Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_015945521.1 DHAF_RS24370 acetaldehyde dehydrogenase (acetylating)
Query= BRENDA::B0K315 (466 letters) >NCBI__GCF_000021925.1:WP_015945521.1 Length = 495 Score = 223 bits (568), Expect = 1e-62 Identities = 142/431 (32%), Positives = 231/431 (53%), Gaps = 14/431 (3%) Query: 33 DLGIFNDVNEAVECAKEAQKKFALMDLEKREEIIAAIREACVNNARLLAEIACSETGRGR 92 DL + AK+AQ + A + E+ ++II + + NA LA++A ETG G+ Sbjct: 7 DLQSVQETRNLARQAKQAQTELAQFNSEQIDKIIRNMVKVAEENAVALAKLAVEETGFGK 66 Query: 93 VEDKVAKNILAAKKTPGTEDLKPTAWTG----DRGLTLVEMA-PVGVIASITPVTNPTAT 147 VEDKV KN A+ T + +KP G D+ ++E+A PVG++ I P TNPT+T Sbjct: 67 VEDKVFKNRFAS--TELYQFIKPMQTIGVIKEDKINKVMEIAEPVGLLMGIVPSTNPTST 124 Query: 148 IINNTISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQTAQ 207 I ++ + A N +VF+PHPSA K + +A +++N+A + GAP ++ I+ P++ Sbjct: 125 TIYKSLIAIKARNGIVFSPHPSALKCTLEAAKLMNDAAVAAGAPANIIGCISKPSMNATN 184 Query: 208 KLMEHPEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIACGAS 267 +LM+ EV M++ TGG A+V+ A GK +G G GN P ++ TADI KA +I + Sbjct: 185 ELMKCDEVAMIIATGGSAMVKAAYSAGKPALGVGPGNVPAYIERTADIPKAVRNIIASKT 244 Query: 268 FDNNLPCIAEKEIIAVERIADTLLERMKREGAYVLHGKDIDRMTELIF-QGGAINKDLIG 326 FDN C +E+ ++ E I + ++E KR+G Y + ++ +++ +F +G A+N ++G Sbjct: 245 FDNGTICASEQSVVVEECIRNQVMEEFKRQGGYFMTPEETEQVGRKLFNRGHAMNAKMVG 304 Query: 327 RDAHFILSQIGIETGKDIRLVV---MPVDVSHPLVYHEQLMPVIPFVTVPTVEEAINLAV 383 R A I + GI ++++ V +PL Y E+L V+ F TV EA +L + Sbjct: 305 RSAADIAAGAGISIPPGTKVLLGEQQGVGEQYPLSY-EKLTTVLAFYTVKDWHEACDLCM 363 Query: 384 KA--EGGNRHTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIGFGGEGYTTFTIAGPT 441 K GG H+ +H++N E FA I V A ++ G+G FT+ T Sbjct: 364 KLLNNGGVGHSLSIHTENPEMAIKFAEKPVFRILVNTASTHGGVGVSTGLAPAFTLGCGT 423 Query: 442 GEGLTSARTFT 452 G ++ T Sbjct: 424 WGGSATSDNVT 434 Lambda K H 0.317 0.133 0.377 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: 510 Number of extensions: 28 Number of successful extensions: 4 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: 466 Length of database: 495 Length adjustment: 34 Effective length of query: 432 Effective length of database: 461 Effective search space: 199152 Effective search space used: 199152 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: 51 (24.3 bits)
Align candidate WP_015945521.1 DHAF_RS24370 (acetaldehyde dehydrogenase (acetylating))
to HMM TIGR02518 (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/TIGR02518.hmm # target sequence database: /tmp/gapView.17527.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02518 [M=488] Accession: TIGR02518 Description: EutH_ACDH: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-226 739.2 7.9 1.3e-226 739.0 7.9 1.0 1 lcl|NCBI__GCF_000021925.1:WP_015945521.1 DHAF_RS24370 acetaldehyde dehydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_015945521.1 DHAF_RS24370 acetaldehyde dehydrogenase (acetylating) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 739.0 7.9 1.3e-226 1.3e-226 1 487 [. 5 489 .. 5 490 .. 0.96 Alignments for each domain: == domain 1 score: 739.0 bits; conditional E-value: 1.3e-226 TIGR02518 1 dkdllsiqevrnlirsakvaqkklaalsqeqidkivkaivdaaeenavklakmaneetGfGkvedkvlk 69 d dl+s+qe+rnl+r+ak+aq +la++ eqidki++++v++aeenav lak a+eetGfGkvedkv+k lcl|NCBI__GCF_000021925.1:WP_015945521.1 5 DYDLQSVQETRNLARQAKQAQTELAQFNSEQIDKIIRNMVKVAEENAVALAKLAVEETGFGKVEDKVFK 73 78******************************************************************* PP TIGR02518 70 nklaakivydsikdmktvGileedkekkvievavpvGvvaglvpstnptstaiyktlisikarnaivls 138 n++a++ +y+ ik m+t+G+++edk +kv+e+a+pvG+++g+vpstnptst+iyk+li+ikarn iv+s lcl|NCBI__GCF_000021925.1:WP_015945521.1 74 NRFASTELYQFIKPMQTIGVIKEDKINKVMEIAEPVGLLMGIVPSTNPTSTTIYKSLIAIKARNGIVFS 142 ********************************************************************* PP TIGR02518 139 phpaakkciietvklirkaaekaGapegiiasltvptiegtnelmknkdtslilatGGeamvkaayssG 207 php+a kc++e++kl+++aa++aGap +ii+++ p++++tnelmk +++++i+atGG+amvkaays+G lcl|NCBI__GCF_000021925.1:WP_015945521.1 143 PHPSALKCTLEAAKLMNDAAVAAGAPANIIGCISKPSMNATNELMKCDEVAMIIATGGSAMVKAAYSAG 211 ********************************************************************* PP TIGR02518 208 kpaiGvGpGngpayieksanvkkavkkildsktfdnGticaseqsvvvekvnkdavveelkkqGayflt 276 kpa+GvGpGn payie++a+++kav++i+ sktfdnGticaseqsvvve++ +++v+ee+k+qG+yf+t lcl|NCBI__GCF_000021925.1:WP_015945521.1 212 KPALGVGPGNVPAYIERTADIPKAVRNIIASKTFDNGTICASEQSVVVEECIRNQVMEEFKRQGGYFMT 280 ********************************************************************* PP TIGR02518 277 eeeaeklgklilrangtmnpkivGksaqeiaklaGltvpedvkvliakenkvgkknpysreklttilaf 345 ee+e++g+ ++ +++mn+k+vG+sa +ia aG+++p kvl++++++vg+++p+s+ekltt+laf lcl|NCBI__GCF_000021925.1:WP_015945521.1 281 PEETEQVGRKLFNRGHAMNAKMVGRSAADIAAGAGISIPPGTKVLLGEQQGVGEQYPLSYEKLTTVLAF 349 ********************************************************************* PP TIGR02518 346 yveedveeacelsielleneGaGhtliihsedkdivrefalkkpvsrllvntgGslGGiGattnlvpal 414 y+++d++eac+l+++ll+n G+Gh+l+ih+e+ ++ +fa +kpv r+lvnt+ + GG+G +t+l+pa+ lcl|NCBI__GCF_000021925.1:WP_015945521.1 350 YTVKDWHEACDLCMKLLNNGGVGHSLSIHTENPEMAIKFA-EKPVFRILVNTASTHGGVGVSTGLAPAF 417 ****************************************.**************************** PP TIGR02518 415 tlGcGavGGsstsdnitpenlinirrvavGvkeledlrkee.ntfatikvasnldvvdkeelieslvkk 482 tlGcG++GGs+tsdn+tp++lini+rva+G+k++++ + + +t+++++ + +e+ i+ lv++ lcl|NCBI__GCF_000021925.1:WP_015945521.1 418 TLGCGTWGGSATSDNVTPMHLINIKRVAYGIKDVTENGNSSyATGDAQQGG--SGGTVSEDRIQALVNE 484 *********************************988664331343333333..334456669******9 PP TIGR02518 483 iiael 487 +++ l lcl|NCBI__GCF_000021925.1:WP_015945521.1 485 VMSLL 489 98766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (488 nodes) Target sequences: 1 (495 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 6.76 // [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