Align Acetaldehyde dehydrogenase 1; EC 1.2.1.10; Acetaldehyde dehydrogenase [acetylating] 1 (uncharacterized)
to candidate WP_050655875.1 C1M55_RS04080 acetaldehyde dehydrogenase (acetylating)
Query= curated2:A1UM81 (310 letters) >NCBI__GCF_002893965.1:WP_050655875.1 Length = 300 Score = 498 bits (1283), Expect = e-146 Identities = 252/301 (83%), Positives = 272/301 (90%), Gaps = 5/301 (1%) Query: 4 KLQVAIVGSGNISTDLLYKLQRSEYLEPRWMIGIDPESEGLARARKLGLETSHEGVDWLL 63 K VAIVGSGNISTDLLYKLQRSE+LEPRWMIGIDPESEGLARARK+GLETS EGVDWLL Sbjct: 3 KASVAIVGSGNISTDLLYKLQRSEWLEPRWMIGIDPESEGLARARKMGLETSAEGVDWLL 62 Query: 64 AQDDKPDLVFEATSAYVHRAAAPRYEEAGIRAIDLTPAAVGPAVIPPANLREHLDAPNVN 123 +Q +KPDLVFEATSAYVHR AAPRYE AGIRAIDLTPAAVGPAV+PPANLREHLDAPNVN Sbjct: 63 SQAEKPDLVFEATSAYVHREAAPRYEAAGIRAIDLTPAAVGPAVVPPANLREHLDAPNVN 122 Query: 124 MITCGGQATIPIVYAVTRAVTEQGGTVPYAEIVASVSSSSAGPGTRANIDEFTKTTSKGV 183 MITCGGQATIPIVYAV+R V V YAEIVASV+S SAGPGTRANIDEFTKTTS+G+ Sbjct: 123 MITCGGQATIPIVYAVSRVV-----DVAYAEIVASVASLSAGPGTRANIDEFTKTTSRGI 177 Query: 184 QTIGGAARGKAIIILNPADPPMIMRDTIFCAIPEDVDRDAIAQSIRDVVAEVQTYVPGYR 243 +TIGGA RGKAIIILNPADPPMIMRDTIFCAIPED D+ AI SI VV ++Q YVPGYR Sbjct: 178 ETIGGAQRGKAIIILNPADPPMIMRDTIFCAIPEDADQAAITDSIHRVVKDIQQYVPGYR 237 Query: 244 LLNDPQFDDPSINSGGQAVVTTFVEVEGAGDYLPPYAGNLDIMTAAAAKVGEEIAKESLS 303 LLN+PQFD+PS+ SGG A VTTFVEVEGAGD+LPPYAGNLDIMTAAA KVGEEIA++ LS Sbjct: 238 LLNEPQFDEPSVVSGGYATVTTFVEVEGAGDFLPPYAGNLDIMTAAATKVGEEIAQKLLS 297 Query: 304 L 304 + Sbjct: 298 V 298 Lambda K H 0.315 0.133 0.381 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: 394 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: 310 Length of database: 300 Length adjustment: 27 Effective length of query: 283 Effective length of database: 273 Effective search space: 77259 Effective search space used: 77259 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: 42 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_050655875.1 C1M55_RS04080 (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.1564389.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-141 456.9 0.2 1.5e-141 456.7 0.2 1.0 1 NCBI__GCF_002893965.1:WP_050655875.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_050655875.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 456.7 0.2 1.5e-141 1.5e-141 1 284 [. 3 296 .. 3 297 .. 0.98 Alignments for each domain: == domain 1 score: 456.7 bits; conditional E-value: 1.5e-141 TIGR03215 1 kvkvaiiGsGnigtdllikllrsevlelallvGidpesdGlararelgvetsaeGvdalleeedi.divfdat 72 k+ vai+GsGni+tdll+kl+rse le+++++Gidpes+Glarar++g+etsaeGvd+ll++ + d+vf+at NCBI__GCF_002893965.1:WP_050655875.1 3 KASVAIVGSGNISTDLLYKLQRSEWLEPRWMIGIDPESEGLARARKMGLETSAEGVDWLLSQAEKpDLVFEAT 75 5789**********************************************************9877******* PP TIGR03215 73 sakahaenaklleelgkividltPaavGpyvvPavnleevldaknvnlvtCgGqatiPivaavsrvakvkyae 145 sa++h+e+a ++e++g+++idltPaavGp vvP+ nl+e+lda+nvn++tCgGqatiPiv+avsrv++v+yae NCBI__GCF_002893965.1:WP_050655875.1 76 SAYVHREAAPRYEAAGIRAIDLTPAAVGPAVVPPANLREHLDAPNVNMITCGGQATIPIVYAVSRVVDVAYAE 148 ************************************************************************* PP TIGR03215 146 ivasiasksaGpgtranideftettskaleqvgGakkgkaiiilnPaePpllmrdtvyalv.eeadeeaieas 217 ivas+as saGpgtranideft+tts+++e++gGa++gkaiiilnPa+Pp++mrdt+++++ e+ad++ai++s NCBI__GCF_002893965.1:WP_050655875.1 149 IVASVASLSAGPGTRANIDEFTKTTSRGIETIGGAQRGKAIIILNPADPPMIMRDTIFCAIpEDADQAAITDS 221 ************************************************************99*********** PP TIGR03215 218 veemveevqkyvpGyrlkqevvld........gekvsvlleveGagdylPkyaGnldiltaaalavaeklaee 282 ++++v+++q+yvpGyrl +e+++d v++++eveGagd+lP yaGnldi+taaa++v+e++a++ NCBI__GCF_002893965.1:WP_050655875.1 222 IHRVVKDIQQYVPGYRLLNEPQFDepsvvsggYATVTTFVEVEGAGDFLPPYAGNLDIMTAAATKVGEEIAQK 294 *****************************985567************************************99 PP TIGR03215 283 ll 284 ll NCBI__GCF_002893965.1:WP_050655875.1 295 LL 296 86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (300 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.46 // [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