Alignments for a candidate for ald-dh-CoA in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Klebsiella variicola At-22

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_012969030.1 KVAR_RS22530 acetaldehyde dehydrogenase (acetylating)

Query= BRENDA::B0K315
         (466 letters)



>NCBI__GCF_000025465.1:WP_012969030.1
          Length = 533

 Score =  191 bits (486), Expect = 4e-53
 Identities = 125/415 (30%), Positives = 207/415 (49%), 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  TGFGNWQDKVLKNRFASLRVYDAIKDMKTVGIIHDDPVKKVMDVGVPLGVICALVPSTNP 121

Query: 145 TATIINNTISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQ 204
           T+T+I   +  L AGNA++F+PHP A++ S KA+EI+  A    GAP G V  I   T++
Sbjct: 122 TSTVIYKALIALKAGNAIIFSPHPGARQCSWKAIEIVKRAAEAAGAPEGCVDGITQLTLE 181

Query: 205 TAQKLMEHPEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIAC 264
              +LM   +V++++ TGG+ +V+ A   G   I  G GN P  ++ +ADI  A  DI  
Sbjct: 182 ATSELMHSKDVSLILATGGEGMVRAAYASGTPTISGGPGNGPAFIERSADIHHAVKDIIT 241

Query: 265 GASFDNNLPCIAEKEIIAVERIADTLLERMKREGAYVLHGKDIDRMTELIFQ-GGAINKD 323
             +FDN + C +E+ II    I D +   ++ +GAY ++  +  +M  L+ +  G IN  
Sbjct: 242 SKTFDNGVICASEQSIIVEGCIYDEVHRELEAQGAYFMNEDEAAKMAALLLRPNGTINPK 301

Query: 324 LIGRDAHFILSQIGIETGKDIRLVVMPVDVSHPL--VYHEQLMPVIPFVTVPTVEEAINL 381
           ++G+ A ++    G       ++++       P      E+L PV+        + A + 
Sbjct: 302 VVGKTALYLSQMAGFCVPASTKVLIAEQTTVSPKNPYSREKLCPVLGLYVAEDWKAACHR 361

Query: 382 AVK--AEGGNRHTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIGFGGEGYTT 434
            V+     G  HT ++H++N + +  F+        + N P+      GG G TT
Sbjct: 362 VVELLTNEGLGHTLVIHTRNQDVIRQFSLEKPVNRILINTPA----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: 537
Number of extensions: 31
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 WP_012969030.1 KVAR_RS22530 (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.843148.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-220  717.0   0.9     8e-220  716.7   0.9    1.1  1  NCBI__GCF_000025465.1:WP_012969030.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_012969030.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.7   0.9    8e-220    8e-220       1     453 [.       5     457 ..       5     531 .. 0.95

  Alignments for each domain:
  == domain 1  score: 716.7 bits;  conditional E-value: 8e-220
                             TIGR02518   1 dkdllsiqevrnlirsakvaqkklaalsqeqidkivkaivdaaeenavklakmaneetGfGkvedkvlknkla 73 
                                           d+dl+s q++r+l+r+ak+aq  la++sq+qid ivk+++++a ++a+ lakma eetGfG ++dkvlkn++a
  NCBI__GCF_000025465.1:WP_012969030.1   5 DNDLQSRQNARELVRNAKKAQAILATFSQQQIDAIVKNVAQEAAHHAEALAKMAAEETGFGNWQDKVLKNRFA 77 
                                           89*********************************************************************** PP

                             TIGR02518  74 akivydsikdmktvGileedkekkvievavpvGvvaglvpstnptstaiyktlisikarnaivlsphpaakkc 146
                                           +  vyd+ikdmktvGi+++d +kkv++v+vp+Gv+ +lvpstnptst+iyk+li++ka+nai++sphp a++c
  NCBI__GCF_000025465.1:WP_012969030.1  78 SLRVYDAIKDMKTVGIIHDDPVKKVMDVGVPLGVICALVPSTNPTSTVIYKALIALKAGNAIIFSPHPGARQC 150
                                           ************************************************************************* PP

                             TIGR02518 147 iietvklirkaaekaGapegiiasltvptiegtnelmknkdtslilatGGeamvkaayssGkpaiGvGpGngp 219
                                             +++++++ aae+aGapeg +  +t +t+e+t elm +kd+slilatGGe+mv+aay+sG+p+i  GpGngp
  NCBI__GCF_000025465.1:WP_012969030.1 151 SWKAIEIVKRAAEAAGAPEGCVDGITQLTLEATSELMHSKDVSLILATGGEGMVRAAYASGTPTISGGPGNGP 223
                                           ************************************************************************* PP

                             TIGR02518 220 ayieksanvkkavkkildsktfdnGticaseqsvvvekvnkdavveelkkqGayflteeeaeklgklilrang 292
                                           a+ie+sa++++avk+i+ sktfdnG+icaseqs++ve +  d+v +el  qGayf+ e+ea k++ l+lr+ng
  NCBI__GCF_000025465.1:WP_012969030.1 224 AFIERSADIHHAVKDIITSKTFDNGVICASEQSIIVEGCIYDEVHRELEAQGAYFMNEDEAAKMAALLLRPNG 296
                                           ************************************************************************* PP

                             TIGR02518 293 tmnpkivGksaqeiaklaGltvpedvkvliakenkvgkknpysreklttilafyveedveeacelsiellene 365
                                           t+npk+vGk+a  ++++aG+ vp++ kvlia++++v+ knpysrekl+++l +yv+ed+++ac++ +ell+ne
  NCBI__GCF_000025465.1:WP_012969030.1 297 TINPKVVGKTALYLSQMAGFCVPASTKVLIAEQTTVSPKNPYSREKLCPVLGLYVAEDWKAACHRVVELLTNE 369
                                           ************************************************************************* PP

                             TIGR02518 366 GaGhtliihsedkdivrefalkkpvsrllvntgGslGGiGattnlvpaltlGcGavGGsstsdnitpenlini 438
                                           G Ghtl+ih++++d++r+f+l+kpv r+l+nt+ +lGGiGattn+ paltlGcGavGG s+sdn++p+nl+ni
  NCBI__GCF_000025465.1:WP_012969030.1 370 GLGHTLVIHTRNQDVIRQFSLEKPVNRILINTPAALGGIGATTNISPALTLGCGAVGGGSSSDNVGPMNLLNI 442
                                           ************************************************************************* PP

                             TIGR02518 439 rrvavGvkeledlrk 453
                                           r+v +Gv+ +++lr 
  NCBI__GCF_000025465.1:WP_012969030.1 443 RKVGYGVRSIDELRA 457
                                           ************985 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.44
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources