Alignments for a candidate for paaK in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Pseudomonas fluorescens GW456-L13

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate PfGW456L13_2428 Phenylacetate-coenzyme A ligase (EC 6.2.1.30) PaaF

Query= SwissProt::O33469
         (439 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428
          Length = 441

 Score =  752 bits (1941), Expect = 0.0
 Identities = 364/426 (85%), Positives = 394/426 (92%)

Query: 11  LLDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAECGAHPDDLTCLEDLAKFPF 70
           +LDP+ETAS+D LRQHQLERLRWSL HAY+NVPLYRQRF   G HPDD+  L+DLAKFPF
Sbjct: 13  VLDPLETASIDELRQHQLERLRWSLNHAYNNVPLYRQRFDALGVHPDDIKSLDDLAKFPF 72

Query: 71  TGKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDINTWANVVARSIRAAG 130
           T K+DLRDNYPYGMFAVP  ++VRLHASSGTTGKPTVVGYTQNDI+TWANVVARSIRAAG
Sbjct: 73  TTKSDLRDNYPYGMFAVPMHDIVRLHASSGTTGKPTVVGYTQNDIDTWANVVARSIRAAG 132

Query: 131 GRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRDFQPDIIMVTP 190
           G +GDKVH+SYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLI+DFQPDIIMVTP
Sbjct: 133 GHRGDKVHISYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIKDFQPDIIMVTP 192

Query: 191 SYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRLGINALDIYGLSEIMGP 250
           SYMLN+ADEIERQGIDPH L LRLGIFGAEPWT ELR +IE R+GI ALDIYGLSEIMGP
Sbjct: 193 SYMLNIADEIERQGIDPHKLALRLGIFGAEPWTAELRSAIEARMGITALDIYGLSEIMGP 252

Query: 251 GVAMECIETKDGPTIWEDHFYPEIIDPVTGEVLPDGQLGELVFTSLSKEALPMVRYRTRD 310
           GVAMEC ETKDGPTIWEDHFYPEIIDPVTGEVLPDGQ+GELVFTSLSKEALPM+RYRTRD
Sbjct: 253 GVAMECAETKDGPTIWEDHFYPEIIDPVTGEVLPDGQMGELVFTSLSKEALPMIRYRTRD 312

Query: 311 LTRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSEMYEIHLYRNG 370
           LTRLLPGTARPMRRI KITGRSDDMLIIRGVNVFPTQIEEQVLK+KQL+E YEIHLYRNG
Sbjct: 313 LTRLLPGTARPMRRIDKITGRSDDMLIIRGVNVFPTQIEEQVLKVKQLAECYEIHLYRNG 372

Query: 371 NLDSVEVHVELRAECQHLDEGQRKLVIGELSKQIKTYIGISTQVHLQACGTLKRSEGKAC 430
           NLDSV+VHVEL+AE QHL + Q+K V GELS+ IKTYIGIS+++ LQ   ++KRSEGKAC
Sbjct: 373 NLDSVDVHVELKAEHQHLGDEQQKAVCGELSRHIKTYIGISSRIVLQPFHSIKRSEGKAC 432

Query: 431 HVYDKR 436
           HV DKR
Sbjct: 433 HVVDKR 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: 788
Number of extensions: 18
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: 441
Length adjustment: 32
Effective length of query: 407
Effective length of database: 409
Effective search space:   166463
Effective search space used:   166463
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 PfGW456L13_2428 (Phenylacetate-coenzyme A ligase (EC 6.2.1.30) PaaF)
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.10664.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.5e-222  724.6   0.0   1.6e-222  724.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428  Phenylacetate-coenzyme A ligase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428  Phenylacetate-coenzyme A ligase (EC 6.2.1.30) PaaF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  724.4   0.0  1.6e-222  1.6e-222       1     422 []      18     438 ..      18     438 .. 0.99

  Alignments for each domain:
  == domain 1  score: 724.4 bits;  conditional E-value: 1.6e-222
                                               TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpl 55 
                                                             e++s delr+ qlerl++s+++ay+nvp yr++fda+gv+pdd+k+l+dlakfp+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428  18 ETASIDELRQHQLERLRWSLNHAYNNVPLYRQRFDALGVHPDDIKSLDDLAKFPF 72 
                                                             799**************************************************** PP

                                               TIGR02155  56 taksdlrdnypfdllavprekvvrvhassGttGkptvvaytqkdldtwsevvars 110
                                                             t+ksdlrdnyp++++avp++++vr+hassGttGkptvv+ytq+d+dtw++vvars
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428  73 TTKSDLRDNYPYGMFAVPMHDIVRLHASSGTTGKPTVVGYTQNDIDTWANVVARS 127
                                                             ******************************************************* PP

                                               TIGR02155 111 lraaGGrkgdllhnayGyGlftGGlGvhyGaeklGatvvpisGGqtekqvqliqd 165
                                                             +raaGG++gd++h++yGyGlftGGlG+hyGae+lG+tv+p+sGGqtekqvqli+d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428 128 IRAAGGHRGDKVHISYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIKD 182
                                                             ******************************************************* PP

                                               TIGR02155 166 fkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearlg 220
                                                             f+pdii+vtpsy+l++++e++r+gidp++ +l+++i+Gaepwt ++r+++ear+g
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428 183 FQPDIIMVTPSYMLNIADEIERQGIDPHKLALRLGIFGAEPWTAELRSAIEARMG 237
                                                             ******************************************************* PP

                                               TIGR02155 221 ikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGe 275
                                                             i+aldiyGlse++GpGva+ec etkdG++iwedhfypeiidp tgevlpdG+ Ge
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428 238 ITALDIYGLSEIMGPGVAMECAETKDGPTIWEDHFYPEIIDPVTGEVLPDGQMGE 292
                                                             ******************************************************* PP

                                               TIGR02155 276 lvfttltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfp 330
                                                             lvft+l+kealp+iryrtrdltrllpgtar+mrr+dki+Grsdd+li+rGvnvfp
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428 293 LVFTSLSKEALPMIRYRTRDLTRLLPGTARPMRRIDKITGRSDDMLIIRGVNVFP 347
                                                             ******************************************************* PP

                                               TIGR02155 331 tqleevllkldklsphyqleltreGaldeltlkvelkdesaalrlleqksllakk 385
                                                             tq+ee +lk+++l+  y+++l r+G+ld++ ++velk e ++l   eq+++++ +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428 348 TQIEEQVLKVKQLAECYEIHLYRNGNLDSVDVHVELKAEHQHLG-DEQQKAVCGE 401
                                                             ***************************************99887.566679**** PP

                                               TIGR02155 386 iekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                                             ++++ik+ +g+s+++ l+   s++rseGka+ vvdkr
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428 402 LSRHIKTYIGISSRIVLQPFHSIKRSEGKACHVVDKR 438
                                                             ************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (441 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: 00:00:00.01
# Mc/sec: 9.87
//
[ok]

This GapMind analysis is from Sep 17 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