Alignments for a candidate for paaK in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Dinoroseobacter shibae DFL-12

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 3610443 Dshi_3824 phenylacetate-CoA ligase (RefSeq)

Query= BRENDA::B4E7B5
         (432 letters)



>FitnessBrowser__Dino:3610443
          Length = 436

 Score =  573 bits (1476), Expect = e-168
 Identities = 280/425 (65%), Positives = 336/425 (79%), Gaps = 1/425 (0%)

Query: 7   LEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFT 66
           L+PIE ASRDE+ ALQL+R+KWSLRHAYD+ P+YR +FD AGVHPDDL+ L DL++FPFT
Sbjct: 11  LDPIEIASRDEIAALQLDRMKWSLRHAYDNVPMYRARFDAAGVHPDDLRDLKDLAKFPFT 70

Query: 67  TKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGA 126
            K DLRD YPFGM AVP+DR+ R+HASSGTTGKPTVV YT  DI+ WA+ +ARS+RA+G 
Sbjct: 71  HKSDLRDHYPFGMSAVPRDRLVRVHASSGTTGKPTVVVYTRHDIEVWADTLARSLRASGL 130

Query: 127 RRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPS 186
           R GD +H +YGYGLFTGGLGAHYG E+ G TVIP GGGQTEKQV LI DFRP  IMVTPS
Sbjct: 131 RAGDMIHNAYGYGLFTGGLGAHYGIEKLGATVIPMGGGQTEKQVSLIHDFRPTAIMVTPS 190

Query: 187 YMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPG 246
           YML+I +   + GLDP QSSL++G+FGAEPWTN MR  +E+   + AVDIYGLSEVMGPG
Sbjct: 191 YMLNILEGFHKAGLDPRQSSLQVGVFGAEPWTNAMRQEVEEAFDMHAVDIYGLSEVMGPG 250

Query: 247 VASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDL 306
           VA+ECVETKDG  +WEDH+YPEIIDP+TGEVL DG  GELVFT+LTKE +P+IRYRTRDL
Sbjct: 251 VANECVETKDGLHVWEDHYYPEIIDPQTGEVLKDGAEGELVFTTLTKEGMPMIRYRTRDL 310

Query: 307 TRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEGP 366
           TRLLPGTAR+MRR+EKITGRSDDMMI+RGVNVFPTQIEEQ++    L P++QI L   G 
Sbjct: 311 TRLLPGTARSMRRIEKITGRSDDMMILRGVNVFPTQIEEQVMATGGLGPYFQIELYTSGR 370

Query: 367 LDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARRV 426
           LD + + VE  P  A D  +   A + L   ++ ++GV+  + V     + RS GKA RV
Sbjct: 371 LDAMRVFVEATP-AAADELSRTAAARVLTKHVRDMVGVSIEVVVGDPGSVARSQGKAVRV 429

Query: 427 VDKRK 431
           +D RK
Sbjct: 430 IDNRK 434


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: 630
Number of extensions: 10
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: 436
Length adjustment: 32
Effective length of query: 400
Effective length of database: 404
Effective search space:   161600
Effective search space used:   161600
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 3610443 Dshi_3824 (phenylacetate-CoA ligase (RefSeq))
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.29785.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.7e-210  684.2   0.1   3.1e-210  684.0   0.1    1.0  1  lcl|FitnessBrowser__Dino:3610443  Dshi_3824 phenylacetate-CoA liga


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610443  Dshi_3824 phenylacetate-CoA ligase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  684.0   0.1  3.1e-210  3.1e-210       1     422 []      15     433 ..      15     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 684.0 bits;  conditional E-value: 3.1e-210
                         TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavprekv 77 
                                       e +s+de+ alql+r+k+s+++ay+nvp+yr++fdaagv+pddl++l+dlakfp+t+ksdlrd ypf++ avpr+++
  lcl|FitnessBrowser__Dino:3610443  15 EIASRDEIAALQLDRMKWSLRHAYDNVPMYRARFDAAGVHPDDLRDLKDLAKFPFTHKSDLRDHYPFGMSAVPRDRL 91 
                                       679************************************************************************** PP

                         TIGR02155  78 vrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGatvvpisGG 154
                                       vrvhassGttGkptvv yt++d+++w++ +arslra+G r+gd++hnayGyGlftGGlG+hyG eklGatv+p+ GG
  lcl|FitnessBrowser__Dino:3610443  92 VRVHASSGTTGKPTVVVYTRHDIEVWADTLARSLRASGLRAGDMIHNAYGYGLFTGGLGAHYGIEKLGATVIPMGGG 168
                                       ***************************************************************************** PP

                         TIGR02155 155 qtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearlgikaldiyGlse 231
                                       qtekqv li+df+p  i+vtpsy+l++le +++ g+dp++ sl+v+++Gaepwt+amr+e+e++++++a+diyGlse
  lcl|FitnessBrowser__Dino:3610443 169 QTEKQVSLIHDFRPTAIMVTPSYMLNILEGFHKAGLDPRQSSLQVGVFGAEPWTNAMRQEVEEAFDMHAVDIYGLSE 245
                                       ***************************************************************************** PP

                         TIGR02155 232 viGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryrtrdltrllpgtartmr 308
                                       v+GpGvanecvetkdGl++wedh+ypeiidp+tgevl dG eGelvfttltke++p+iryrtrdltrllpgtar+mr
  lcl|FitnessBrowser__Dino:3610443 246 VMGPGVANECVETKDGLHVWEDHYYPEIIDPQTGEVLKDGAEGELVFTTLTKEGMPMIRYRTRDLTRLLPGTARSMR 322
                                       ***************************************************************************** PP

                         TIGR02155 309 rmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkvelkdesaalrlleqksllakk 385
                                       r++ki+Grsdd++ilrGvnvfptq+ee +++++ l+p +q+el  +G+ld + + ve+ + +a+     ++++ a+ 
  lcl|FitnessBrowser__Dino:3610443 323 RIEKITGRSDDMMILRGVNVFPTQIEEQVMATGGLGPYFQIELYTSGRLDAMRVFVEATPAAADEL---SRTAAARV 396
                                       ***********************************************************9887776...55566899 PP

                         TIGR02155 386 iekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                       + k+++++vgvs++v + +pgs+ rs+Gka rv+d+r
  lcl|FitnessBrowser__Dino:3610443 397 LTKHVRDMVGVSIEVVVGDPGSVARSQGKAVRVIDNR 433
                                       9**********************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.45
//
[ok]

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

Downloads

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

Related tools

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