Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate BWI76_RS03590 BWI76_RS03590 acetaldehyde dehydrogenase (acetylating)
Query= BRENDA::B0K315 (466 letters) >FitnessBrowser__Koxy:BWI76_RS03590 Length = 533 Score = 198 bits (503), Expect = 4e-55 Identities = 131/415 (31%), Positives = 210/415 (50%), Gaps = 13/415 (3%) Query: 28 EKDNPDLGIFNDVNEAVECAKEAQKKFALMDLEKREEIIAAIREACVNNARLLAEIACSE 87 E DN DL + E V AK+AQ A ++ + I+ + + ++A LA++A E Sbjct: 3 ELDN-DLQSRQNARELVRNAKKAQAILATFSQQQIDAIVKNVAQEAAHHAEALAKMAAEE 61 Query: 88 TGRGRVEDKVAKNILAAKKT-PGTEDLKPTAWTGDRGLTLVEMA--PVGVIASITPVTNP 144 TG G +DKV KN A+ + +D+K D + V P+GVI ++ P TNP Sbjct: 62 TGFGNWQDKVLKNRFASLRVYDAIKDMKTVGIIHDDQVQKVMDVGVPLGVICALVPSTNP 121 Query: 145 TATIINNTISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQ 204 T+T+I T+ L AGNA++F+PHP A++ S KA+EI+ A GAP G V +I+ T++ Sbjct: 122 TSTVIYKTLIALKAGNAIIFSPHPGARQCSWKAIEIVKRAAEAAGAPAGSVDAISQLTLE 181 Query: 205 TAQKLMEHPEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIAC 264 +LM +V++++ TGG+ +V+ A G I G GN P ++ +ADI A DI Sbjct: 182 ATSELMHSKDVSLILATGGEGMVRAAYASGTPTISGGPGNGPAFIERSADIPHAVKDIIT 241 Query: 265 GASFDNNLPCIAEKEIIAVERIADTLLERMKREGAYVLHGKDIDRMTELIFQ-GGAINKD 323 +FDN + C +E+ II I D + ++ +GAY ++ + +M L+ + G IN Sbjct: 242 SKTFDNGVICASEQSIIVERCIYDEVHRELEAQGAYFMNESEAAKMAALLLRPNGTINPK 301 Query: 324 LIGRDAHFILSQIGIETGKDIR-LVVMPVDVSHPLVY-HEQLMPVIPFVTVPTVEEAINL 381 ++G+ A ++ G R L+ VSH Y E+L PV+ + A Sbjct: 302 VVGKTALYLSQMAGFCVPASTRVLIAEQTTVSHTNPYSREKLCPVLGLYVEEDWKAACQR 361 Query: 382 AVK--AEGGNRHTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIGFGGEGYTT 434 V+ G HT ++H++N + + F + N P+ GG G TT Sbjct: 362 VVELLTNEGLGHTLVIHTRNQDVIRQFCLEKPVNRILINTPA----ALGGIGATT 412 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: 550 Number of extensions: 30 Number of successful extensions: 3 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: 533 Length adjustment: 34 Effective length of query: 432 Effective length of database: 499 Effective search space: 215568 Effective search space used: 215568 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: 52 (24.6 bits)
Align candidate BWI76_RS03590 BWI76_RS03590 (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.26856.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-220 718.2 2.0 3.2e-220 718.0 2.0 1.1 1 lcl|FitnessBrowser__Koxy:BWI76_RS03590 BWI76_RS03590 acetaldehyde dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS03590 BWI76_RS03590 acetaldehyde dehydrogenase (acetylating) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 718.0 2.0 3.2e-220 3.2e-220 1 453 [. 5 457 .. 5 531 .. 0.96 Alignments for each domain: == domain 1 score: 718.0 bits; conditional E-value: 3.2e-220 TIGR02518 1 dkdllsiqevrnlirsakvaqkklaalsqeqidkivkaivdaaeenavklakmaneetGfGkvedkvlknk 71 d+dl+s q++r+l+r+ak+aq la++sq+qid ivk+++++a ++a+ lakma eetGfG ++dkvlkn+ lcl|FitnessBrowser__Koxy:BWI76_RS03590 5 DNDLQSRQNARELVRNAKKAQAILATFSQQQIDAIVKNVAQEAAHHAEALAKMAAEETGFGNWQDKVLKNR 75 89********************************************************************* PP TIGR02518 72 laakivydsikdmktvGileedkekkvievavpvGvvaglvpstnptstaiyktlisikarnaivlsphpa 142 +a+ vyd+ikdmktvGi+++d+++kv++v+vp+Gv+ +lvpstnptst+iyktli++ka+nai++sphp lcl|FitnessBrowser__Koxy:BWI76_RS03590 76 FASLRVYDAIKDMKTVGIIHDDQVQKVMDVGVPLGVICALVPSTNPTSTVIYKTLIALKAGNAIIFSPHPG 146 *********************************************************************** PP TIGR02518 143 akkciietvklirkaaekaGapegiiasltvptiegtnelmknkdtslilatGGeamvkaayssGkpaiGv 213 a++c +++++++ aae+aGap g + ++ +t+e+t elm +kd+slilatGGe+mv+aay+sG+p+i lcl|FitnessBrowser__Koxy:BWI76_RS03590 147 ARQCSWKAIEIVKRAAEAAGAPAGSVDAISQLTLEATSELMHSKDVSLILATGGEGMVRAAYASGTPTISG 217 *********************************************************************** PP TIGR02518 214 GpGngpayieksanvkkavkkildsktfdnGticaseqsvvvekvnkdavveelkkqGayflteeeaeklg 284 GpGngpa+ie+sa++++avk+i+ sktfdnG+icaseqs++ve++ d+v +el qGayf+ e ea k++ lcl|FitnessBrowser__Koxy:BWI76_RS03590 218 GPGNGPAFIERSADIPHAVKDIITSKTFDNGVICASEQSIIVERCIYDEVHRELEAQGAYFMNESEAAKMA 288 *********************************************************************** PP TIGR02518 285 klilrangtmnpkivGksaqeiaklaGltvpedvkvliakenkvgkknpysreklttilafyveedveeac 355 l+lr+ngt+npk+vGk+a ++++aG+ vp++ +vlia++++v+++npysrekl+++l +yveed+++ac lcl|FitnessBrowser__Koxy:BWI76_RS03590 289 ALLLRPNGTINPKVVGKTALYLSQMAGFCVPASTRVLIAEQTTVSHTNPYSREKLCPVLGLYVEEDWKAAC 359 *********************************************************************** PP TIGR02518 356 elsielleneGaGhtliihsedkdivrefalkkpvsrllvntgGslGGiGattnlvpaltlGcGavGGsst 426 ++ +ell+neG Ghtl+ih++++d++r+f l+kpv r+l+nt+ +lGGiGattn++paltlGcGavGG s+ lcl|FitnessBrowser__Koxy:BWI76_RS03590 360 QRVVELLTNEGLGHTLVIHTRNQDVIRQFCLEKPVNRILINTPAALGGIGATTNITPALTLGCGAVGGGSS 430 *********************************************************************** PP TIGR02518 427 sdnitpenlinirrvavGvkeledlrk 453 sdn++p+nl+nir+v +Gv+ +++lr lcl|FitnessBrowser__Koxy:BWI76_RS03590 431 SDNVGPMNLLNIRKVGYGVRSIDELRA 457 ***********************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (488 nodes) Target sequences: 1 (533 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: 00:00:00.02 # Mc/sec: 10.97 // [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