Alignments for a candidate for paaK in Marinomonas arctica 328

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Marinomonas arctica 328

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_111606234.1 DK187_RS04940 phenylacetate--CoA ligase

Query= SwissProt::O33469
         (439 letters)



>NCBI__GCF_003259225.1:WP_111606234.1
          Length = 439

 Score =  690 bits (1780), Expect = 0.0
 Identities = 327/427 (76%), Positives = 376/427 (88%)

Query: 12  LDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAECGAHPDDLTCLEDLAKFPFT 71
           LDPMETAS+D LR HQLERL+W+++HAY+NVP+Y+QRF + G HPDD+  L+DLAK PFT
Sbjct: 12  LDPMETASIDELRAHQLERLQWTVRHAYNNVPMYKQRFDQLGLHPDDIKTLDDLAKLPFT 71

Query: 72  GKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDINTWANVVARSIRAAGG 131
            K+DLRDNYPYGMFA P  +VVRLHASSGTTGKPTVVGYTQNDI+ WAN+VARSIRAAGG
Sbjct: 72  TKSDLRDNYPYGMFATPMNQVVRLHASSGTTGKPTVVGYTQNDIDNWANIVARSIRAAGG 131

Query: 132 RKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRDFQPDIIMVTPS 191
           RKGD +H +YGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQV+LI+DFQPDIIMVTPS
Sbjct: 132 RKGDMLHNAYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVRLIQDFQPDIIMVTPS 191

Query: 192 YMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRLGINALDIYGLSEIMGPG 251
           YMLNL DE+E+QGIDP  LKLRLGIFGAEPWT ELRRS+E+R GI A+DIYGLSEIMGPG
Sbjct: 192 YMLNLLDEMEKQGIDPLGLKLRLGIFGAEPWTQELRRSVEERAGIRAMDIYGLSEIMGPG 251

Query: 252 VAMECIETKDGPTIWEDHFYPEIIDPVTGEVLPDGQLGELVFTSLSKEALPMVRYRTRDL 311
           VAMEC E++DGPT+WEDHFYPEI+DP TGEVLPDG++GELVFTSLSKEALPM+RYRTRDL
Sbjct: 252 VAMECAESQDGPTVWEDHFYPEIVDPNTGEVLPDGEMGELVFTSLSKEALPMIRYRTRDL 311

Query: 312 TRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSEMYEIHLYRNGN 371
           TRLLPGTAR MRRI KITGRSDDM+IIRGVNVFPTQIEE+V+K+   SE YEIHLYR GN
Sbjct: 312 TRLLPGTARRMRRIDKITGRSDDMMIIRGVNVFPTQIEEEVIKVNHFSESYEIHLYRKGN 371

Query: 372 LDSVEVHVELRAECQHLDEGQRKLVIGELSKQIKTYIGISTQVHLQACGTLKRSEGKACH 431
           +DS++VHVELR +C   DE +    I EL   +K+ +GIS  V L+  G++ RSEGKA H
Sbjct: 372 MDSMDVHVELRPDCAGFDEQEINDAINELRHHVKSSVGISISVKLREIGSIARSEGKAKH 431

Query: 432 VYDKRLA 438
           VYD+R++
Sbjct: 432 VYDERIS 438


Lambda     K      H
   0.320    0.138    0.415 

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: 766
Number of extensions: 27
Number of successful extensions: 1
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: 439
Length of database: 439
Length adjustment: 32
Effective length of query: 407
Effective length of database: 407
Effective search space:   165649
Effective search space used:   165649
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_111606234.1 DK187_RS04940 (phenylacetate--CoA ligase)
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))

# 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/TIGR02155.hmm
# target sequence database:        /tmp/gapView.1083939.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02155  [M=422]
Accession:   TIGR02155
Description: PA_CoA_ligase: phenylacetate-CoA ligase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-222  723.4   0.0   3.8e-222  723.2   0.0    1.0  1  NCBI__GCF_003259225.1:WP_111606234.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003259225.1:WP_111606234.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  723.2   0.0  3.8e-222  3.8e-222       1     422 []      16     436 ..      16     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 723.2 bits;  conditional E-value: 3.8e-222
                             TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavp 73 
                                           e++s delra qlerl+++v++ay+nvp+y+++fd++g++pdd+k+l+dlak+p+t+ksdlrdnyp++++a+p
  NCBI__GCF_003259225.1:WP_111606234.1  16 ETASIDELRAHQLERLQWTVRHAYNNVPMYKQRFDQLGLHPDDIKTLDDLAKLPFTTKSDLRDNYPYGMFATP 88 
                                           799********************************************************************** PP

                             TIGR02155  74 rekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGa 146
                                           +++vvr+hassGttGkptvv+ytq+d+d+w+++vars+raaGGrkgd+lhnayGyGlftGGlG+hyGae+lG+
  NCBI__GCF_003259225.1:WP_111606234.1  89 MNQVVRLHASSGTTGKPTVVGYTQNDIDNWANIVARSIRAAGGRKGDMLHNAYGYGLFTGGLGAHYGAERLGC 161
                                           ************************************************************************* PP

                             TIGR02155 147 tvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearl 219
                                           tv+p+sGGqtekqv+liqdf+pdii+vtpsy+l+ll+e++++gidp    l+++i+Gaepwt+++r+ +e+r+
  NCBI__GCF_003259225.1:WP_111606234.1 162 TVIPMSGGQTEKQVRLIQDFQPDIIMVTPSYMLNLLDEMEKQGIDPLGLKLRLGIFGAEPWTQELRRSVEERA 234
                                           ************************************************************************* PP

                             TIGR02155 220 gikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryr 292
                                           gi+a+diyGlse++GpGva+ec e++dG+++wedhfypei+dp+tgevlpdGe Gelvft+l+kealp+iryr
  NCBI__GCF_003259225.1:WP_111606234.1 235 GIRAMDIYGLSEIMGPGVAMECAESQDGPTVWEDHFYPEIVDPNTGEVLPDGEMGELVFTSLSKEALPMIRYR 307
                                           ************************************************************************* PP

                             TIGR02155 293 trdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkve 365
                                           trdltrllpgtar mrr+dki+Grsdd++i+rGvnvfptq+ee ++k+++ s  y+++l r+G++d++ ++ve
  NCBI__GCF_003259225.1:WP_111606234.1 308 TRDLTRLLPGTARRMRRIDKITGRSDDMMIIRGVNVFPTQIEEEVIKVNHFSESYEIHLYRKGNMDSMDVHVE 380
                                           ************************************************************************* PP

                             TIGR02155 366 lkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                           l+++ a  +++e +    +++++++k+ vg+s++v+l e gs+ rseGkak v+d r
  NCBI__GCF_003259225.1:WP_111606234.1 381 LRPDCAGFDEQEIN-DAINELRHHVKSSVGISISVKLREIGSIARSEGKAKHVYDER 436
                                           ****9998866555.66799***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (439 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: 00:00:00.00
# Mc/sec: 23.06
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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