Alignments for a candidate for paaK in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Dechlorosoma suillum PS

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate Dsui_1441 Dsui_1441 phenylacetate-CoA ligase

Query= SwissProt::Q9L9C1
         (440 letters)



>FitnessBrowser__PS:Dsui_1441
          Length = 434

 Score =  641 bits (1654), Expect = 0.0
 Identities = 308/429 (71%), Positives = 364/429 (84%), Gaps = 2/429 (0%)

Query: 11  LEPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKSLADLAKFPFT 70
           L+ IE AS+DE+ ALQ+ERL+W+++HAY+NVPHYR  FDA+GVHPDD  SL DL KFPFT
Sbjct: 8   LDAIENASRDEITALQVERLRWTLKHAYDNVPHYRAKFDAQGVHPDDFHSLDDLRKFPFT 67

Query: 71  AKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTWATVVARSIRASGG 130
            K DLRDNYPF MFA PRE+V RVHASSGTTGKPTVVGYT KDIDTWA ++ARSI A+GG
Sbjct: 68  TKQDLRDNYPFKMFATPREEVVRVHASSGTTGKPTVVGYTQKDIDTWAHLMARSIYAAGG 127

Query: 131 RAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLIQDFKPDIIMVTPS 190
           R GD++H+AYGYGLFTGGLGAHYGAE LGCTV+PMSGGQTEKQ+QLI DF P IIM TPS
Sbjct: 128 RRGDIIHVAYGYGLFTGGLGAHYGAEALGCTVIPMSGGQTEKQVQLIADFAPRIIMCTPS 187

Query: 191 YMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDIYGLSEVMGPG 250
           YML + DE +R G+DP  TSL++GI GAEPWT  MR  +E   GIDAVDIYGLSEVMGPG
Sbjct: 188 YMLNIADEFKRQGMDPRGTSLRIGIHGAEPWTDGMRQEIENLLGIDAVDIYGLSEVMGPG 247

Query: 251 VANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAMPVIRYRTRDL 310
           VANECIE+KDGPVIWEDHFYPEIIDP+TGEVLP+GS+GELVFT+L+KEA+PV+RYRTRDL
Sbjct: 248 VANECIESKDGPVIWEDHFYPEIIDPNTGEVLPEGSQGELVFTSLSKEALPVVRYRTRDL 307

Query: 311 TRLLPPTARSMRRMAKITGRSDDMLIIRGVNLFPTQVEELICKNPKLAPQYLLEVDKDGH 370
           TRLL PT+RS RR+ KITGRSDDMLIIRGVN+FP+Q+EELI K  KL+  YLLEV +DGH
Sbjct: 308 TRLLTPTSRSFRRIGKITGRSDDMLIIRGVNVFPSQIEELILKQAKLSGHYLLEVARDGH 367

Query: 371 MDTLTVKVEINPEANVGRHPEQKEALAKELQHDIKTFIGVSAKVHVCEPFAIERVTIGKA 430
           +D++TV VE+ PE  +    E KE +A ELQH IK++IG+S +V + E   IER ++GKA
Sbjct: 368 LDSITVNVEMKPEFGIATAAE-KEYVAHELQHHIKSYIGISTQVRIVEVGGIER-SVGKA 425

Query: 431 KRVVDRRPK 439
           KRV+D+RP+
Sbjct: 426 KRVIDKRPR 434


Lambda     K      H
   0.318    0.137    0.406 

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: 696
Number of extensions: 18
Number of successful extensions: 3
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: 440
Length of database: 434
Length adjustment: 32
Effective length of query: 408
Effective length of database: 402
Effective search space:   164016
Effective search space used:   164016
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 Dsui_1441 Dsui_1441 (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.29592.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.4e-229  746.9   0.0   2.7e-229  746.8   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_1441  Dsui_1441 phenylacetate-CoA liga


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1441  Dsui_1441 phenylacetate-CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  746.8   0.0  2.7e-229  2.7e-229       1     422 []      12     432 ..      12     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 746.8 bits;  conditional E-value: 2.7e-229
                         TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavprekv 77 
                                       e++s+de++alq+erl++++k+ay+nvp+yr++fda+gv+pdd+++l+dl+kfp+t+k+dlrdnypf+++a+pre+v
  lcl|FitnessBrowser__PS:Dsui_1441  12 ENASRDEITALQVERLRWTLKHAYDNVPHYRAKFDAQGVHPDDFHSLDDLRKFPFTTKQDLRDNYPFKMFATPREEV 88 
                                       789************************************************************************** PP

                         TIGR02155  78 vrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGatvvpisGG 154
                                       vrvhassGttGkptvv+ytqkd+dtw++++ars++aaGGr+gd++h+ayGyGlftGGlG+hyGae lG+tv+p+sGG
  lcl|FitnessBrowser__PS:Dsui_1441  89 VRVHASSGTTGKPTVVGYTQKDIDTWAHLMARSIYAAGGRRGDIIHVAYGYGLFTGGLGAHYGAEALGCTVIPMSGG 165
                                       ***************************************************************************** PP

                         TIGR02155 155 qtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearlgikaldiyGlse 231
                                       qtekqvqli df p+ii++tpsy+l++++e+kr+g+dp+ +sl+++i Gaepwt+ mr+e+e+ lgi+a+diyGlse
  lcl|FitnessBrowser__PS:Dsui_1441 166 QTEKQVQLIADFAPRIIMCTPSYMLNIADEFKRQGMDPRGTSLRIGIHGAEPWTDGMRQEIENLLGIDAVDIYGLSE 242
                                       ***************************************************************************** PP

                         TIGR02155 232 viGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryrtrdltrllpgtartmr 308
                                       v+GpGvanec+e+kdG+viwedhfypeiidp+tgevlp+G++Gelvft+l+kealpv+ryrtrdltrll +t+r+ r
  lcl|FitnessBrowser__PS:Dsui_1441 243 VMGPGVANECIESKDGPVIWEDHFYPEIIDPNTGEVLPEGSQGELVFTSLSKEALPVVRYRTRDLTRLLTPTSRSFR 319
                                       ***************************************************************************** PP

                         TIGR02155 309 rmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkvelkdesaalrlleqksllakk 385
                                       r+ ki+Grsdd+li+rGvnvfp+q+ee++lk+ kls+hy le+ r+G+ld++t++ve+k+e   ++   +k+ +a++
  lcl|FitnessBrowser__PS:Dsui_1441 320 RIGKITGRSDDMLIIRGVNVFPSQIEELILKQAKLSGHYLLEVARDGHLDSITVNVEMKPEFGIAT-AAEKEYVAHE 395
                                       *************************************************************98877.667779**** PP

                         TIGR02155 386 iekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                       ++++ik+ +g+s++v++ve g +ers Gkakrv+dkr
  lcl|FitnessBrowser__PS:Dsui_1441 396 LQHHIKSYIGISTQVRIVEVGGIERSVGKAKRVIDKR 432
                                       ************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (434 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: 00:00:00.01
# Mc/sec: 10.67
//
[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