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_1443 Dsui_1443 phenylacetate-CoA ligase

Query= SwissProt::Q9L9C1
         (440 letters)



>FitnessBrowser__PS:Dsui_1443
          Length = 438

 Score =  594 bits (1531), Expect = e-174
 Identities = 285/429 (66%), Positives = 350/429 (81%), Gaps = 3/429 (0%)

Query: 12  EPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKSLADLAKFPFTA 71
           E I +AS+DE+ ALQL+RL+ S+RHAYE VPH R  FDA GVHPDDLK+LADLA+FPFT 
Sbjct: 12  ERIARASRDEIAALQLKRLQQSLRHAYEKVPHTRAKFDAHGVHPDDLKTLADLARFPFTG 71

Query: 72  KGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTWATVVARSIRASGGR 131
           K DLRDNYP+G+FAVP   + RVHASSGTTGKPTVVGYT  DID WA ++AR++RA+G  
Sbjct: 72  KQDLRDNYPYGLFAVPMRDIVRVHASSGTTGKPTVVGYTAGDIDRWADIMARALRAAGAG 131

Query: 132 AGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLIQDFKPDIIMVTPSY 191
             D+VH+A+GYGLFTGGLG HYG E+LG T VP+SGGQTE+Q+QLI DFKP +++VTPSY
Sbjct: 132 PEDIVHVAHGYGLFTGGLGVHYGVERLGATAVPVSGGQTERQVQLIADFKPTVLVVTPSY 191

Query: 192 MLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDIYGLSEVMGPGV 251
            L + DE E  G D   +SL++G+FGAEPW ++MRA +E R GI A+D+YGLSEVMGPGV
Sbjct: 192 ALNLADECEHQGFDLAGSSLRIGLFGAEPWGESMRAEIERRFGIAAMDLYGLSEVMGPGV 251

Query: 252 ANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAMPVIRYRTRDLT 311
           A+ECIE++DGP IWEDHFYPEIIDP+TGEVLPDG+ GELVFT+LTKE MPV+RYRTRDLT
Sbjct: 252 ASECIESRDGPTIWEDHFYPEIIDPNTGEVLPDGAHGELVFTSLTKEGMPVVRYRTRDLT 311

Query: 312 RLLPPTARSMRRMAKITGRSDDMLIIRGVNLFPTQVEELICKNPKLAPQYLLEVDKDGHM 371
            LLPPTARS RR+ KITGRSDDMLIIRGVN+FP+Q+EE + K  +L+P Y LEV ++GH+
Sbjct: 312 TLLPPTARSFRRIGKITGRSDDMLIIRGVNVFPSQIEEFVLKQAELSPHYQLEVWREGHL 371

Query: 372 DTLTVKVEINPE-ANVGRHPEQKEALAKELQHDIKTFIGVSAKVHVCEPFAIERVTIGKA 430
           D L ++VE+ PE AN G H    E  A+ELQH IK++IG+S +V V    +IER   GKA
Sbjct: 372 DKLDIRVELKPEFANAGTH--VSEQAARELQHHIKSYIGISTRVRVEAVGSIERAVGGKA 429

Query: 431 KRVVDRRPK 439
           +RVVD+RP+
Sbjct: 430 RRVVDKRPQ 438


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: 709
Number of extensions: 21
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: 440
Length of database: 438
Length adjustment: 32
Effective length of query: 408
Effective length of database: 406
Effective search space:   165648
Effective search space used:   165648
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_1443 Dsui_1443 (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.23979.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.3e-211  688.5   0.0   1.6e-211  688.3   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_1443  Dsui_1443 phenylacetate-CoA liga


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1443  Dsui_1443 phenylacetate-CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  688.3   0.0  1.6e-211  1.6e-211       2     422 .]      16     436 ..      15     436 .. 0.99

  Alignments for each domain:
  == domain 1  score: 688.3 bits;  conditional E-value: 1.6e-211
                         TIGR02155   2 klsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavprekvv 78 
                                       ++s+de+ alql+rl+ s+++aye+vp+ r++fda gv+pddlk+l+dla+fp+t k+dlrdnyp++l+avp+ ++v
  lcl|FitnessBrowser__PS:Dsui_1443  16 RASRDEIAALQLKRLQQSLRHAYEKVPHTRAKFDAHGVHPDDLKTLADLARFPFTGKQDLRDNYPYGLFAVPMRDIV 92 
                                       689************************************************************************** PP

                         TIGR02155  79 rvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGatvvpisGGq 155
                                       rvhassGttGkptvv+yt+ d+d w++++ar+lraaG  ++d++h+a+GyGlftGGlGvhyG e+lGat vp+sGGq
  lcl|FitnessBrowser__PS:Dsui_1443  93 RVHASSGTTGKPTVVGYTAGDIDRWADIMARALRAAGAGPEDIVHVAHGYGLFTGGLGVHYGVERLGATAVPVSGGQ 169
                                       ***************************************************************************** PP

                         TIGR02155 156 tekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearlgikaldiyGlsev 232
                                       te+qvqli dfkp +++vtpsy+l+l++e +++g d +  sl+++++Gaepw e mr+e+e+r+gi a+d+yGlsev
  lcl|FitnessBrowser__PS:Dsui_1443 170 TERQVQLIADFKPTVLVVTPSYALNLADECEHQGFDLAGSSLRIGLFGAEPWGESMRAEIERRFGIAAMDLYGLSEV 246
                                       ***************************************************************************** PP

                         TIGR02155 233 iGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryrtrdltrllpgtartmrr 309
                                       +GpGva ec+e++dG++iwedhfypeiidp+tgevlpdG +Gelvft+ltke++pv+ryrtrdlt llp+tar+ rr
  lcl|FitnessBrowser__PS:Dsui_1443 247 MGPGVASECIESRDGPTIWEDHFYPEIIDPNTGEVLPDGAHGELVFTSLTKEGMPVVRYRTRDLTTLLPPTARSFRR 323
                                       ***************************************************************************** PP

                         TIGR02155 310 mdkikGrsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkvelkdesaalrlleqksllakki 386
                                       + ki+Grsdd+li+rGvnvfp+q+ee +lk+ +lsphyqle+ reG+ld+l ++velk+e a++ +++++ + a+++
  lcl|FitnessBrowser__PS:Dsui_1443 324 IGKITGRSDDMLIIRGVNVFPSQIEEFVLKQAELSPHYQLEVWREGHLDKLDIRVELKPEFANAGTHVSE-QAAREL 399
                                       *************************************************************999988876.789*** PP

                         TIGR02155 387 ekkikaevgvsvdvelvepgsler.seGkakrvvdkr 422
                                       +++ik+ +g+s++v++ + gs+er   Gka+rvvdkr
  lcl|FitnessBrowser__PS:Dsui_1443 400 QHHIKSYIGISTRVRVEAVGSIERaVGGKARRVVDKR 436
                                       ************************8899********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (438 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.65
//
[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