Alignments for a candidate for paaK in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Halomonas desiderata SP1

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_010626092.1 BZY95_RS06840 phenylacetate--CoA ligase

Query= SwissProt::O33469
         (439 letters)



>NCBI__GCF_002151265.1:WP_010626092.1
          Length = 437

 Score =  636 bits (1640), Expect = 0.0
 Identities = 315/429 (73%), Positives = 356/429 (82%)

Query: 8   DRALLDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAECGAHPDDLTCLEDLAK 67
           + + LD ME AS+D LR  QL+RLRWSLKHAYDNVP YR  F   G HP+D+  L DL K
Sbjct: 9   NNSALDQMELASLDELRATQLKRLRWSLKHAYDNVPFYRHVFDGAGVHPEDVKSLADLGK 68

Query: 68  FPFTGKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDINTWANVVARSIR 127
            PFT K DLRD+YP+GMFA P  E+VR+HASSGTTG+PTVVGYTQ DI+TWA+VVARSIR
Sbjct: 69  LPFTTKADLRDHYPFGMFATPMSEIVRVHASSGTTGQPTVVGYTQRDIDTWADVVARSIR 128

Query: 128 AAGGRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRDFQPDIIM 187
           AAGG + DKVHV+YGYGLFTGGLGAHYGAERLGC VIPMSGGQTEKQVQLIRDF+P+IIM
Sbjct: 129 AAGGTRNDKVHVAYGYGLFTGGLGAHYGAERLGCAVIPMSGGQTEKQVQLIRDFEPNIIM 188

Query: 188 VTPSYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRLGINALDIYGLSEI 247
           VTPSYMLN+ADE+ERQGIDPH L LR GIFGAEPWT  +R ++EQRLGI+ALDIYGLSE+
Sbjct: 189 VTPSYMLNIADEMERQGIDPHKLPLRAGIFGAEPWTGSMRTALEQRLGIDALDIYGLSEV 248

Query: 248 MGPGVAMECIETKDGPTIWEDHFYPEIIDPVTGEVLPDGQLGELVFTSLSKEALPMVRYR 307
           MGPGV MEC+ETKDGPTIWEDHFYPEIIDPVTGEVLPDG+ GELVFT+L+KEALP++RYR
Sbjct: 249 MGPGVGMECLETKDGPTIWEDHFYPEIIDPVTGEVLPDGEYGELVFTTLTKEALPVIRYR 308

Query: 308 TRDLTRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSEMYEIHLY 367
           TRDLTRLLPGTARPMRRI KITGRSDDMLIIRGVNVFPTQIEEQ+LKI+ LS  YEI + 
Sbjct: 309 TRDLTRLLPGTARPMRRIDKITGRSDDMLIIRGVNVFPTQIEEQILKIEGLSPHYEIEVG 368

Query: 368 RNGNLDSVEVHVELRAECQHLDEGQRKLVIGELSKQIKTYIGISTQVHLQACGTLKRSEG 427
           R GNLD+V V VE  +     D    + + G L   IKTY+GISTQV + +   + RS G
Sbjct: 369 RQGNLDTVCVRVEACSNDVARDPSACEQLAGRLRHAIKTYVGISTQVDVCSVEDVMRSVG 428

Query: 428 KACHVYDKR 436
           KA  V D R
Sbjct: 429 KAKRVKDLR 437


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: 742
Number of extensions: 25
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: 437
Length adjustment: 32
Effective length of query: 407
Effective length of database: 405
Effective search space:   164835
Effective search space used:   164835
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_010626092.1 BZY95_RS06840 (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.22700.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-221  719.8   0.0   4.6e-221  719.7   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_010626092.1  BZY95_RS06840 phenylacetate--CoA


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_010626092.1  BZY95_RS06840 phenylacetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  719.7   0.0  4.6e-221  4.6e-221       1     422 []      17     437 .]      17     437 .] 0.99

  Alignments for each domain:
  == domain 1  score: 719.7 bits;  conditional E-value: 4.6e-221
                                 TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdl 69 
                                               e +sldelra ql+rl++s+k+ay+nvp+yr+ fd agv+p+d+k+l+dl k+p+t+k dlrd ypf++
  lcl|NCBI__GCF_002151265.1:WP_010626092.1  17 ELASLDELRATQLKRLRWSLKHAYDNVPFYRHVFDGAGVHPEDVKSLADLGKLPFTTKADLRDHYPFGM 85 
                                               6799***************************************************************** PP

                                 TIGR02155  70 lavprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvh 138
                                               +a+p+ ++vrvhassGttG+ptvv+ytq+d+dtw++vvars+raaGG ++d++h+ayGyGlftGGlG+h
  lcl|NCBI__GCF_002151265.1:WP_010626092.1  86 FATPMSEIVRVHASSGTTGQPTVVGYTQRDIDTWADVVARSIRAAGGTRNDKVHVAYGYGLFTGGLGAH 154
                                               ********************************************************************* PP

                                 TIGR02155 139 yGaeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepw 207
                                               yGae+lG++v+p+sGGqtekqvqli+df+p+ii+vtpsy+l++++e++r+gidp++  l+ +i+Gaepw
  lcl|NCBI__GCF_002151265.1:WP_010626092.1 155 YGAERLGCAVIPMSGGQTEKQVQLIRDFEPNIIMVTPSYMLNIADEMERQGIDPHKLPLRAGIFGAEPW 223
                                               ********************************************************************* PP

                                 TIGR02155 208 teamrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGel 276
                                               t  mr++le+rlgi+aldiyGlsev+GpGv++ec+etkdG++iwedhfypeiidp tgevlpdGe Gel
  lcl|NCBI__GCF_002151265.1:WP_010626092.1 224 TGSMRTALEQRLGIDALDIYGLSEVMGPGVGMECLETKDGPTIWEDHFYPEIIDPVTGEVLPDGEYGEL 292
                                               ********************************************************************* PP

                                 TIGR02155 277 vfttltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsp 345
                                               vfttltkealpviryrtrdltrllpgtar+mrr+dki+Grsdd+li+rGvnvfptq+ee +lk++ lsp
  lcl|NCBI__GCF_002151265.1:WP_010626092.1 293 VFTTLTKEALPVIRYRTRDLTRLLPGTARPMRRIDKITGRSDDMLIIRGVNVFPTQIEEQILKIEGLSP 361
                                               ********************************************************************* PP

                                 TIGR02155 346 hyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGk 414
                                               hy++e+ r+G+ld+++++ve+ ++ +a    +  ++la ++++ ik+ vg+s++v +++   + rs Gk
  lcl|NCBI__GCF_002151265.1:WP_010626092.1 362 HYEIEVGRQGNLDTVCVRVEACSNDVAR-DPSACEQLAGRLRHAIKTYVGISTQVDVCSVEDVMRSVGK 429
                                               *********************9776655.5788889********************************* PP

                                 TIGR02155 415 akrvvdkr 422
                                               akrv d+r
  lcl|NCBI__GCF_002151265.1:WP_010626092.1 430 AKRVKDLR 437
                                               ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (437 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: 7.87
//
[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