GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ald-dh-CoA in Klebsiella michiganensis M5al

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate BWI76_RS03590 BWI76_RS03590 acetaldehyde dehydrogenase (acetylating)

Query= BRENDA::B0K315
         (466 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS03590 BWI76_RS03590 acetaldehyde
           dehydrogenase (acetylating)
          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.20842.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.62
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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