Alignments for a candidate for ald-dh-CoA in Photobacterium jeanii R-40508

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Photobacterium jeanii R-40508

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_068333577.1 A3K86_RS16475 acetaldehyde dehydrogenase (acetylating)

Query= BRENDA::B0K315
         (466 letters)



>NCBI__GCF_001650345.1:WP_068333577.1
          Length = 563

 Score =  202 bits (515), Expect = 2e-56
 Identities = 132/430 (30%), Positives = 221/430 (51%), Gaps = 20/430 (4%)

Query: 33  DLGIFNDVNEAVECAKEAQKKFALMDLEKREEIIAAIREACVNNARLLAEIACSETGRGR 92
           DL       E V+ AK AQ++FA +  ++ ++I+A I      +A  LA+ A  ETG GR
Sbjct: 6   DLQSIQAARELVKNAKNAQRQFAKLSQQQVDKIVAHIAAEAARHAEPLAKAAHEETGFGR 65

Query: 93  VEDKVAKNILAAKKT-PGTEDLKPTAWTGDRGLTLVEMA--PVGVIASITPVTNPTATII 149
            +DKV KN+ A+ +      D+K      D     V     P+GVI ++ P TNPT+TI 
Sbjct: 66  WQDKVLKNLFASTQVHEHIRDMKTVGIIADDSANKVMDVGVPLGVITALVPSTNPTSTIF 125

Query: 150 NNTISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQTAQKL 209
             T+  L AGNA++F+PHP+AK  S +A+E++  A  + GAP G+V  +   T+Q  + L
Sbjct: 126 YKTLIALKAGNAIIFSPHPNAKVCSQQAIEVVKRAAQEAGAPAGIVDGVTLLTMQATETL 185

Query: 210 MEHPEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIACGASFD 269
           M+  +V++++ TGG+ +V+ A   G   I  G GN P  ++ +A++ +A  DI    +FD
Sbjct: 186 MKSKDVSLILATGGEGMVRAAYASGTPTISGGPGNGPAFIERSANVPQAVKDIITSKTFD 245

Query: 270 NNLPCIAEKEIIAVERIADTLLERMKREGAYVLHGKDIDRMTELIFQ-GGAINKDLIGRD 328
           N + C +E+ II    I D + + + R+GAY+++ ++ +++  L+ +  G IN +++G+ 
Sbjct: 246 NGVICASEQSIIVERCIYDQVHQELIRQGAYLMNEQESEKLAALLLRPNGMINPEMVGQC 305

Query: 329 AHFILSQIGIETGKDIRLVVMPVDVSHPL--VYHEQLMPVIPFVTVPTVEE------AIN 380
           A  +  + G        ++V P     P      E+L PV+       VEE      A  
Sbjct: 306 ALTVAQKAGFSVPAHTTVLVSPQTTVSPKNPYSREKLCPVLGLY----VEEDWHTACARV 361

Query: 381 LAVKAEGGNRHTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIGFGGEGYTTFTI--- 437
           + +    G  HT ++H++N + +  FA        + N P+  G G G     T  +   
Sbjct: 362 MELLTNEGMGHTLVIHTQNTDIVREFALEKPVFRMLVNTPAALG-GIGATSNLTPALTLG 420

Query: 438 AGPTGEGLTS 447
            G  G G +S
Sbjct: 421 CGALGGGSSS 430


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: 603
Number of extensions: 33
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 466
Length of database: 563
Length adjustment: 35
Effective length of query: 431
Effective length of database: 528
Effective search space:   227568
Effective search space used:   227568
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_068333577.1 A3K86_RS16475 (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.2661166.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-218  710.4   4.1   7.3e-218  710.2   4.1    1.1  1  NCBI__GCF_001650345.1:WP_068333577.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001650345.1:WP_068333577.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  710.2   4.1  7.3e-218  7.3e-218       1     465 [.       4     468 ..       4     561 .. 0.94

  Alignments for each domain:
  == domain 1  score: 710.2 bits;  conditional E-value: 7.3e-218
                             TIGR02518   1 dkdllsiqevrnlirsakvaqkklaalsqeqidkivkaivdaaeenavklakmaneetGfGkvedkvlknkla 73 
                                           dkdl+siq +r+l+++ak+aq+++a+lsq+q+dkiv  i+ +a  +a+ lak a+eetGfG+++dkvlkn +a
  NCBI__GCF_001650345.1:WP_068333577.1   4 DKDLQSIQAARELVKNAKNAQRQFAKLSQQQVDKIVAHIAAEAARHAEPLAKAAHEETGFGRWQDKVLKNLFA 76 
                                           9************************************************************************ PP

                             TIGR02518  74 akivydsikdmktvGileedkekkvievavpvGvvaglvpstnptstaiyktlisikarnaivlsphpaakkc 146
                                           ++ v++ i+dmktvGi+ +d  +kv++v+vp+Gv+++lvpstnptst+ yktli++ka+nai++sphp+ak c
  NCBI__GCF_001650345.1:WP_068333577.1  77 STQVHEHIRDMKTVGIIADDSANKVMDVGVPLGVITALVPSTNPTSTIFYKTLIALKAGNAIIFSPHPNAKVC 149
                                           ************************************************************************* PP

                             TIGR02518 147 iietvklirkaaekaGapegiiasltvptiegtnelmknkdtslilatGGeamvkaayssGkpaiGvGpGngp 219
                                             +++++++ aa++aGap gi+  +t +t+++t+ lmk+kd+slilatGGe+mv+aay+sG+p+i  GpGngp
  NCBI__GCF_001650345.1:WP_068333577.1 150 SQQAIEVVKRAAQEAGAPAGIVDGVTLLTMQATETLMKSKDVSLILATGGEGMVRAAYASGTPTISGGPGNGP 222
                                           ************************************************************************* PP

                             TIGR02518 220 ayieksanvkkavkkildsktfdnGticaseqsvvvekvnkdavveelkkqGayflteeeaeklgklilrang 292
                                           a+ie+sanv++avk+i+ sktfdnG+icaseqs++ve++  d+v +el +qGay++ e+e+ekl+ l+lr+ng
  NCBI__GCF_001650345.1:WP_068333577.1 223 AFIERSANVPQAVKDIITSKTFDNGVICASEQSIIVERCIYDQVHQELIRQGAYLMNEQESEKLAALLLRPNG 295
                                           ************************************************************************* PP

                             TIGR02518 293 tmnpkivGksaqeiaklaGltvpedvkvliakenkvgkknpysreklttilafyveedveeacelsiellene 365
                                            +np++vG+ a ++a+ aG++vp++  vl++ +++v+ knpysrekl+++l +yveed++ ac + +ell+ne
  NCBI__GCF_001650345.1:WP_068333577.1 296 MINPEMVGQCALTVAQKAGFSVPAHTTVLVSPQTTVSPKNPYSREKLCPVLGLYVEEDWHTACARVMELLTNE 368
                                           ************************************************************************* PP

                             TIGR02518 366 GaGhtliihsedkdivrefalkkpvsrllvntgGslGGiGattnlvpaltlGcGavGGsstsdnitpenlini 438
                                           G+Ghtl+ih+++ divrefal+kpv r+lvnt+ +lGGiGat nl+paltlGcGa+GG s+sdn++p+nl+n+
  NCBI__GCF_001650345.1:WP_068333577.1 369 GMGHTLVIHTQNTDIVREFALEKPVFRMLVNTPAALGGIGATSNLTPALTLGCGALGGGSSSDNVGPMNLLNV 441
                                           ************************************************************************* PP

                             TIGR02518 439 rrvavGvkeledlrkeentfatikvas 465
                                           r+v +Gv+ +e+lr+ ++ +a++ +a+
  NCBI__GCF_001650345.1:WP_068333577.1 442 RKVGYGVRSIEELRQPTAPAASVSAAT 468
                                           **************9988866655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (488 nodes)
Target sequences:                          1  (563 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 18.65
//
[ok]

This GapMind analysis is from Sep 24 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:

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 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