Alignments for a candidate for paaK in Sphingomonas wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Sphingomonas wittichii RW1

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_011952291.1 SWIT_RS07330 phenylacetate--CoA ligase

Query= BRENDA::B4E7B5
         (432 letters)



>NCBI__GCF_000016765.1:WP_011952291.1
          Length = 429

 Score =  551 bits (1421), Expect = e-161
 Identities = 284/421 (67%), Positives = 326/421 (77%), Gaps = 8/421 (1%)

Query: 13  ASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFTTKGDLR 72
           A+  EL ALQLERLK +L HAY +SP Y + FD AGV PDDL TLADL+RFPFTTK DLR
Sbjct: 9   ANLAELRALQLERLKSTLAHAYANSPHYAKAFDAAGVTPDDLTTLADLARFPFTTKADLR 68

Query: 73  DSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGARRGDKV 132
            +YPFGMFAVPQ+++SRIHASSGTTGKPTVVGYT  DI+TWA+LVARSI AAG R G K 
Sbjct: 69  ATYPFGMFAVPQEQVSRIHASSGTTGKPTVVGYTKRDIETWASLVARSIHAAGGRPGMKA 128

Query: 133 HVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIA 192
            +SYGYGLFTGGLGAHYGAE  G TVIP  GGQTEKQVQLI DF+PDIIMVTPSYML+I 
Sbjct: 129 QISYGYGLFTGGLGAHYGAEALGCTVIPMSGGQTEKQVQLICDFKPDIIMVTPSYMLAIL 188

Query: 193 DEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPGVASECV 252
           DE  RQG+DP  SSL+ GIFGAEPWT  MR  +E+   I A DIYGLSEVMGPGVA E V
Sbjct: 189 DEFRRQGIDPRASSLKYGIFGAEPWTEAMRREVEEAFDIKACDIYGLSEVMGPGVAQEFV 248

Query: 253 ETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPG 312
            ++ GPTIWEDHFYPE+I+P TGEVLPDGE GELVFTSLTK+ALPIIRYRTRDLTRLLPG
Sbjct: 249 ASQAGPTIWEDHFYPEVINPATGEVLPDGEEGELVFTSLTKQALPIIRYRTRDLTRLLPG 308

Query: 313 TARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGPLDVLTL 372
               MRRM KITGRSDDM+I+RGVNVFPTQIEEQ+LK   LAPH+++ +T+ G +D + +
Sbjct: 309 IEVPMRRMAKITGRSDDMLIIRGVNVFPTQIEEQVLKCEGLAPHFEVEITRPGRMDEVLI 368

Query: 373 NVE---PCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRVVDK 429
            VE    C ET       +     LA  +K +IG++A   ++    + RS GKA RV D 
Sbjct: 369 IVERRLDCDETRGGAEGAR-----LAGYVKEVIGISARTRIVESGALPRSSGKAARVRDL 423

Query: 430 R 430
           R
Sbjct: 424 R 424


Lambda     K      H
   0.319    0.137    0.404 

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: 627
Number of extensions: 13
Number of successful extensions: 2
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: 432
Length of database: 429
Length adjustment: 32
Effective length of query: 400
Effective length of database: 397
Effective search space:   158800
Effective search space used:   158800
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_011952291.1 SWIT_RS07330 (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.26808.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-208  676.9   0.0   5.2e-208  676.7   0.0    1.0  1  lcl|NCBI__GCF_000016765.1:WP_011952291.1  SWIT_RS07330 phenylacetate--CoA 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016765.1:WP_011952291.1  SWIT_RS07330 phenylacetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  676.7   0.0  5.2e-208  5.2e-208       4     422 .]      10     424 ..       8     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 676.7 bits;  conditional E-value: 5.2e-208
                                 TIGR02155   4 sldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllav 72 
                                               +l elralqlerlk+++++ay n p+y kafdaagv pddl +l+dla+fp+t+k dlr  ypf+++av
  lcl|NCBI__GCF_000016765.1:WP_011952291.1  10 NLAELRALQLERLKSTLAHAYANSPHYAKAFDAAGVTPDDLTTLADLARFPFTTKADLRATYPFGMFAV 78 
                                               5789***************************************************************** PP

                                 TIGR02155  73 prekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGa 141
                                               p+e+v r+hassGttGkptvv+yt++d++tw+++vars++aaGGr+g++  ++yGyGlftGGlG+hyGa
  lcl|NCBI__GCF_000016765.1:WP_011952291.1  79 PQEQVSRIHASSGTTGKPTVVGYTKRDIETWASLVARSIHAAGGRPGMKAQISYGYGLFTGGLGAHYGA 147
                                               ********************************************************************* PP

                                 TIGR02155 142 eklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwtea 210
                                               e lG+tv+p+sGGqtekqvqli dfkpdii+vtpsy+la+l+e++r+gidp+  slk++i+Gaepwtea
  lcl|NCBI__GCF_000016765.1:WP_011952291.1 148 EALGCTVIPMSGGQTEKQVQLICDFKPDIIMVTPSYMLAILDEFRRQGIDPRASSLKYGIFGAEPWTEA 216
                                               ********************************************************************* PP

                                 TIGR02155 211 mrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvft 279
                                               mr+e+e++++ika diyGlsev+GpGva+e v ++ G++iwedhfype+i+p tgevlpdGeeGelvft
  lcl|NCBI__GCF_000016765.1:WP_011952291.1 217 MRREVEEAFDIKACDIYGLSEVMGPGVAQEFVASQAGPTIWEDHFYPEVINPATGEVLPDGEEGELVFT 285
                                               ********************************************************************* PP

                                 TIGR02155 280 tltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyq 348
                                               +ltk+alp+iryrtrdltrllpg   +mrrm+ki+Grsdd+li+rGvnvfptq+ee +lk + l+ph++
  lcl|NCBI__GCF_000016765.1:WP_011952291.1 286 SLTKQALPIIRYRTRDLTRLLPGIEVPMRRMAKITGRSDDMLIIRGVNVFPTQIEEQVLKCEGLAPHFE 354
                                               ********************************************************************* PP

                                 TIGR02155 349 leltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGkakr 417
                                               +e+tr G++de+ + ve + +  ++r   +      ++   +k+ +g+s++ ++ve+g+l+rs Gka r
  lcl|NCBI__GCF_000016765.1:WP_011952291.1 355 VEITRPGRMDEVLIIVERRLDCDETRGGAEG----ARLAGYVKEVIGISARTRIVESGALPRSSGKAAR 419
                                               *******************999999977666....6788899*************************** PP

                                 TIGR02155 418 vvdkr 422
                                               v d+r
  lcl|NCBI__GCF_000016765.1:WP_011952291.1 420 VRDLR 424
                                               ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (429 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.66
//
[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