:WP_012277178.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 478.7 1.4 3.1e-148 3.1e-148 1 284 [. 4 292 .. 4 293 .. 0.97 Alignments for each domain: == domain 1 score: 478.7 bits; conditional E-value: 3.1e-148 TIGR03215 1 kvkvaiiGsGnigtdllikllrsevlelallvGidpesdGlararelgvetsaeGvdalleee...didivfd 70 k+k+a+iGsGnigtdll+kl+rs+vle++++vGidpesdGlara+ +g++++a+G+++ll +i+i+fd NCBI__GCF_000019185.1:WP_012277178.1 4 KIKCALIGSGNIGTDLLYKLMRSDVLEPVWMVGIDPESDGLARAKAAGLKVTADGINGLLPFVeadEIKIAFD 76 79********************************************************987555559****** PP TIGR03215 71 atsakahaenaklleelgkividltPaavGpyvvPavnleevldak.nvnlvtCgGqatiPivaavsrvakvk 142 atsa++haen+++l+elg+++idltPaa+Gp++vP+vnl++ ++ n+n+vtCgGqatiP+vaavsrv+ v+ NCBI__GCF_000019185.1:WP_012277178.1 77 ATSAYVHAENSRKLNELGVVMIDLTPAAIGPFCVPPVNLSQLDENVkNINMVTCGGQATIPMVAAVSRVQAVE 149 ****************************************9876544************************** PP TIGR03215 143 yaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalv.eeadeeai 214 y+eiva+++s+s+Gpgtr+nideft+tt+ a+eq+gGa+kgkaii++nPaePpllmrdt+++l+ e++de+ai NCBI__GCF_000019185.1:WP_012277178.1 150 YGEIVATVSSRSVGPGTRQNIDEFTRTTAGAVEQIGGAEKGKAIIVINPAEPPLLMRDTIHCLTkEQPDEQAI 222 ***************************************************************9899****** PP TIGR03215 215 easveemveevqkyvpGyrlkqevvldgekvsvlleveGagdylPkyaGnldiltaaalavaeklaeell 284 +asv+em+e+vq+yvpGy+lk+ +v+dg+kv+++leveG gdylPkyaGnldi+taaa+++ae+la+++l NCBI__GCF_000019185.1:WP_012277178.1 223 TASVHEMIEQVQQYVPGYTLKNGPVFDGRKVTIFLEVEGLGDYLPKYAGNLDIMTAAAARTAEMLASKML 292 ******************************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (307 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: 12.57 // [ok]
This GapMind analysis is from Sep 24 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