Align Acetaldehyde dehydrogenase 2; EC 1.2.1.10; Acetaldehyde dehydrogenase [acetylating] 2 (uncharacterized)
to candidate RR42_RS31855 RR42_RS31855 acetaldehyde dehydrogenase
Query= curated2:Q396N9 (299 letters) >FitnessBrowser__Cup4G11:RR42_RS31855 Length = 303 Score = 509 bits (1310), Expect = e-149 Identities = 252/292 (86%), Positives = 271/292 (92%) Query: 1 MKKIKCALIGPGNIGTDLLYKLRRSTVLEPVWMVGVDPASDGLARAREFGLKTTDKGVDG 60 M KIKCALIGPGNIGTDLLYKLRRST+LEPVWMVGVDPASDGLARARE GLKTTD+G+DG Sbjct: 1 MAKIKCALIGPGNIGTDLLYKLRRSTILEPVWMVGVDPASDGLARARELGLKTTDQGLDG 60 Query: 61 LLPHVAADEIRIAFDATSAYVHRDNSDKLTALGVKMIDLTPAAIGPYCVPPVNLDAHLDS 120 LL H+AAD+IRIAFDATSAYVHR +SD+LTA GV++IDLTPAAIGP+CVPPVNLD HL S Sbjct: 61 LLAHLAADDIRIAFDATSAYVHRQHSDQLTARGVRVIDLTPAAIGPFCVPPVNLDEHLGS 120 Query: 121 AQTNVNMVTCGGQATIPMVYAVSRVQPVAYGEIVATVSSRSVGPGTRKNIDEFTRTTSGA 180 NVNMVTCGGQATIPMVYAVSRVQ VAYGEIVATVSSRSVGPGTR+NIDEFTRTT+GA Sbjct: 121 NAMNVNMVTCGGQATIPMVYAVSRVQAVAYGEIVATVSSRSVGPGTRRNIDEFTRTTAGA 180 Query: 181 IEQVGGARKGKAIIVINPAEPPLIMRDTIHCLTDGPPDVDAITASVHAMVKEVQRYVPGY 240 IEQVGGAR+GKAIIVINPAEPPLIMRDTIHCLT+ PDVDAITASVH M+ EV++YVPGY Sbjct: 181 IEQVGGARQGKAIIVINPAEPPLIMRDTIHCLTEDEPDVDAITASVHDMIAEVRQYVPGY 240 Query: 241 TLKNGPVFDGNRVSVFMEVEGLGDYLPKYAGNLDIMTAAAAATAERFAEQML 292 TLKNGPVFDG RVS+FMEVEGLGDYLP+YAGNLDIMTAAAA TAER ML Sbjct: 241 TLKNGPVFDGKRVSIFMEVEGLGDYLPRYAGNLDIMTAAAARTAERIGAAML 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: 389 Number of extensions: 8 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: 299 Length of database: 303 Length adjustment: 27 Effective length of query: 272 Effective length of database: 276 Effective search space: 75072 Effective search space used: 75072 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 RR42_RS31855 RR42_RS31855 (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.14169.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-146 473.2 0.3 1.6e-146 473.1 0.3 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS31855 RR42_RS31855 acetaldehyde dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS31855 RR42_RS31855 acetaldehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.1 0.3 1.6e-146 1.6e-146 1 283 [. 3 291 .. 3 293 .. 0.98 Alignments for each domain: == domain 1 score: 473.1 bits; conditional E-value: 1.6e-146 TIGR03215 1 kvkvaiiGsGnigtdllikllrsevlelallvGidpesdGlararelgvetsaeGvdalleee...did 66 k+k+a+iG+Gnigtdll+kl rs+ le++++vG+dp+sdGlararelg++t+++G+d+ll++ di+ lcl|FitnessBrowser__Cup4G11:RR42_RS31855 3 KIKCALIGPGNIGTDLLYKLRRSTILEPVWMVGVDPASDGLARARELGLKTTDQGLDGLLAHLaadDIR 71 79*********************************************************9987778*** PP TIGR03215 67 ivfdatsakahaenaklleelgkividltPaavGpyvvPavnleevldak..nvnlvtCgGqatiPiva 133 i+fdatsa++h++++++l++ g++vidltPaa+Gp++vP+vnl+e+l ++ nvn+vtCgGqatiP+v+ lcl|FitnessBrowser__Cup4G11:RR42_RS31855 72 IAFDATSAYVHRQHSDQLTARGVRVIDLTPAAIGPFCVPPVNLDEHLGSNamNVNMVTCGGQATIPMVY 140 **********************************************977666***************** PP TIGR03215 134 avsrvakvkyaeivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtv 202 avsrv+ v+y+eiva+++s+s+Gpgtr+nideft+tt+ a+eqvgGa++gkaii++nPaePpl+mrdt+ lcl|FitnessBrowser__Cup4G11:RR42_RS31855 141 AVSRVQAVAYGEIVATVSSRSVGPGTRRNIDEFTRTTAGAIEQVGGARQGKAIIVINPAEPPLIMRDTI 209 ********************************************************************* PP TIGR03215 203 yalv.eeadeeaieasveemveevqkyvpGyrlkqevvldgekvsvlleveGagdylPkyaGnldilta 270 ++l+ +e+d +ai+asv++m++ev++yvpGy+lk+ +v+dg++vs+++eveG gdylP+yaGnldi+ta lcl|FitnessBrowser__Cup4G11:RR42_RS31855 210 HCLTeDEPDVDAITASVHDMIAEVRQYVPGYTLKNGPVFDGKRVSIFMEVEGLGDYLPRYAGNLDIMTA 278 ****899************************************************************** PP TIGR03215 271 aalavaeklaeel 283 aa+++ae++ +++ lcl|FitnessBrowser__Cup4G11:RR42_RS31855 279 AAARTAERIGAAM 291 *******998776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (303 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: 9.22 // [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