Alignments for a candidate for ald-dh-CoA in Desulfitobacterium hafniense DCB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Desulfitobacterium hafniense DCB-2

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_011462303.1 DHAF_RS24440 acetaldehyde dehydrogenase (acetylating)

Query= metacyc::STM2463-MONOMER
         (467 letters)



>NCBI__GCF_000021925.1:WP_011462303.1
          Length = 513

 Score =  169 bits (427), Expect = 3e-46
 Identities = 126/403 (31%), Positives = 201/403 (49%), Gaps = 28/403 (6%)

Query: 43  AKRAQQGLKSVAMRQLAIHAIREAGE--KHARELAELAVSETGMGRVDDKFAKNV----- 95
           A+ AQ+ L + +  +L     R AGE  K+ARELA ++  ETG G+  DK+ KN+     
Sbjct: 21  AREAQKALATFSQEKLDRIVERMAGEVVKYARELAMMSHEETGFGKWQDKYIKNIFASDF 80

Query: 96  --AQARGTPGVECLSPQVLTGDNGLTLIENAPWGVVASVTPSTNPAATVINNAISLIAAG 153
              + R    V  ++          TL    P GV+ ++ PSTNP +T I   +  I +G
Sbjct: 81  LCKKIRKMKVVGIIAED----KENQTLDVGVPVGVIVALLPSTNPVSTAIYKTLIAIKSG 136

Query: 154 NSVVFAPHPAAKKVSQRAITLLNQAVVAAGGPENLLVTVANPDIETAQRLFKYPGIGLLV 213
           N++VF+PHP AKK ++R + +L +   A+G P   +       +E    L  +    L++
Sbjct: 137 NAIVFSPHPKAKKTTRRVLEILVRTAEASGLPCGAIGYQRTQALEGTLGLMNHKDTALII 196

Query: 214 VTGGEAVVDAARKHTNKRLIAAGAGNPPVVVDETADLPRAAQSIVKGASFDNNIICADEK 273
           VTG   +V AA     K  I  G GN P  ++ +AD+ +A   I+   +FD+ I+ A E+
Sbjct: 197 VTGVPKLVKAAYA-AGKPTIYGGPGNGPAFIERSADIKQAVADIITSRTFDHGIVSASEQ 255

Query: 274 VLIVVDSVADELMRLMEGQHAVKLTAAQAEQLQPVLLKNIDERGKGTVSRDWVGRDAGKI 333
            ++  + +ADE+ + + G     L+  +AEQL  + L     R  G+V+ D VG+ A ++
Sbjct: 256 SVVAEECIADEVRQELRGNGGYFLSEEEAEQLGKLFL-----RPDGSVNPDIVGKSAVEL 310

Query: 334 AAAIGLNVPDQTRLLFVE----TPANHPFAVTEMMMPVLPVVRVANVEEAIALAVQ--LE 387
           A  IG+ V + T++L  E    +P N P+A  E + PVL      +   A    ++  L 
Sbjct: 311 ARKIGITVSENTKVLISEQKFVSPTN-PYA-KEKLCPVLAFYVEKDWFNACEKCIELLLN 368

Query: 388 GGCHHTAAMHSRNIDNMNQMANAIDTSIFVKNGPCIAGLGLGG 430
            G  HT  +HSRN   + + A     S  + N P   G G+GG
Sbjct: 369 DGRGHTLVIHSRNEQVIREFALKKPVSRVLVNTPATLG-GIGG 410


Lambda     K      H
   0.317    0.131    0.370 

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: 483
Number of extensions: 26
Number of successful extensions: 5
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: 467
Length of database: 513
Length adjustment: 34
Effective length of query: 433
Effective length of database: 479
Effective search space:   207407
Effective search space used:   207407
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_011462303.1 DHAF_RS24440 (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.14464.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.2e-199  647.6   0.1   8.7e-199  647.3   0.1    1.0  1  lcl|NCBI__GCF_000021925.1:WP_011462303.1  DHAF_RS24440 acetaldehyde dehydr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_011462303.1  DHAF_RS24440 acetaldehyde dehydrogenase (acetylating)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  647.3   0.1  8.7e-199  8.7e-199       1     482 [.       5     506 ..       5     509 .. 0.94

  Alignments for each domain:
  == domain 1  score: 647.3 bits;  conditional E-value: 8.7e-199
                                 TIGR02518   1 dkdllsiqevrnlirsakvaqkklaalsqeqidkivkaivdaaeenavklakmaneetGfGkvedkvlk 69 
                                               d+dll+iqe+r li++a++aqk la++sqe++d+iv+ ++ +  + a +la m++eetGfGk++dk +k
  lcl|NCBI__GCF_000021925.1:WP_011462303.1   5 DNDLLAIQEARILIENAREAQKALATFSQEKLDRIVERMAGEVVKYARELAMMSHEETGFGKWQDKYIK 73 
                                               89******************************************************************* PP

                                 TIGR02518  70 nklaakivydsikdmktvGileedkekkvievavpvGvvaglvpstnptstaiyktlisikarnaivls 138
                                               n +a+ ++ + i+ mk vGi+ edke++ ++v+vpvGv+++l+pstnp staiyktli+ik++naiv+s
  lcl|NCBI__GCF_000021925.1:WP_011462303.1  74 NIFASDFLCKKIRKMKVVGIIAEDKENQTLDVGVPVGVIVALLPSTNPVSTAIYKTLIAIKSGNAIVFS 142
                                               ********************************************************************* PP

                                 TIGR02518 139 phpaakkciietvklirkaaekaGapegiiasltvptiegtnelmknkdtslilatGGeamvkaayssG 207
                                               php+akk++ +  +++  +ae++G p g+i+   + ++egt  lm +kdt+li+ tG + +vkaay++G
  lcl|NCBI__GCF_000021925.1:WP_011462303.1 143 PHPKAKKTTRRVLEILVRTAEASGLPCGAIGYQRTQALEGTLGLMNHKDTALIIVTGVPKLVKAAYAAG 211
                                               ********************************************************************* PP

                                 TIGR02518 208 kpaiGvGpGngpayieksanvkkavkkildsktfdnGticaseqsvvvekvnkdavveelkkqGayflt 276
                                               kp+i  GpGngpa+ie+sa++k+av +i+ s+tfd+G++ aseqsvv e++  d+v +el+ +G+yfl+
  lcl|NCBI__GCF_000021925.1:WP_011462303.1 212 KPTIYGGPGNGPAFIERSADIKQAVADIITSRTFDHGIVSASEQSVVAEECIADEVRQELRGNGGYFLS 280
                                               ********************************************************************* PP

                                 TIGR02518 277 eeeaeklgklilrangtmnpkivGksaqeiaklaGltvpedvkvliakenkvgkknpysreklttilaf 345
                                               eeeae+lgkl lr++g++np+ivGksa e+a+  G+tv+e+ kvli+++  v+ +npy++ekl+++laf
  lcl|NCBI__GCF_000021925.1:WP_011462303.1 281 EEEAEQLGKLFLRPDGSVNPDIVGKSAVELARKIGITVSENTKVLISEQKFVSPTNPYAKEKLCPVLAF 349
                                               ********************************************************************* PP

                                 TIGR02518 346 yveedveeacelsielleneGaGhtliihsedkdivrefalkkpvsrllvntgGslGGiGattnlvpal 414
                                               yve+d+ +ace++iell n+G Ghtl+ihs++++++refalkkpvsr+lvnt+ +lGGiG ttnl pal
  lcl|NCBI__GCF_000021925.1:WP_011462303.1 350 YVEKDWFNACEKCIELLLNDGRGHTLVIHSRNEQVIREFALKKPVSRVLVNTPATLGGIGGTTNLFPAL 418
                                               ********************************************************************* PP

                                 TIGR02518 415 tlGcGavGGsstsdnitpenlinirrvavGvkeledlrkeentfatikvasnldvv............. 470
                                               tlGcGavGG  tsdn++p+nlinir+v +Gv++led+    +      v s++++              
  lcl|NCBI__GCF_000021925.1:WP_011462303.1 419 TLGCGAVGGGFTSDNVSPLNLINIRKVGYGVRKLEDITCGVQA---ESVGSSESAGltrltglngslcp 484
                                               *************************************854443...22222222222344566677777 PP

                                 TIGR02518 471 ..........dkeelieslvkk 482
                                                         d +el+e+l+++
  lcl|NCBI__GCF_000021925.1:WP_011462303.1 485 gpgypkertqDLNELLETLLEQ 506
                                               7777665555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (488 nodes)
Target sequences:                          1  (513 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: 12.47
//
[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