Alignments for a candidate for paaK in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Marinobacter adhaerens HP15

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate GFF2752 HP15_2696 phenylacetate-CoA ligase

Query= SwissProt::O33469
         (439 letters)



>FitnessBrowser__Marino:GFF2752
          Length = 436

 Score =  642 bits (1657), Expect = 0.0
 Identities = 316/425 (74%), Positives = 357/425 (84%), Gaps = 1/425 (0%)

Query: 12  LDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAECGAHPDDLTCLEDLAKFPFT 71
           LD METAS+D LR  QL+RLRWS+ HAY NVP YR+ F + G  P D+  LEDLAK PFT
Sbjct: 11  LDRMETASIDELRHEQLQRLRWSVVHAYTNVPFYRKAFDDQGLKPMDINSLEDLAKVPFT 70

Query: 72  GKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDINTWANVVARSIRAAGG 131
            K DLRDNYP+GMFA P  +VVR+HASSGTTGKPTVVGYTQ+DINTWA++VARSIRA GG
Sbjct: 71  TKADLRDNYPFGMFATPMSDVVRVHASSGTTGKPTVVGYTQSDINTWADIVARSIRAGGG 130

Query: 132 RKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRDFQPDIIMVTPS 191
            +GDKVHV+YGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLI+DF+PDIIMVTPS
Sbjct: 131 SRGDKVHVAYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIKDFEPDIIMVTPS 190

Query: 192 YMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRLGINALDIYGLSEIMGPG 251
           YMLN+ADE+ERQGIDPH L LRLGIFGAEPWT+ +R  IE+RLGI ALDIYGLSE+MGPG
Sbjct: 191 YMLNIADEMERQGIDPHKLPLRLGIFGAEPWTNAMRSEIEERLGIEALDIYGLSEVMGPG 250

Query: 252 VAMECIETKDGPTIWEDHFYPEIIDPVTGEVLPDGQLGELVFTSLSKEALPMVRYRTRDL 311
           V MECIETKDGPTIWEDHFYPEII+P TGEVLPDG+ GELVFTSL+K ALP++RYRTRDL
Sbjct: 251 VGMECIETKDGPTIWEDHFYPEIINPETGEVLPDGEYGELVFTSLTKVALPILRYRTRDL 310

Query: 312 TRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSEMYEIHLYRNGN 371
           TRLLPGTARPMRRI KITGRSDDMLIIRGVNVFP+QIEEQVLK + L+  YEI +Y+ GN
Sbjct: 311 TRLLPGTARPMRRIDKITGRSDDMLIIRGVNVFPSQIEEQVLKCEALAPHYEIEVYKEGN 370

Query: 372 LDSVEVHVELRAECQHLDEGQRKLVIGELSKQIKTYIGISTQVHLQACGTLKRSEGKACH 431
           LD V++  EL+       E  R     EL+  IK+YIGIST+V +     L RSEGKA  
Sbjct: 371 LDCVDIRTELKPGVTDTPE-SRAAAAKELAHHIKSYIGISTRVEVVETNRLARSEGKAKR 429

Query: 432 VYDKR 436
           V+D+R
Sbjct: 430 VFDRR 434


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: 723
Number of extensions: 24
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: 439
Length of database: 436
Length adjustment: 32
Effective length of query: 407
Effective length of database: 404
Effective search space:   164428
Effective search space used:   164428
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 GFF2752 HP15_2696 (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.5386.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.7e-222  722.9   0.0   5.3e-222  722.7   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF2752  HP15_2696 phenylacetate-CoA liga


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2752  HP15_2696 phenylacetate-CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  722.7   0.0  5.3e-222  5.3e-222       1     422 []      15     434 ..      15     434 .. 0.99

  Alignments for each domain:
  == domain 1  score: 722.7 bits;  conditional E-value: 5.3e-222
                           TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavpre 75 
                                         e++s delr  ql+rl++sv +ay nvp+yrkafd++g+kp d+++l+dlak+p+t+k dlrdnypf+++a+p+ 
  lcl|FitnessBrowser__Marino:GFF2752  15 ETASIDELRHEQLQRLRWSVVHAYTNVPFYRKAFDDQGLKPMDINSLEDLAKVPFTTKADLRDNYPFGMFATPMS 89 
                                         799************************************************************************ PP

                           TIGR02155  76 kvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGatvvp 150
                                         +vvrvhassGttGkptvv+ytq d++tw+++vars+ra GG++gd++h+ayGyGlftGGlG+hyGae+lG+tv+p
  lcl|FitnessBrowser__Marino:GFF2752  90 DVVRVHASSGTTGKPTVVGYTQSDINTWADIVARSIRAGGGSRGDKVHVAYGYGLFTGGLGAHYGAERLGCTVIP 164
                                         *************************************************************************** PP

                           TIGR02155 151 isGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearlgikald 225
                                         +sGGqtekqvqli+df+pdii+vtpsy+l++++e++r+gidp++  l+++i+Gaepwt+amr+e+e+rlgi+ald
  lcl|FitnessBrowser__Marino:GFF2752 165 MSGGQTEKQVQLIKDFEPDIIMVTPSYMLNIADEMERQGIDPHKLPLRLGIFGAEPWTNAMRSEIEERLGIEALD 239
                                         *************************************************************************** PP

                           TIGR02155 226 iyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryrtrdltrll 300
                                         iyGlsev+GpGv++ec+etkdG++iwedhfypeii+petgevlpdGe Gelvft+ltk alp++ryrtrdltrll
  lcl|FitnessBrowser__Marino:GFF2752 240 IYGLSEVMGPGVGMECIETKDGPTIWEDHFYPEIINPETGEVLPDGEYGELVFTSLTKVALPILRYRTRDLTRLL 314
                                         *************************************************************************** PP

                           TIGR02155 301 pgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkvelkdesaalrl 375
                                         pgtar+mrr+dki+Grsdd+li+rGvnvfp+q+ee +lk + l+phy++e+ +eG+ld + ++ elk+    +++
  lcl|FitnessBrowser__Marino:GFF2752 315 PGTARPMRRIDKITGRSDDMLIIRGVNVFPSQIEEQVLKCEALAPHYEIEVYKEGNLDCVDIRTELKPGV--TDT 387
                                         *******************************************************************765..556 PP

                           TIGR02155 376 leqksllakkiekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                          e++++ ak++ ++ik+ +g+s++ve+ve+  l rseGkakrv+d+r
  lcl|FitnessBrowser__Marino:GFF2752 388 PESRAAAAKELAHHIKSYIGISTRVEVVETNRLARSEGKAKRVFDRR 434
                                         699999***************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (436 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: 00:00:00.01
# Mc/sec: 10.41
//
[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