Alignments for a candidate for paaK in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Pseudomonas putida KT2440

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate PP_3279 PP_3279 phenylacetate-CoA ligase

Query= SwissProt::O33469
         (439 letters)



>FitnessBrowser__Putida:PP_3279
          Length = 439

 Score =  872 bits (2252), Expect = 0.0
 Identities = 426/439 (97%), Positives = 433/439 (98%)

Query: 1   MNMYHDADRALLDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAECGAHPDDLT 60
           MNMYHDADRALLDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAE G HPDDL 
Sbjct: 1   MNMYHDADRALLDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAEYGIHPDDLK 60

Query: 61  CLEDLAKFPFTGKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDINTWAN 120
           CLEDLAKFPFTGKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDI+TWAN
Sbjct: 61  CLEDLAKFPFTGKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDIDTWAN 120

Query: 121 VVARSIRAAGGRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRD 180
           VVARSIRAAGGRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRD
Sbjct: 121 VVARSIRAAGGRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRD 180

Query: 181 FQPDIIMVTPSYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRLGINALD 240
           F PDIIMVTPSYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQR+GINALD
Sbjct: 181 FHPDIIMVTPSYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRMGINALD 240

Query: 241 IYGLSEIMGPGVAMECIETKDGPTIWEDHFYPEIIDPVTGEVLPDGQLGELVFTSLSKEA 300
           IYGLSEIMGPGVAMECIETKDGPTIWEDHFYPEIIDP TGEVLPDGQLGELVFTSLSKEA
Sbjct: 241 IYGLSEIMGPGVAMECIETKDGPTIWEDHFYPEIIDPATGEVLPDGQLGELVFTSLSKEA 300

Query: 301 LPMVRYRTRDLTRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSE 360
           LPMVRYRTRDLTRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSE
Sbjct: 301 LPMVRYRTRDLTRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSE 360

Query: 361 MYEIHLYRNGNLDSVEVHVELRAECQHLDEGQRKLVIGELSKQIKTYIGISTQVHLQACG 420
           +YEIHLYRNGNLDSV+VHVELRAECQHLDEGQRKLV+GELSKQIKTYIGISTQVHLQ CG
Sbjct: 361 LYEIHLYRNGNLDSVQVHVELRAECQHLDEGQRKLVVGELSKQIKTYIGISTQVHLQPCG 420

Query: 421 TLKRSEGKACHVYDKRLAS 439
           TLKRSEGKACHV+D+RLAS
Sbjct: 421 TLKRSEGKACHVFDRRLAS 439


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: 911
Number of extensions: 22
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 PP_3279 PP_3279 (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.21153.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.2e-223  725.6   0.0   8.1e-223  725.4   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3279  PP_3279 phenylacetate-CoA ligase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3279  PP_3279 phenylacetate-CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  725.4   0.0  8.1e-223  8.1e-223       1     422 []      16     436 ..      16     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 725.4 bits;  conditional E-value: 8.1e-223
                           TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavpre 75 
                                         e++s+d lr+ qlerl++s+k+ay+nvp yr++f + g++pddlk l+dlakfp+t k+dlrdnyp++++avp+e
  lcl|FitnessBrowser__Putida:PP_3279  16 ETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAEYGIHPDDLKCLEDLAKFPFTGKNDLRDNYPYGMFAVPQE 90 
                                         799************************************************************************ PP

                           TIGR02155  76 kvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGatvvp 150
                                         +vvr+hassGttGkptvv+ytq+d+dtw++vvars+raaGGrkgd++h++yGyGlftGGlG+hyGae+lG+tv+p
  lcl|FitnessBrowser__Putida:PP_3279  91 EVVRLHASSGTTGKPTVVGYTQNDIDTWANVVARSIRAAGGRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIP 165
                                         *************************************************************************** PP

                           TIGR02155 151 isGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearlgikald 225
                                         +sGGqtekqvqli+df+pdii+vtpsy+l+l++e++r+gidp+d  l+++i+Gaepwt+++r+ +e+r+gi+ald
  lcl|FitnessBrowser__Putida:PP_3279 166 MSGGQTEKQVQLIRDFHPDIIMVTPSYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRMGINALD 240
                                         *************************************************************************** PP

                           TIGR02155 226 iyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryrtrdltrll 300
                                         iyGlse++GpGva+ec+etkdG++iwedhfypeiidp tgevlpdG+ Gelvft+l+kealp++ryrtrdltrll
  lcl|FitnessBrowser__Putida:PP_3279 241 IYGLSEIMGPGVAMECIETKDGPTIWEDHFYPEIIDPATGEVLPDGQLGELVFTSLSKEALPMVRYRTRDLTRLL 315
                                         *************************************************************************** PP

                           TIGR02155 301 pgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkvelkdesaalrl 375
                                         pgtar+mrr+ ki+Grsdd+li+rGvnvfptq+ee +lk+++ls  y+++l r+G+ld++ ++vel+ e ++l+ 
  lcl|FitnessBrowser__Putida:PP_3279 316 PGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSELYEIHLYRNGNLDSVQVHVELRAECQHLD- 389
                                         ***********************************************************************999. PP

                           TIGR02155 376 leqksllakkiekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                         + q++l+  +++k+ik+ +g+s++v+l+ +g+l+rseGka+ v+d+r
  lcl|FitnessBrowser__Putida:PP_3279 390 EGQRKLVVGELSKQIKTYIGISTQVHLQPCGTLKRSEGKACHVFDRR 436
                                         667779***************************************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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.58
//
[ok]

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

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

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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